Descriptor: "MESH: Genome, Bacterial" - Searchworks@Jio Institute Digital Library Search Results

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192 results on '"MESH: Genome, Bacterial"'

1. Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity

Author: William Rostain, Theophile Grebert, Danylo Vyhovskyi, Paula Thiel Pizarro, Gatwa Tshinsele-Van Bellingen, Lun Cui, David Bikard, Biologie de Synthèse - Synthetic biology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), European Research Council [677823], European Research Council [101044479], Agence Nationale de la Recherche [ANR-10-LABX-62-IBEID]. Funding for open access charge: Institut Pasteur., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016)
Subjects: MESH: CRISPR-Cas Systems, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH: Escherichia coli, MESH: Endonucleases, [SDV]Life Sciences [q-bio], MESH: Promoter Regions, Genetic, Genetics, MESH: Genetic Engineering, MESH: Animals, MESH: Genes, Bacterial, MESH: Genome, Bacterial, MESH: Mammals
Abstract: Genetic tools derived from the Cas9 RNA-guided nuclease are providing essential capabilities to study and engineer bacteria. While the importance of off-target effects was noted early in Cas9’s application to mammalian cells, off-target cleavage by Cas9 in bacterial genomes is easily avoided due to their smaller size. Despite this, several studies have reported experimental setups in which Cas9 expression was toxic, even when using the catalytic dead variant of Cas9 (dCas9). Specifically, dCas9 was shown to be toxic when in complex with guide RNAs sharing specific PAM (protospacer adjacent motif)-proximal sequence motifs. Here, we demonstrate that this toxicity is caused by off-target binding of Cas9 to the promoter of essential genes, with silencing of off-target genes occurring with as little as 4 nt of identity in the PAM-proximal sequence. Screens performed in various strains of Escherichia coli and other enterobacteria show that the nature of toxic guide RNAs changes together with the evolution of sequences at off-target positions. These results highlight the potential for Cas9 to bind to hundreds of off-target positions in bacterial genomes, leading to undesired effects. This phenomenon must be considered in the design and interpretation of CRISPR–Cas experiments in bacteria.
Published: 2023

2. A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains

Author: Hennart Melanie, Guglielmini Julien, Bridel Sébastien, Maiden Martin C.J., Jolley Keith A., Criscuolo Alexis, Brisse Sylvain, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Sorbonne Université (SU), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Department of Zoology [Oxford], University of Oxford, M.H. was supported financially by the PhD grant 'Codes4strains' from the European Joint Programme One Health, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 773830. This work was supported financially by the French Government’s Investissement d’Avenir program Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62-IBEID) and by an award from the Bill and Melinda Gates Foundation (INV-025280). BIGSdb development is funded by a Wellcome Trust Biomedical Resource grant (218205/Z/19/Z). This work used the computational and storage services provided by the IT department at Institut Pasteur. This research was funded, in whole or in part, by Institut Pasteur and by European Union’s Horizon 2020 research and innovation programme.For the purpose of open access, the authors have applied a CC-BY public copyright license to any Author Manuscript version arising from this submission., This work builds partly on the classical 7-gene MLST database, which has been curated by Virginie Passet, Radek Izdebski, Carla Rodrigues, and Federica Palma. We thank Adrien Le Meur for help with the genome data set constitution and initial analyses of intra-outbreak variation., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health)(2018)
Subjects: Genotype, MESH: Klebsiella pneumoniae, Computational biology, Biology, MESH: Genome, Bacterial, Genome, MESH: Genotype, Taxonomy (general), Genetics, genomic classification, strain nomenclature, Taxonomic rank, MESH: Phylogeny, Nomenclature, Molecular Biology, Phylogeny, Ecology, Evolution, Behavior and Systematics, Phylogenetic tree, Strain (biology), MESH: Genomics, Genomics, genomic library, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], pathogen tracking, Klebsiella pneumoniae, microevolution, international harmonization, MESH: Multilocus Sequence Typing, Multilocus sequence typing, Identification (biology), Genome, Bacterial, Multilocus Sequence Typing
Abstract: Sublineages within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and industrial or public health applications. Whereas the classification and naming of prokaryotes is unified at the species level and higher taxonomic ranks, universally accepted definitions of sublineages within species are largely missing, which introduces confusion in population biology and epidemiological surveillance.Here we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threatKlebsiella pneumoniaeas a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LIN). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infra-specific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL sublineages (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users’ genomic sequences identification.The proposed strain taxonomy combines two phylogenetically informative barcodes systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.
Published: 2022

3. The seventh pandemic of cholera in Europe revisited by microbial genomics

Author: Radu Cojocaru, Anatoly N. Kravetz, Daniela Cristea, Jean Rauzier, Clifford G. Clark, Olivier Gascuel, Marie-Laure Quilici, François-Xavier Weill, Elisabeth Njamkepo, Adriana Simona Ciontea, Monakhova Ev, Maria Damian, Mihaela Oprea, Anna Zhukova, Cantacuzino National Medico-Military Institute for Research Development [Bucharest], Cantacuzino Institute [Romania], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris] (IP), Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, National Microbiology Laboratory [Winnipeg, Canada], Public Health Agency of Canada, Kiev Research Institute of Epidemiology and Infectious Diseases, Rostov-on-Don Research Institute for Plague Control, National Centre for Public Health [Chisinau, Republic of Moldova], This study was supported by the Institut Pasteur, Cantacuzino NMMIRD, Santé publiqueFrance, the Fondation Le Roch-Les Mousquetaires, the French government’s Investisse-ment d’Avenir programme, Laboratoire d’Excellence‘Integrative Biology of EmergingInfectious Diseases’(grant number ANR-10-LABX-62-IBEID), and'Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations'(INCEPTION, grant number PIA/ANR-16-CONV-0005). D.C. was supported by a trai-neeship grant from the Calmette and Yersin Program of the Institut Pasteur InternationalNetwork. M.O. was supported by a mobility grant from the Romanian Ministry of Research and Innovation CNCS - UEFISCDI, project no. 495/2018, within PNCDI III.The Institut Pasteur Biomics platform is supported by France Génomique (ANR10-INBS-09-08) and IBISA. We thank I. Najjar and L. Lemée for sequencing the isolates., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Epidemiology, Black sea region, General Physics and Astronomy, MESH: Genome, Bacterial, Ribotyping, El Tor, West africa, Cholera, Pandemic, Socioeconomics, MESH: Phylogeny, lcsh:Science, Vibrio cholerae, Phylogeny, MESH: Evolution, Molecular, Multidisciplinary, Middle East, biology, MESH: Genomics, Genomics, 3. Good health, Europe, Geography, MESH: Human Migration, MESH: History, 20th Century, Pathogens, MESH: History, 21st Century, MESH: Pandemics, Science, Human Migration, 030106 microbiology, History, 21st Century, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Spatio-Temporal Analysis, MESH: Spatio-Temporal Analysis, MESH: Cholera, Drug Resistance, Bacterial, MESH: Drug Resistance, Bacterial, medicine, Humans, Clinical microbiology, Pandemics, MESH: Humans, Outbreak, MESH: Ribotyping, General Chemistry, History, 20th Century, medicine.disease, biology.organism_classification, Microbial genomics, Bacterial genes, 030104 developmental biology, lcsh:Q, MESH: Europe, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial, MESH: Vibrio cholerae
Abstract: In 1970, the seventh pandemic of cholera (7 P) reached both Africa and Europe. Between 1970 and 2011, several European countries reported cholera outbreaks of a few to more than 2,000 cases. We report here a whole-genome analysis of 1,324 7 P V. cholerae El Tor (7 PET) isolates, including 172 from autochthonous sporadic or outbreak cholera cases occurring between 1970 and 2011 in Europe, providing insight into the spatial and temporal spread of this pathogen across Europe. In this work, we show that the 7 PET lineage was introduced at least eight times into two main regions: Eastern and Southern Europe. Greater recurrence of the disease was observed in Eastern Europe, where it persisted until 2011. It was introduced into this region from Southern Asia, often circulating regionally in the countries bordering the Black Sea, and in the Middle East before reaching Eastern Africa on several occasions. In Southern Europe, the disease was mostly seen in individual countries during the 1970s and was imported from North and West Africa, except in 1994, when cholera was imported into Albania and Italy from the Black Sea region. These results shed light on the geographic course of cholera during the seventh pandemic and highlight the role of humans in its global dissemination., Since 1970, several cholera outbreaks caused by the “seventh pandemic” (7PET) lineage have been reported in Europe. Here, the authors demonstrate that the outbreaks were caused by repeated introductions of 7PET into Europe, rather than local environmental sources.
Published: 2020

4. Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae

Author: Claudio Bandi, Xiaoli Cao, Davide Sassera, Ana Cristina Gales, Sion C. Bayliss, Stefano Pongolini, Sylvain Brisse, Ryoichi Saito, Stefano Gaiarsa, Francesco Comandatore, Edward J. Feil, Erika Scaltriti, Università degli Studi di Milano [Milano] (UNIMI), Università degli Studi di Pavia, University of Bath [Bath], Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), Fondazione IRCCS Policlinico San Matteo [Pavia], Università di Pavia, Nanjing Medical University, Federal University of Sao Paulo (Unifesp), Tokyo Medical and Dental University [Japan] (TMDU), Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris], Work supported by the Romeo ed Enrica Invernizzi Foundation., Università degli Studi di Milano = University of Milan (UNIMI), Università degli Studi di Pavia = University of Pavia (UNIPV), and Institut Pasteur [Paris] (IP)
Subjects: Klebsiella pneumoniae, Lineage (evolution), Population, MESH: Klebsiella pneumoniae, large recombination, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, MESH: Genome, Bacterial, Genome, Gene flow, chemistry.chemical_compound, 03 medical and health sciences, clonal group 258, Genotype, Genetics, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Recombination, Genetic, 0303 health sciences, education.field_of_study, MESH: Humans, 030306 microbiology, MESH: Clone Cells, biology.organism_classification, 3. Good health, Clone Cells, Klebsiella Infections, MESH: Klebsiella Infections, chemistry, MESH: Recombination, Genetic, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, DNA, Recombination, Genome, Bacterial, Research Article
Abstract: Klebsiella pneumoniae (Kp) is one of the most important nosocomial pathogens world-wide, being responsible for frequent hospital outbreaks and causing sepsis and multi-organ infections with a high mortality rate and frequent hospital outbreaks. The most prevalent and widely disseminated lineage of K. pneumoniae is clonal group 258 (CG258), which includes the highly resistant “high-risk” genotypes ST258 and ST11. Recent studies revealed that very large recombination events have occurred during the recent emergence of Kp lineages. A striking example is provided by ST258, which has undergone a recombination event that replaced over 1 Mb of the genome with DNA from an unrelated Kp donor. Although several examples of this phenomenon have been documented in Kp and other bacterial species, the significance of these very large recombination events for the emergence of either hyper-virulent or resistant clones remains unclear. Here we present an analysis of 834 Kp genomes that provides data on the frequency of these very large recombination events (defined as those involving >100Kb), their distribution within the genome, and the dynamics of gene flow within the Kp population. We note that very large recombination events occur frequently, and in multiple lineages, and that the majority of recombinational exchanges are clustered within two overlapping genomic regions, which result to be involved by recombination events with different frequencies. Our results also indicate that certain non-CG258 lineages are more likely to act as donors to CG258 recipients than others. Furthermore, comparison of gene content in CG258 and non-CG258 strains agrees with this pattern, suggesting that the success of a large recombination depends on gene composition in the exchanged genomic portion.Author SummaryKlebsiella pneumoniae (Kp) is an opportunistic bacterial pathogen, a major cause of deadly infections and outbreaks in hospitals worldwide. This bacterium is able to exchange large genomic portions (up to a fourth of the entire genome) within a single recombination event. Indeed, the most epidemiologically important Kp clone, is actually a hybrid which emerged after a > 1Mb recombination event. In this work, we investigated how recombinations affected the evolution of the most studied Kp Clonal Group, CG258. We found that large recombinations occurred frequently during Kp evolution, and occurred preferentially in a well-delimited genomic region. Furthermore, we found that four epidemiologically important clones emerged after large recombinations. We identified the donors of several large recombinations: despite many Kp lineages acted as donors during CG258 evolution, two of them have been involved more frequently. We hypothesize that the observed pattern of donors-recipients in recombinations, and the presence of a large recombinogenic region in Kp genome, could be related to gene composition. Indeed, genomic analyses showed a pattern compatible with this hypothesis, suggesting that gene content can represent a main factor in the success of a large recombination.
Published: 2019

5. CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers

Author: Jean-Philippe Vernadet, Christine Pourcel, David Couvin, Marie Touchon, Gilles Vergnaud, Nicolas Villeriot, Claire Toffano-Nioche, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Unité Transmission, Réservoir et Diversité des Pathogènes [Pasteur Guadeloupe, France] (TReD-Path), Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut Français de Bioinformatique (IFB) [ANR-11-INSB-0013]. Funding for open access charge: CNRS., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Séquence, Structure et Fonction des ARN (SSFA), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transposable element, MESH: CRISPR-Cas Systems, MESH: Genome, Archaeal, [SDV]Life Sciences [q-bio], CRISPR-Associated Proteins, Computational biology, MESH: Genome, Bacterial, Genome, 03 medical and health sciences, MESH: Software, Plasmid, Phylogenetics, Genome, Archaeal, Databases, Genetic, Genetics, CRISPR, Database Issue, Clustered Regularly Interspaced Short Palindromic Repeats, MESH: Phylogeny, Gene, MESH: Databases, Genetic, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, Bacteria, 030306 microbiology, MESH: CRISPR-Associated Proteins, Palindrome, Prokaryote, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Archaea, MESH: Bacteria, MESH: Archaea, MESH: Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, Genome, Bacterial, Software
Abstract: In Archaea and Bacteria, the arrays called CRISPRs for ‘clustered regularly interspaced short palindromic repeats’ and the CRISPR associated genes or cas provide adaptive immunity against viruses, plasmids and transposable elements. Short sequences called spacers, corresponding to fragments of invading DNA, are stored in-between repeated sequences. The CRISPR–Cas systems target sequences homologous to spacers leading to their degradation. To facilitate investigations of CRISPRs, we developed 12 years ago a website holding the CRISPRdb. We now propose CRISPRCasdb, a completely new version giving access to both CRISPRs and cas genes. We used CRISPRCasFinder, a program that identifies CRISPR arrays and cas genes and determine the system's type and subtype, to process public whole genome assemblies. Strains are displayed either in an alphabetic list or in taxonomic order. The database is part of the CRISPR-Cas++ website which also offers the possibility to analyse submitted sequences and to download programs. A BLAST search against lists of repeats and spacers extracted from the database is proposed. To date, 16 990 complete prokaryote genomes (16 650 bacteria from 2973 species and 340 archaea from 300 species) are included. CRISPR–Cas systems were found in 36% of Bacteria and 75% of Archaea strains. CRISPRCasdb is freely accessible at https://crisprcas.i2bc.paris-saclay.fr/.
Published: 2019

6. Strainberry: automated strain separation in low-complexity metagenomes using long reads

Author: Vicedomini, Riccardo, Quince, Christopher, Darling, Aaron E., Chikhi, Rayan, Algorithmes pour les séquences biologiques - Sequence Bioinformatics, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Warwick Medical School, University of Warwick [Coventry], Earlham Institute [Norwich], Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), iThree Institute, University of Technology Sydney (UTS), R.V. and R.C. are funded by ANR INCEPTION (PIA/ANR-16-CONV-0005) and R.C. by ANR PRAIRIE (ANR-19-P3IA-0001) and ANR SeqDigger (ANR-19-CE45-0008). C.Q. is funded through 'Strain resolved metagenomics for medical microbiology' MRC MR/S037195/1 and the 'CLIMB-BIG-DATA' consortium MR/T030062/1. A.E.D.’s contributions to this research were supported in part by the Australian Government through the Australian Research Council Discovery Projects funding scheme (project DP180101506)., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), ANR-19-CE45-0008,SeqDigger,Moteur de recherche de donne´es de se´quenc¸age en ge´nomique environnementale(2019), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Bacteria, Bioinformatics, Science, MESH: Genomics, Computational Biology, High-Throughput Nucleotide Sequencing, Genomics, MESH: Metagenome, MESH: Genome, Bacterial, Article, MESH: Bacteria, Species Specificity, Genome assembly algorithms, Metagenome, MESH: Species Specificity, Metagenomics, MESH: Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: High-Throughput Nucleotide Sequencing, Software, Genome, Bacterial, MESH: Computational Biology
Abstract: High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities., Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and reconstruct strain genomes from single-sample low-complexity microbiomes.
Published: 2021

7. Host Colonization as a Major Evolutionary Force Favoring the Diversity and the Emergence of the Worldwide Multidrug-Resistant Escherichia coli ST131

Author: Guillaume Dalmasso, Richard Bonnet, Marisa Haenni, Racha Beyrouthy, Jean-Yves Madec, Marie-Hélène Nicolas-Chanoine, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Centre National de Référence de la Résistance aux Antibiotiques [CHU Clermont-Ferrand] (CNR), CHU Clermont-Ferrand, Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, JPIAMR program TransComp-ESC-R, and ANR-16-JPEC-0002,ST131TS,Escherichia coli ST131: a model for high-risk transmission dynamics of antimicrobial resistance(2016)
Subjects: Male, antibiotic resistance, ST131, Virulence Factors, extended-spectrum beta-lactamase, Virulence, Population genetics, Biology, MESH: Genome, Bacterial, medicine.disease_cause, Global Health, Genome, Microbiology, Birds, Evolution, Molecular, one health, Mice, Dogs, Virology, Drug Resistance, Multiple, Bacterial, medicine, Escherichia coli, Animals, Humans, Evolutionary dynamics, MESH: Evolution, Molecular, veterinary microbiology, Escherichia coli Infections, genome analysis, Disease Reservoirs, Genetics, MESH: Disease Reservoirs, MESH: Escherichia coli, Host (biology), host colonization, veterinary epidemiology, population genetics, population structure, MESH: Drug Resistance, Multiple, Bacterial, Pathogenicity island, QR1-502, virulence, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Host-Pathogen Interactions, extended-spectrum betalactamase, Adaptation, Genome, Bacterial, Research Article
Abstract: International audience; The emergence of multidrug-resistant Escherichia coli ST131 is a major worldwide public health problem in humans. According to the "one health" approach, this study investigated animal reservoirs of ST131, their relationships with human strains, and the genetic features associated with host colonization. High-quality genomes originating from human, avian, and canine hosts were classified on the basis of their accessory gene content using pangenomic. Pangenomic clusters and subclusters were specifi- cally and significantly associated with hosts. The functions of clustering accessory genes were mainly enriched in functions involved in DNA acquisition, interactions, and virulence (e.g., pathogenesis, response to biotic stimulus and interaction between organisms). Accordingly, networks of cooccurrent host interaction factors were significantly associated with the pangenomic clusters and the originating hosts. The avian strains exhibited a specific content in virulence factors. Rarely found in humans, they corresponded to pathovars responsible for severe human infections. An emerging subcluster significantly associated with both human and canine hosts was evidenced. This ability to significantly colonize canine hosts in addition to humans was associated with a specific content in virulence factors (VFs) and metabolic functions encoded by a new pathogenicity island in ST131 and an improved fitness that is probably involved in its emergence. Overall, VF content, unlike the determinants of antimicrobial resistance, appeared as a key actor of bacterial host adaptation. The host dimension emerges as a major driver of genetic evolution that shapes ST131 genome, enhances its diversity, and favors its dissemination.IMPORTANCE Until now, there has been no indication that the evolutionary dynamics of Escherichia coli ST131 may reflect independent and host-specific adaptation of this lineage outside humans. In contrast, the limited number of ST131 reports in animals supported the common view that it rather reflects a spillover of the human sector. This study uncovered a link between host, ST131 population structure, and virulence factor content which appeared to reflect adaptation to hosts. This study helps to better understand the reservoir of ST131, the putative transmission flux, associated risks and the evolutionary dynamics of this bacterial population and highlights a paradigm in which host colonization stands as a key ecological force of the ST131 evolution.
Published: 2021

8. Phenotypic and genomic hallmarks of a novel, potentially pathogenic rapidly growing Mycobacterium species related to the Mycobacterium fortuitum complex

Author: Roland Brosch, Reem Gharbi, Besma Mhenni, Varun Khanna, Wafa Frigui, Helmi Mardassi, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique (LR11IPT01), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Université de Tunis El Manar (UTM), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pathogénomique mycobactérienne intégrée - Integrated Mycobacterial Pathogenomics, This study was funded by the Tunisian Ministry of Higher Education and Scientific Research (LR16IPT01)., and We thank Christiane Bouchier and Laurence Ma, from the Biomics platform of the Institut Pasteur, Paris, for library construction and genome sequencing, and Sinda Zarouk from Institut Pasteur, Tunis, for sample logistics.
Subjects: 0301 basic medicine, MESH: Mycobacterium fortuitum, Gene Transfer, Horizontal, Virulence Factors, Science, [SDV]Life Sciences [q-bio], 030106 microbiology, Mycobacterium Infections, Nontuberculous, Virulence, Locus (genetics), Human pathogen, MESH: Molecular Sequence Annotation, Biology, MESH: Genome, Bacterial, MESH: Phenotype, Microbiology, Article, 03 medical and health sciences, Genetics, Humans, MESH: Phylogeny, Gene, Phylogeny, MESH: Virulence Factors, Whole genome sequencing, Multidisciplinary, MESH: Humans, Mycobacterium fortuitum, MESH: Genomics, Computational Biology, Molecular Sequence Annotation, Genomics, MESH: Mycobacterium Infections, Nontuberculous, Phenotype, Mycobacterium fortuitum Complex, MESH: Gene Transfer, Horizontal, 030104 developmental biology, Horizontal gene transfer, Medicine, Genome, Bacterial, MESH: Computational Biology
Abstract: Previously, we have identified a putative novel rapidly growing Mycobacterium species, referred to as TNTM28, recovered from the sputum of an apparently immunocompetent young man with an underlying pulmonary disease. Here we provide a thorough characterization of TNTM28 genome sequence, which consists of one chromosome of 5,526,191 bp with a 67.3% G + C content, and a total of 5193 predicted coding sequences. Phylogenomic analyses revealed a deep-rooting relationship to the Mycobacterium fortuitum complex, thus suggesting a new taxonomic entity. TNTM28 was predicted to be a human pathogen with a probability of 0.804, reflecting the identification of several virulence factors, including export systems (Sec, Tat, and ESX), a nearly complete set of Mce proteins, toxin-antitoxins systems, and an extended range of other genes involved in intramacrophage replication and persistence (hspX, ahpC, sodA, sodC, katG, mgtC, ClpR, virS, etc.), some of which had likely been acquired through horizontal gene transfer. Such an arsenal of potential virulence factors, along with an almost intact ESX-1 locus, might have significantly contributed to TNTM28 pathogenicity, as witnessed by its ability to replicate efficiently in macrophages. Overall, the identification of this new species as a potential human pathogen will help to broaden our understanding of mycobacterial pathogenesis.
Published: 2021

9. Highly Resistant Cholera Outbreak Strain in Zimbabwe

Author: Andrew Tarupiwa, Anthony M. Smith, Sekesai Mtapuri-Zinyowera, François-Xavier Weill, Portia Manangazira, Tapfumanei Mashe, Prosper Chonzi, Daryl Domman, Isaac K. Phiri, Masindi Ramudzulu, Elisabeth Njamkepo, Kudzai P.E. Masunda, Ministry of Health and Child Care [Harare], The University of New Mexico [Albuquerque], Beatrice Road Infectious Diseases Hospital [Harare, Zimbabwé], Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris] (IP), National Institute for Communicable Diseases [Johannesburg] (NICD), and Institut Pasteur [Paris]
Subjects: DNA, Bacterial, Zimbabwe, Drug resistance, 030204 cardiovascular system & hematology, MESH: Genome, Bacterial, medicine.disease_cause, Genome, Cholera outbreak, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, Cholera, MESH: Cholera, Phylogenetics, MESH: Anti-Bacterial Agents, Drug Resistance, Bacterial, MESH: Drug Resistance, Bacterial, medicine, Humans, 030212 general & internal medicine, MESH: Disease Outbreaks, MESH: Phylogeny, Vibrio cholerae, Phylogeny, ComputingMilieux_MISCELLANEOUS, MESH: Humans, business.industry, Strain (biology), Outbreak, General Medicine, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virology, Anti-Bacterial Agents, 3. Good health, MESH: Zimbabwe, business, Genome, Bacterial, MESH: Vibrio cholerae
Abstract: Highly Resistant Cholera Outbreak Strain in Zimbabwe Whole genomes of 11 Vibrio cholerae O1 isolates from the 2018–2019 outbreak in Zimbabwe were sequenced to investigate the determinants of antimi...
Published: 2020

10. The impact of genetic diversity on gene essentiality within the E. coli species

Author: Rousset, François, Caballero, José, Piastra-Facon, Florence, Fernández-Rodríguez, Jesús, Clermont, Olivier, Denamur, Erick, Rocha, Eduardo, Bikard, David, Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris] (IP), Collège Doctoral, Sorbonne Université (SU), Eligo Bioscience, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 677823), by the French Government’s Investissement d’Avenir programme and by Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID). F.R. is supported by a doctoral scholarship from Ecole Normale Supérieure. E.D. was partially supported by the ‘Fondation pour la Recherche Médicale’ (Equipe FRM 2016, grant no. DEQ20161136698). E.P.C.R. was partially supported by the ‘Fondation pour la Recherche Médicale’ (Equipe FRM EQU201903007835)., We thank B. Dupuy for sharing the use of the anaerobic chamber, as well as O. Tenaillon, P.-A. Kaminsky, G. Sezonov, A. Danchin and A. Calvo-Villamañan for useful discussions. We thank the P2M platform (Institut Pasteur, Paris, France) for genome sequencing and V. Briolat from the Biomics platform, C2RT, Institut Pasteur, Paris, France, supported by France Génomique (ANR-10-INBS-09-09) and IBISA. We also thank J. Rodríguez-Beltrán and S. Brisse for providing a strain of Citrobacter freundii and Klebsiella pneumoniae, respectively, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016), Bikard, David, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Study of the interplay between CRISPR interference and DNA repair pathways towards the development of novel CRISPR tools - CRISPAIR - - H20202016-03-01 - 2021-02-28 - 677823 - VALID, Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Gene Expression, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: DNA Transposable Elements, MESH: Genetic Fitness, MESH: Escherichia coli, MESH: Species Specificity, MESH: Genetic Variation, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Genome, Bacterial, MESH: Phylogeny, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Genes, Essential
Abstract: International audience; Bacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have unraveled genes required for fitness in various experimental conditions at the genome scale, most studies have focused on single model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell remains largely under-investigated. Here, we developed a new CRISPR interference platform for highthroughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of ~3,400 nearly ubiquitous genes in 3 growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens revealed extensive variations in gene essentiality between strains and conditions. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how prophage-encoded defense systems against phage infection can trigger the essentiality of persistent genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species under diverse conditions.
Published: 2021

11. Listeria spp. Isolated from Tonsils of Wild Deer and Boars: Genomic Characterization

Author: Carla Palacios-Gorba, Juan J. Quereda, Marc Lecuit, Jesús Gomis, María L. Mocé, Ángel Gómez-Martín, Alexandre Leclercq, E. Jiménez-Trigos, Alexandra Moura, Universidad Cardenal Herrera-CEU (CEU-UCH), Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Service des Maladies infectieuses et tropicales [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), This work was supported by Generalitat Valenciana (project reference GV/2018/A/183) and by the Spanish Ministry of Science and Innovation (project reference PID2019-110764RA-I00) (J.J.Q.), Institut Pasteur, Inserm, and Santé Publique France. J. J. Quereda is supported by a 'Ramón y Cajal' contract of the Spanish Ministry of Science, Innovation and Universities (RYC-2018-024985-I). C. Palacios-Gorba is supported by a predoctoral contract from the Universidad Cardenal Herrera-CEU., We thank Hélène Bracq-Dieye, Nathalie Tessaud-Rita, Pierre Thouvenot, and Guillaume Vales (Institut Pasteur, Paris, France) for DNA extraction and the P2M platform (Institut Pasteur, Paris, France) for genome sequencing., DIAKITE, andrée, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)
Subjects: [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV]Life Sciences [q-bio], medicine.disease_cause, MESH: Genome, Bacterial, Applied Microbiology and Biotechnology, MESH: Listeria, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Animals, MESH: Phylogeny, Pathogen, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Ecology, Public and Environmental Health Microbiology, [SDV.BA]Life Sciences [q-bio]/Animal biology, MESH: Feces, 3. Good health, wild animal, [SDV] Life Sciences [q-bio], MESH: Multilocus Sequence Typing, MESH: Palatine Tonsil, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Listeria ivanovii, MESH: Whole Genome Sequencing, Biotechnology, Population, MESH: Deer, Biology, Microbiology, 03 medical and health sciences, Listeria monocytogenes, medicine, education, Feces, 030304 developmental biology, 030306 microbiology, biology.organism_classification, Pathogenicity island, MESH: Sus scrofa, virulence, MESH: Listeriosis, tonsil, Listeria, Multilocus sequence typing, cgMLST, WGS, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Food Science
Abstract: Listeria monocytogenes is a major human and animal foodborne pathogen. However, data from environmental reservoirs remain scarce. Here, we used whole-genome sequencing to characterize Listeria species isolates recovered over 1 year from wild animals in their natural habitats in Spain. Three different Listeria spp. (L. monocytogenes [n = 19], Listeria ivanovii subsp. londoniensis [n = 4], and Listeria innocua [n = 3]) were detected in 23 animal tonsils (9 deer, 14 wild boars) and 2 feeding troughs. No Listeria species was detected in feces. L. monocytogenes was detected in tonsils of 44.4% (8 out of 18) of deer and 40.7% (11 out of 27) of wild boars. L. monocytogenes isolates belonged to 3 different core genome multilocus sequence typing (cgMLST) types (CTs) of 3 distinct sublineages (SL1, SL387, and SL155) from lineages I and II. While cgMLST type L1-SL1-ST1-CT5279 (IVb; clonal complex 1 [CC1]) occurred only in one animal, types L1-SL387-ST388-CT5239 (IVb; CC388) and L2-SL155-ST155-CT1170 (IIa; CC155) were retrieved from multiple animals. In addition, L1-SL387-ST388-CT5239 (IVb; CC388) isolates were collected 1 year apart, revealing their long-term occurrence within the animal population and/or environmental reservoir. The presence of identical L. monocytogenes strains in deer and wild boars suggests contamination from a common food or environmental source, although interhost transmission cannot be excluded. Pathogenicity islands LIPI-1, LIPI-3, and LIPI-4 were present in 100%, 5%, and 79% of the L. monocytogenes isolates, respectively, and all L. monocytogenes lineage II isolates (n = 3) carried SSI-1 stress islands. This study highlights the need for monitoring L. monocytogenes environmental contamination and the importance of tonsils as a possible L. monocytogenes intrahost reservoir. IMPORTANCEListeria monocytogenes is a foodborne bacterial pathogen responsible for listeriosis. Whole-genome sequencing has been extensively used in public health and food industries to characterize circulating Listeria isolates, but genomic data on isolates occurring in natural environments and wild animals are still scarce. Here, we show that wild animals carry pathogenic Listeria and that the same genotypes can be found at different time points in different host species. This work highlights the need of Listeria species monitoring of environmental contamination and the importance of tonsils as a possible L. monocytogenes intrahost reservoir.
Published: 2021

12. The Persistence of Staphylococcus aureus in Pressure Ulcers: A Colonising Role

Author: Catherine Dunyach-Remy, Marion Chateauraynaud, Anthony Gelis, Madjid Morsli, Jean-Philippe Lavigne, Alex Yahiaoui-Martinez, Albert Sotto, Martin Fayolle, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Virulence bactérienne et maladies infectieuses (VBMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), This research was funded by the French Society of Pressure Ulcer, and the UniversityHospital of Nîmes (2014-A00534-43), and Retiveau, Nolwenn
Subjects: Chronic wound, Staphylococcus aureus, MESH: Pressure Ulcer, MESH: Staphylococcal Infections, Virulence, MESH: Biofilms, QH426-470, MESH: Virulence, medicine.disease_cause, MESH: Genome, Bacterial, Persistence (computer science), Microbiology, Persistence, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Genetics, MESH: Staphylococcus aureus, chronic wound, Genetics (clinical), Chronic wounds, MESH: Aged, MESH: Humans, MESH: Middle Aged, biology, Strain (chemistry), Decubitus pressure ulcers, Biofilm, Colonisation, MESH: Adult, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Male, colonisation, decubitus pressure ulcers, persistence, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine.symptom, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Staphylococcus, MESH: Female, Bacteria
Abstract: Decubitus pressure ulcers (PU) are a major complication of immobilised patients. Staphylococcus aureus is one of the most frequently detected microorganisms in PU samples; however, its persistence and role in the evolution of these wounds is unknown. In this study, we analysed S. aureus strains isolated from PU biopsies at inclusion and day 28. Eleven S. aureus (21.1%) were detected in 52 patients at inclusion. Only six PUs (11.5%) continued to harbour this bacterium at day 28. Using a whole genome sequencing approach (Miseq®, Illumina), we confirmed that these six S. aureus samples isolated at D28 were the same strain as that isolated at inclusion, with less than 83 bp difference. Phenotypical studies evaluating the growth profiles (Infinite M Mano, Tecan®) and biofilm formation (Biofilm Ring Test®) did not detect any significant difference in the fitness of the pairs of S. aureus. However, using the Caenorhabditis elegans killing assay, a clear decrease of virulence was observed between strains isolated at D28 compared with those isolated at inclusion, regardless of the clinical evolution of the PU. Moreover, all strains at inclusion were less virulent than a control S. aureus strain, i.e., NSA739. An analysis of polymicrobial communities of PU (by metabarcoding approach), in which S. aureus persisted, demonstrated no impact of Staphylococcus genus on PU evolution. Our study suggested that S. aureus presented a colonising profile on PU with no influence on wound evolution.
Published: 2021

13. Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage

Author: Carla Rodrigues, Sylvain Brisse, Virginie Passet, Camille d’Humières, Grégory Papin, Etienne Ruppé, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris], Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported financially by the French Government’s Investissement d’Avenir program Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID). C.R. was financially supported by the MedVetKlebs project, a component of European Joint Programme One Health EP, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 773830., We thank the ‘Plateforme de Microbiologie Mutualisée’ of Institut Pasteur for genomic sequencing., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health EJP)(2018), Institut Pasteur [Paris] (IP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), European Project: 773830,H2020-SFS-2017-1,MedVetKlebs (a component of European Joint Programme One Health)(2018), Brisse, Sylvain, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, and Klebsiella pneumoniae: from ecology to source attribution and transmission control - MedVetKlebs (a component of European Joint Programme One Health) - - H2020-SFS-2017-12018-01-01 - 2019-12-31 - 773830 - VALID
Subjects: Klebsiella, Europe, community-acquired infection, hypervirulence, genomics, recombination, virulence plasmid, Klebsiella pneumoniae, MESH: Klebsiella pneumoniae, Virulence, [SDV.BID]Life Sciences [q-bio]/Biodiversity, MESH: Virulence, MESH: Genome, Bacterial, Yersiniabactin, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, Ampicillin, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Bacterial Proteins, 030304 developmental biology, MESH: Virulence Factors, 0303 health sciences, MESH: Humans, biology, 030306 microbiology, General Medicine, MESH: Serogroup, MESH: Drug Resistance, Multiple, Bacterial, biology.organism_classification, MESH: DNA, Bacterial, 3. Good health, Multiple drug resistance, MESH: France, MESH: Klebsiella Infections, chemistry, MESH: Community-Acquired Infections, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Aerobactin, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.BID] Life Sciences [q-bio]/Biodiversity, medicine.drug
Abstract: Klebsiella pneumoniae (Kp) reference strain Kp52.145 is widely used in experimental Klebsiella pathophysiology. Since 1935, only one other strain of the same sublineage (sequence type ST66, capsular serotype K2) was isolated (AJ210, Australia). Here, we describe a community-acquired invasive infection caused by a ST66-K2 Kp strain in France. Four hypermucoviscous Kp isolates responsible for acute otitis media, meningitis, bacteraemia and bacteriuria, respectively, were obtained from a patient with a history of chronic alcoholism and diabetes mellitus, and infected with HIV. The isolates were characterized by phenotypic and genomic methods. The four genetically identical ST66-K2 isolates presented a full antimicrobial susceptibility profile, including to ampicillin, corresponding to a single strain (SB5881), which was more closely related to AJ210 (135 SNPs) than to Kp52.145 (388 SNPs). Colibactin and yersiniabactin gene clusters were present on the integrative and conjugative element ICEKp10 in the chromosome. The two plasmids from Kp52.145 were detected in SB5881. In addition to carrying genes for virulence factors RmpA, aerobactin and salmochelin, plasmid II has acquired in SB5881, the conjugation machinery gene cluster from plasmid I. We report the first case of community-acquired infection caused by a hypervirulent ST66-K2 Kp strain in Europe. This demonstrates the long-term persistence of the high-virulence and laboratory model ST66-K2 sublineage. The combination of a conjugative apparatus and major virulence genes on a single plasmid may contribute to the co-occurrence of hypervirulence and multidrug resistance in single Kp strains.
Published: 2020

14. A synthesis of bacterial and archaeal phenotypic trait data

Author: Ross Corkrey, David Danko, Joshua S. Madin, T. B. K. Reddy, Mark Westoby, Sara Vieira-Silva, Thomas M. Schmidt, Eduardo P. C. Rocha, Martin K. M. Engqvist, Matthew A. Richards, Noah Fierer, Lisa R. Moore, Alice R. Wattam, Fran Supek, Maria Brbic, Heba Shaaban, Michael R. Gillings, Christopher E. Mason, David A. Westfall, Nikos C. Kyrpides, Daniel A. Nielsen, Maulik Shukla, Elena Litchman, Kyle F. Edwards, Jemma L. Geoghegan, Sasha G. Tetu, Søren Laurentius Nielsen, Nathan D. Price, Ian T. Paulsen, University of Hawai‘i [Mānoa] (UHM), Macquarie University [Sydney], Rudjer Boskovic Institute [Zagreb], University of Tasmania [Hobart, Australia] (UTAS), Weill Cornell Medicine [New York], Chalmers University of Technology [Gothenburg, Sweden], University of Colorado [Boulder], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Michigan State University [East Lansing], Michigan State University System, Roskilde University, Institute for Systems Biology [Seattle] (ISB), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, Argonne National Laboratory [Lemont] (ANL), Institute for Research in Biomedicine [Barcelona, Spain] (IRB), University of Barcelona-Barcelona Institute of Science and Technology (BIST), Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Virginia [Charlottesville], Weill Cornell Medicine [Cornell University], Cornell University [New York], Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and University of Virginia
Subjects: Statistics and Probability, Data Descriptor, MESH: Genome, Archaeal, Library and Information Sciences, MESH: Genome, Bacterial, MESH: Phenotype, Genome, Education, Microbial ecology, 03 medical and health sciences, Genome, Archaeal, Abundance (ecology), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Ecosystem, MESH: Ecosystem, lcsh:Science, 030304 developmental biology, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Bacteria, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Human Genome, Bacterial, Phenotypic trait, biology.organism_classification, Phenotype, Archaea, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, MESH: Bacteria, Habitat, Evolutionary biology, Archaeal, MESH: Archaea, Trait, lcsh:Q, Statistics, Probability and Uncertainty, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial, Information Systems, Biotechnology
Abstract: A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients., Measurement(s)Trait • phenotypic trait • quantitative genomic traitTechnology Type(s)digital curationFactor Type(s)habitat • speciesSample Characteristic - OrganismArchaea • BacteriaSample Characteristic - Locationglobal Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12221732
Published: 2020

15. Genome-based insights into the resistomes and mobilomes of two Providencia rettgeri strains isolated from wound infections in Madagascar

Author: Jean-Marc Collard, Lovasoa Ramparany, Pierrette Landrie Simo Tchuinte, Elisoa Ratsima, Frédérique Randrianirina, Mamitina Alain Noah Rabenandrasana, Vincent Enouf, Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Pasteur International Bioresources network (PIBNet), Institut Pasteur [Paris] (IP), This study was conducted during a postdoctoral internship supported by a Postdoctoral Grant CALMETTE and YERSIN from the Institute Pasteur Department of International Affairs., and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, Antimicrobial resistance, MESH: Genome, Bacterial, Genome, MESH: Madagascar, 0302 clinical medicine, Plasmid, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Bacterial, Providencia rettgeri, Immunology and Allergy, MESH: Genomic Islands, 030212 general & internal medicine, Insertion sequence, MESH: Phylogeny, MESH: High-Throughput Nucleotide Sequencing, Phylogeny, Wound infections, Genetics, MESH: Microbial Sensitivity Tests, biology, High-Throughput Nucleotide Sequencing, QR1-502, Anti-Bacterial Agents, Gene cassette, Horizontal gene transfer, MESH: Whole Genome Sequencing, Plasmids, Microbiology (medical), MESH: Interspersed Repetitive Sequences, Gene Transfer, Horizontal, Genomic Islands, 030106 microbiology, Immunology, Microbial Sensitivity Tests, Providencia, MESH: Providencia, Microbiology, 03 medical and health sciences, MESH: Plasmids, Intensive care, MESH: Anti-Bacterial Agents, Madagascar, MESH: Spain, MESH: United States, MESH: Wound Infection, Humans, Intensive care unit, MESH: Humans, Whole Genome Sequencing, MESH: Drug Resistance, Multiple, Bacterial, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, United States, MESH: Gene Transfer, Horizontal, Interspersed Repetitive Sequences, Spain, Wound Infection, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Mobile genetic elements, Genome, Bacterial
Abstract: Objectives A molecular analysis was performed of two Providencia rettgeri (P. rettgeri) strains (Pr 297 and Pr 269) collected in 2007 and 2009 from wound swabs of patients admitted to the intensive care units at Joseph Ravoangy Andrianavalona hospital and the Military Hospital in Antananarivo, Madagascar. Methods The two P. rettgeri isolates were subjected to susceptibility testing. Whole genome sequencing was performed to characterise the antibiotic resistance genes, genomic islands and mobilomes (integrons, plasmids and insertion sequences). Results All isolates were found to be multidrug-resistant. Antibiotic-resistant genes described were amongst eight different classes of antimicrobial agents. Thirty insertion sequences and twelve genomic islands were predicted in each genome. Class 1 and class 2 integrons were found in both genomes, with gene cassette regions encompassing arr-2 - cmlA5 - blaOXA-10 - ant (3”)-Ia and dfrA1 - sat2 - ant (3”)-Ia – orfX, respectively. IncA/C2, ColM and ColE1-like plasmids were described harbouring blaCMY-30, qnrD and aac(6’)-Ib-cr4 genes, respectively. Phylogenetic analysis showed that Pr 297 and Pr 269 isolates were genetically identical and clustered with P. rettgeri strains described in the USA and Spain. Conclusions It is believed that this is the first molecular characterisation of wound infection pathogens from Madagascan patients and the first description of P. rettgeri co-producing CMY-30, OXA-10 and AAC(6’)-Ib-cr4 enzymes. The diversity of the resistance determinants and mobile genetic elements was probably due to extensive horizontal gene transfer events, highlighting the need to conduct further molecular monitoring studies to understand the genomic plasticity of resistant bacteria in Madagascan hospitals.
Published: 2020

16. Evolution of virulence in the Mycobacterium tuberculosis complex

Author: Mickael Orgeur, Roland Brosch, Pathogénomique mycobactérienne intégrée - Integrated Mycobacterial Pathogenomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), upport by grants from the Agence National de Recherche (ANR-10-LABX-62-IBEID, ANR-16-CE15-0003 and ANR-16-CE35-0009) and from the Fondation pour la Recherche Médicale (SPF20160936136 and DEQ20130326471) are gratefully acknowledged., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CE15-0003,MTBLipVir,Analyse multi-échelle et multidisciplinaire des mécanismes intimes d'action des lipides de virulence de l'enveloppe de Mycobacterium tuberculosis(2016), ANR-16-CE35-0009,TBemerg,Naissance d'un tueur: facteurs génétiques et adaptations métaboliques impliquées dans l'émergence des bacilles tuberculeux épidémiques(2016), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), MESH: Mycobacterium tuberculosis, Tuberculosis, Virulence Factors, 030106 microbiology, Population, Virulence, Human pathogen, MESH: Virulence, MESH: Genome, Bacterial, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Microbiology, Evolution, Molecular, Mycobacterium tuberculosis, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylogenetics, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, Humans, MESH: Tuberculosis, MESH: Phylogeny, education, Phylogeny, MESH: Evolution, Molecular, MESH: Virulence Factors, Genetics, education.field_of_study, MESH: Humans, biology, MESH: Host-Pathogen Interactions, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Infectious Diseases, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Mycobacterium tuberculosis complex, Host-Pathogen Interactions, Genome, Bacterial, Mycobacterium
Abstract: International audience; Mycobacterium tuberculosis, the causative agent of human tuberculosis is one of the most widely spread human pathogens. It has succeeded to infect a quarter of the global human population by developing most sophisticated ways to circumvent innate and adaptive immune defences. This highly specialized, major human pathogen has evolved from a pool of ancestral environmental mycobacteria, whose extant representatives are known under the name of Mycobacterium canettii. Recent whole genome analyses in combination with different phenotypic screens have provided key insights into the evolution of M. tuberculosis and closely related members regrouped in the M. tuberculosis complex (MTBC). They have also elucidated novel virulence determinants that are essential for these obligate pathogens. In this review, we present the most recent evolutionary models of the MTBC and various factors that have contributed to the outstanding evolutionary success of the tuberculosis agent.
Published: 2018

17. Culex pipiens crossing type diversity is governed by an amplified and polymorphic operon of Wolbachia

Author: Bonneau, Manon, Atyame Nten, Célestine, Beji, Marwa, Justy, Fabienne, Cohen-Gonsaud, Martin, Sicard, Mathieu, Weill, Mylène, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IRD-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Sequencing data were produced through the technical facilities of the LabEX 'Centre Méditerranéen de l'Environnement et de la Biodiversité' in the GENSEQ plateform. This work was funded by the French ANR (project 'CIAWOL' ANR-16-CE02-0006-01 and ANR-10-BINF-0003)., ANR-16-CE02-0006,CIAWOL,Bases moléculaire et cellulaire de la diversité phénotypique de l'incompatibilté cytoplasmique chez les insectes(2016), ANR-10-BINF-0003,Bip:Bip,Paradigme d'inference bayesienne pour la Biologie structurale in silico(2010), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: MESH: Operon, MESH: Host Specificity, MESH: Sequence Homology, Amino Acid, Science, [SDV]Life Sciences [q-bio], MESH: Sequence Alignment, MESH: Amino Acid Sequence, MESH: Culex, MESH: Base Sequence, MESH: Genome, Bacterial, MESH: Drosophila melanogaster, MESH: Polymorphism, Genetic, parasitic diseases, MESH: Animals, lcsh:Science, MESH: Bacterial Proteins, reproductive and urinary physiology, MESH: Symbiosis, MESH: Crosses, Genetic, MESH: Male, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Wolbachia, bacteria, lcsh:Q, MESH: Female, MESH: Toxin-Antitoxin Systems
Abstract: International audience; Culex pipiens mosquitoes are infected with Wolbachia (wPip) that cause an important diversity of cytoplasmic incompatibilities (CIs). Functional transgenic studies have implicated the cidA-cidB operon from wPip and its homolog in wMel in CI between infected Drosophila males and uninfected females. However, the genetic basis of the CI diversity induced by different Wolbachia strains was unknown. We show here that the remarkable diversity of CI in the C. pipiens complex is due to the presence, in all tested wPip genomes, of several copies of the cidA-cidB operon, which undergoes diversification through recombination events. In 183 isofemale lines of C. pipiens collected worldwide, specific variations of the cidA-cidB gene repertoires are found to match crossing types. The diversification of cidA-cidB is consistent with the hypothesis of a toxin–antitoxin system in which the gene cidB co-diversifies with the gene cidA, particularly in putative domains of reciprocal interactions.
Published: 2018

18. Genomic history of the seventh pandemic of cholera in Africa

Author: François-Xavier Weill, Karen H. Keddy, Mireille Dosso, Sandra Moore, Anne Laure Page, Renaud Piarroux, Jean Michel Fournier, Antoinette Ngandjio, Monakhova Ev, Julian Parkhill, Sébastien Breurec, Monzer Hamze, Nizar Fawal, Henrik Salje, Fati Sidikou, Elisabeth Njamkepo, Asish K. Mukhopadhyay, Maria Damian, Gordon Dougan, Kathryn E. Holt, Marie Laure Quilici, Daryl Domman, Raymond Bercion, Jean Rauzier, Martin A. Mengel, Cheryl L. Tarr, Patrick A. D. Grimont, Benoit Garin, Laurence Bonte, Goutam Chowdhury, Roland Grunow, Jean Louis Koeck, Berthe Marie Njanpop-Lafourcade, Guillaume Sapriel, Myriam Henkens, Carlo Pazzani, Christiane Bouchier, Ankur Mutreja, Nicholas R. Thomson, Francisco J. Luquero, Thandavarayan Ramamurthy, Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris] (IP), The Wellcome Trust Sanger Institute [Cambridge], Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, National Institute for Communicable Diseases [Johannesburg] (NICD), University of the Witwatersrand [Johannesburg] (WITS), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), Hôpital de la Timone [CHU - APHM] (TIMONE), Université de la Méditerranée - Aix-Marseille 2, Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur de Dakar, Epicentre [Paris] [Médecins Sans Frontières], Centre Pasteur du Cameroun, Institut Pasteur de Côte d'Ivoire, Rostov-on-Don Research Institute for Plague Control, Génomique (Plate-Forme) - Genomics Platform, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), University of Cambridge [UK] (CAM), Translational Health Science and Technology Institute [Faridabad] (THSTI), Robert Koch Institute [Berlin] (RKI), Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Cantacuzino Institute [Romania], Agence de Médecine Préventive, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université Libanaise, Médecins Sans Frontières Belgique, National Institute of Cholera and Enteric Diseases, Hôpital Bouffard - Centre Hospitalier des Armées Bouffard [Djibouti], Service de Santé des Armées, Centre National de Référence des Vibrions et du Choléra - National Reference Center Vibrios and Cholera (CNR), Biodiversité des Bactéries Pathogènes Émergentes, University of Melbourne, London School of Hygiene and Tropical Medicine (LSHTM), This study was supported by the Institut Pasteur and the Institut Pasteur International Network, the Institut de Veille Sanitaire, the French government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant no. ANR-10-LABX-62-IBEID), the Fondation Le Roch-Les Mousquetaires, the Wellcome Trust through grant 098051 to the Sanger Institute, and the Indian Council of Medical Research, New Delhi, India., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Bari Aldo Moro (UNIBA), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Weill, François-Xavier [0000-0001-9941-5799], Domman, Daryl [0000-0001-5389-9185], Njamkepo, Elisabeth [0000-0001-6791-6003], Tarr, Cheryl [0000-0001-6290-365X], Fawal, Nizar [0000-0002-9914-0315], Keddy, Karen H [0000-0001-8640-2235], Salje, Henrik [0000-0003-3626-4254], Bercion, Raymond [0000-0002-0466-0407], Luquero, Francisco J [0000-0003-0885-8418], Ngandjio, Antoinette [0000-0001-9777-3656], Dosso, Mireille [0000-0003-4744-8235], Monakhova, Elena [0000-0002-9216-7777], Bouchier, Christiane [0000-0003-3549-1543], Pazzani, Carlo [0000-0003-0414-2965], Grunow, Roland [0000-0001-8966-8469], Sidikou, Fati [0000-0002-0269-5454], Njanpop-Lafourcade, Berthe-Marie [0000-0001-6211-6402], Page, Anne-Laure [0000-0001-7952-3178], Koeck, Jean-Louis [0000-0002-6493-3905], Dougan, Gordon [0000-0003-0022-965X], Grimont, Patrick AD [0000-0002-6264-136X], Parkhill, Julian [0000-0002-7069-5958], Holt, Kathryn E [0000-0003-3949-2471], Piarroux, Renaud [0000-0002-4151-4134], Thomson, Nicholas R [0000-0002-4432-8505], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, MESH: Pandemics, Asia, Lineage (genetic), Genomic data, Zoology, MESH: Vibrio cholerae O1, Biology, MESH: Genome, Bacterial, medicine.disease_cause, Africa, Southern, West africa, 03 medical and health sciences, Cholera, MESH: Cholera, Phylogenetics, MESH: Africa, Western, parasitic diseases, Pandemic, medicine, Humans, MESH: Phylogeny, Pandemics, Phylogeny, MESH: Africa, Eastern, MESH: Humans, Multidisciplinary, MESH: Asia, Transmission (medicine), MESH: Genomics, Vibrio cholerae O1, Genomics, Africa, Eastern, medicine.disease, 3. Good health, Africa, Western, 030104 developmental biology, Vibrio cholerae, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Africa, Southern, Genome, Bacterial
Abstract: Wave upon wave of diseaseThe cholera pathogen,Vibrio cholerae, is considered to be ubiquitous in water systems, making the design of eradication measures apparently fruitless. Nevertheless, local and globalVibriopopulations remain distinct. Now, Weillet al.and Dommanet al.show that a surprising diversity between continents has been established. Latin America and Africa bear different variants of cholera toxin with different transmission dynamics and ecological niches. The data are not consistent with the establishment of long-term reservoirs of pandemic cholera or with a relationship to climate events.Science, this issue p.785, p.789
Published: 2017

19. Genome characteristics of Bordetella pertussis isolates from Tunisia

Author: Sylvain Brisse, Ikram Ben Fraj, Hanen Smaoui, Valérie Bouchez, Amel Kechrid, Université de Tunis El Manar (UTM), Béchir Hamza Children's Hospital, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris], Centre National de Référence de la Coqueluche et autres bordetelloses (CNR), This research received no specific grant. It was supported financially by Institut Pasteur support to the research unit Biodiversity and Epidemiology of Bacterial Pathogens., and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Microbiology (medical), Bordetella pertussis, MESH: Sequence Analysis, DNA, Tunisia, [SDV]Life Sciences [q-bio], 030106 microbiology, Population, genomic epidemiology, MESH: Virulence, MESH: Virulence Factors, Bordetella, phylogeny, MESH: Genome, Bacterial, Microbiology, Genome, MESH: Bordetella pertussis, 03 medical and health sciences, Immunity, medicine, MESH: Molecular Epidemiology, MESH: Genetic Variation, education, MESH: Phylogeny, Whooping cough, education.field_of_study, MESH: Humans, biology, Phylogenetic tree, Transmission (medicine), Strain (biology), MESH: Bacterial Outer Membrane Proteins, MESH: Infant, Newborn, General Medicine, MESH: Whooping Cough, biology.organism_classification, medicine.disease, Virology, MESH: DNA, Bacterial, MESH: Infant, 3. Good health, 030104 developmental biology, MESH: Pertussis Vaccine, MESH: Tunisia, MESH: Antigens, Bacterial
Abstract: The genomic sequence data generated in this work were submitted to the European Nucleotide Archive and are available from the International Nucleotide Sequence Database Collaboration (NCBI/ENA/DDBJ) databases under project accession number PRJEB27412 and run data accession numbers ERS2572942 to ERS2572951.; International audience; The recent increase in pertussis cases observed in some countries may have several causes, including the evolution of Bordetella pertussis populations towards escape of vaccine-induced immunity. Most genomic studies of B. pertussis isolates performed so far are from countries that use acellular vaccines. The objective was to analyse genomic sequences of isolates collected during the 2014 whooping cough epidemic in Tunisia, a country where whole-cell vaccines are used. Ten Tunisian isolates and four vaccine strains were sequenced and compared to 169 isolates from countries where acellular vaccines are used. Phylogenetic analysis showed that Tunisian isolates are diverse, demonstrating a multi-strain 2014 epidemic peak, and are intermixed with those circulating in other world regions, showing inter-country transmission. Consistently, Tunisian isolates have antigen variant composition observed in other world regions. No pertactin-deficient strain was observed. The Tunisian B. pertussis population appears to be largely connected with populations from other countries.
Published: 2019

20. The use of genomic DNA sequences as type material for valid publication of bacterial species names will have severe implications for clinical microbiology and related disciplines

Author: Magne Bisgaard, J. Michael Janda, Niels Nørskov-Lauritsen, Henrik Christensen, Alexandr Nemec, Dominique Clermont, Frans A. G. Reubsaet, Jörg Overmann, Edward R. B. Moore, Lenie Dijkshoorn, Bisgaard Consulting, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU), Collection de l'Institut Pasteur (CIP), Institut Pasteur [Paris], Leiden University Medical Center (LUMC), Kern County Public Health Laboratory [Bakersfield], University of Gothenburg (GU), Laboratory of Bacterial Genetics, National Institute of Public Health, Department of Clinical Microbiology, Aarhus University Hospital, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), Braunschweig University of Technology, National Institute of Public Health and the Environment (NIPHE), University of Copenhagen = Københavns Universitet (UCPH), Institut Pasteur [Paris] (IP), and Universiteit Leiden
Subjects: DNA, Bacterial, Microbiology (medical), MESH: Terminology as Topic, MESH: Bacterial Infections, [SDV]Life Sciences [q-bio], Computational biology, Biology, MESH: Genome, Bacterial, 03 medical and health sciences, Type (biology), Terminology as Topic, MESH: Publishing, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Publishing, 0303 health sciences, Bacteria, 030306 microbiology, Bacterial Infections, General Medicine, MESH: DNA, Bacterial, 3. Good health, genomic DNA, Clinical microbiology, MESH: Bacteria, Infectious Diseases, [SDE]Environmental Sciences, Genome, Bacterial
Abstract: International audience
Published: 2019

21. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

Author: Daniel J. Wilson, Frank Møller Aarestrup, Rene S. Hendriksen, Dorte Lau Baggesen, Ole Lund, David W. Ussery, Se-Ran Jun, Simon Le Hello, Pimlapas Leekitcharoenphon, Derrick W. Crook, François-Xavier Weill, Center for Biological Sequence Analysis [Lyngby], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Institut Pasteur [Paris] (IP), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, John Radcliffe Hospital [Oxford University Hospital], The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford, This study was supported by the Center for Genomic Epidemiology (09-067103/DSF) (www.genomicepidemiology.org). D.J.W. is a Sir HenryDale Fellow, jointly funded by the Wellcome Trust and the Royal Society (grant 101237/Z/13/Z).The Wellcome Trust and the Royal Society provided funding to Daniel J. Wilson under grant number 101237/Z/13/Z. Center for Genomic Epidemiology (CGE) provided funding to Pimlapas Leekitcharoenphon under grant number 09-067103/DSF., Technical University of Denmark [Lyngby] (DTU), Institut Pasteur [Paris], and University of Oxford [Oxford]
Subjects: 0301 basic medicine, Serotype, Salmonella typhimurium, MESH: Sequence Analysis, DNA, Salmonella, MESH: Swine Diseases, Swine, animal diseases, MESH: Global Health, MESH: Genome, Bacterial, medicine.disease_cause, Global Health, Applied Microbiology and Biotechnology, law.invention, MESH: Genotype, law, Genomic island, Drug Resistance, Multiple, Bacterial, Genotype, MESH: Animals, Spotlight, MESH: Swine, MESH: Evolution, Molecular, Genetics, Swine Diseases, Molecular Epidemiology, MESH: Molecular Typing, Ecology, biology, Phylogenetic tree, MESH: Polymorphism, Single Nucleotide, 3. Good health, Phylogeography, Transmission (mechanics), MESH: Phylogeography, Salmonella enterica, Salmonella Infections, Biotechnology, MESH: Salmonella Infections, Animal, 030106 microbiology, Polymorphism, Single Nucleotide, Evolution, Molecular, 03 medical and health sciences, MESH: Spatio-Temporal Analysis, Spatio-Temporal Analysis, medicine, MESH: Molecular Epidemiology, Animals, Humans, Evolutionary and Genomic Microbiology, Salmonella Infections, Animal, MESH: Humans, MESH: Salmonella Infections, Molecular epidemiology, MESH: Salmonella typhimurium, MESH: Drug Resistance, Multiple, Bacterial, Sequence Analysis, DNA, biology.organism_classification, Virology, Molecular Typing, 030104 developmental biology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Genome, Bacterial, Food Science
Abstract: It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315 S . Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ∼1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ∼1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ∼1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonella from pig herds in Denmark from 1996 to 2000. The results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections.
Published: 2019

22. Crosstalk between Entamoeba histolytica and the human intestinal tract during amoebiasis

Author: Elisabeth Labruyère, Nancy Guillén, Jean-Christophe Olivo-Marin, Roman Thibeaux, Analyse d'images biologiques - Biological Image Analysis (BIA), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie Cellulaire du Parasitisme, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie des Interactions Hôte-Parasite - Biology of Host-Parasite Interactions, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This work was funded by the Institut Pasteur (through grants PTR-178 and PTR 392), the French National Agency for Research (ANR, through grants ANR-MIE-08 Intestinalamibe and ANR-2010-GENM-0011-01, GENAMIBE), and the French Parasitology consortium Labex ParaFrap (through the grant ANR-11-LABX0024)., We acknowledge the contribution of the Institut Pasteur's Transcriptome and EpiGenome Facility and Imagopole to data analysis and microscopy images. We thank the DIM Ile-de-France program for support us in the acquisition of the two-photon microscope., ANR-08-MIEN-0017,INTESTINALAMIBE,Analyse moléculaire et cellulaire de la mobilité et du processus infectieux de Entamoeba histolytica pendant l'amibiase(2008), ANR-10-GENM-0011,GENAMIBE,Comprendre la pathogenicité de Entamoeba par l'utilisation de la transcriptomique et la phylogénétique comparatives(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, MESH: Inflammation, MESH: Genome, Bacterial, MESH: Amebiasis / physiopathology, Entamoeba, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Animals, colon explants, Intestinal Mucosa, MESH: Intestinal Mucosa / parasitology, Entamoeba histolytica, Amebiasis, MESH: Colon / parasitology, Intestinal epithelium, 3. Good health, Crosstalk (biology), Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Lytic cycle, MESH: Host-Parasite Interactions, Signal Transduction, MESH: Intestinal Mucosa / physiology, Colon, 030106 microbiology, Virulence, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Host-Parasite Interactions, Microbiology, 03 medical and health sciences, Immune system, parasitic diseases, medicine, MESH: Colon / cytology, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, Humans, Amoebiasis, MESH: Entamoeba histolytica / pathogenicity, Inflammation, MESH: Humans, MESH: Transcriptome, medicine.disease, biology.organism_classification, MESH: Signal Transduction, 030104 developmental biology, Animal Science and Zoology, Parasitology, Transcriptome, MESH: Amebiasis / parasitology, Genome, Bacterial
Abstract: The protozoan parasite Entamoeba histolytica is the microbial agent of amoebiasis – an infection that is endemic worldwide and is associated with high morbidity and mortality rates. As the disease develops, virulent E. histolytica deplete the mucus layer, interact with the intestinal epithelium, and then degrade the colonic mucosa and disrupt the extracellular matrix (ECM). Our research demonstrated that virulent parasites with an invasive phenotype display rapid, highly specific changes in their transcriptome (notably for essential factors involved in carbohydrate metabolism and the processing of glycosylated residues). Moreover, combined activation of parasite and host lytic enzymes leads to the destruction of the intestinal parenchyma. Together, these enzymes degrade the mucus layer and the ECM, and trigger the inflammatory response essential to the development of amoebiasis.
Published: 2019

23. Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics

Author: Farida Zinini, Olivier Schiettekatte, Mathieu Picardeau, Julien Guglielmini, Sylvain Brisse, Pascale Bourhy, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre Collaborateur FAO/OMS pour l'épidémiologie de la leptospirose, Institut Pasteur [Paris], Biologie des Spirochètes / Biology of Spirochetes, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, This work was supported in part by a donation from Foundation MSD to the ‘PIBnet’ programme of Institut Pasteur, by Public Health France (SPF), and by Institut Pasteur through grant PTR 30-2017. This work was part of the PhD thesis of O. S. who received financial support from 'Universite ́ Paris Diderot' and 'Sorbonne Paris Cite ́'. The funders had no role in the design, conduct or conclusions of the study., We thank the technicians of the National Reference Center for Leptospirosis, in particular Céline Lorioux, for cultures and typing of Leptospira strains, and Evelyne Bégaud and Chantal Bizet from Collection de l’Institut Pasteur (CIP) for providing type and reference strains. We thank Cyrille Goarant (Institut Pasteur de Nouméa, New Caledonia), Anissa Amara Korba (Institut Pasteur d’Alger, Algeria), Fairuz Amran (Institute for Medical Research, Malaysia), Toshiyuki Masuzawa (Chiba Institute of Science, Japan), Vasantha Kumari Neela (Universiti Putra Malaysia, Malaysia) and Alejandro Buschiazzo, Leticia Zarantonelli and the consortium 'Grupo de Trabajo Interinstitucional de Leptospirosis' (Institut Pasteur Montevideo/UdelaR/ INIA/MGAP, Uruguay) for sharing Leptospira isolates. We also thank Vincent Enouf and the team of core facility P2M (Institut Pasteur, Mutualized Platform for Microbiology) for genomic sequencing., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, MESH: Leptospira/isolation & purification, [SDV]Life Sciences [q-bio], RC955-962, MESH: Genome, Bacterial, Pathology and Laboratory Medicine, Disease Outbreaks, MESH: Genotype, 0302 clinical medicine, Arctic medicine. Tropical medicine, Medicine and Health Sciences, MESH: Animals, MESH: Disease Outbreaks, MESH: Phylogeny, Phylogeny, Data Management, Leptospira, Geography, Phylogenetic tree, Phylogenetic Analysis, Genomics, MESH: Leptospira/classification, Bacterial Pathogens, Phylogenetics, Leptospira Interrogans, Phylogeography, MESH: Multilocus Sequence Typing, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Biogeography, Medical Microbiology, Pathogens, Public aspects of medicine, RA1-1270, MESH: Leptospirosis/microbiology, MESH: Whole Genome Sequencing, Leptospira interrogans, Research Article, Computer and Information Sciences, Genotyping, MESH: Leptospira/genetics, Genotype, 030231 tropical medicine, Environment, Biology, Serogroup, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Genetics, Animals, Humans, Leptospirosis, Evolutionary Systematics, MESH: Environment, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, Taxonomy, Whole genome sequencing, Evolutionary Biology, MESH: Humans, Whole Genome Sequencing, Bacteria, Population Biology, Ecology and Environmental Sciences, Organisms, Public Health, Environmental and Occupational Health, Correction, Biology and Life Sciences, Computational Biology, MESH: Serogroup, Genome Analysis, biology.organism_classification, bacterial infections and mycoses, 030104 developmental biology, Genetic Loci, Evolutionary biology, Earth Sciences, Multilocus sequence typing, Genome, Bacterial, Population Genetics, Multilocus Sequence Typing
Abstract: Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to, Author summary Leptospirosis, caused by pathogenic Leptospira strains, is an emerging bacterial zoonotic disease mostly affecting humans in tropical countries. Despite its public health importance, little is known about the strains that are circulating worldwide due to the lack of a universal common language on strain types. In this work we describe a new strain genotyping and classification system that is highly standardized, thus facilitating global collaboration, and that can discriminate all members of the Leptospira genus at high resolution. We then examine the genetic diversity of Leptospira strains from different origins. This study provides a framework for optimizing diagnostic methods and epidemiological surveillance of leptospirosis.
Published: 2019

24. Atypical Hemolytic Listeria innocua Isolates Are Virulent, albeit Less than Listeria monocytogenes

Author: Alexandra Moura, Alexandre Leclercq, Morgane Lavina, Olivier Disson, Athmanya K. Eshwar, Marc Lecuit, Maria Fredriksson-Ahomaa, Pierre Thouvenot, Lei Huang, Roger Stephan, Centre National de Référence Listeria - Biologie des Infections (CNRL), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre collaborateur de l'OMS Listeria - Biologie des Infections (CCOMS), Biologie des Infections - Biology of Infection, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, Université Paris Diderot - Paris 7 (UPD7), University of Helsinki, Institute for Food Safety and Hygiene, University of Zürich [Zürich] (UZH), Service des Maladies infectieuses et tropicales [CHU Necker], Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP]-Institut des Maladies Génétiques Imagine [Paris], Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Institut des Maladies Génétiques Imagine [Paris], Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), University of Zurich, Freitag, Nancy E, and Lecuit, Marc
Subjects: inlA, L innocua, [SDV]Life Sciences [q-bio], 2405 Parasitology, LIPI, MESH: Virulence, medicine.disease_cause, MESH: Genome, Bacterial, MESH: Listeria monocytogenes, MESH: Bird Diseases, Feces, listeriosis, MESH: Listeria, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Ducks, MESH: Genomic Islands, MESH: Animals, Galliformes, MESH: Phylogeny, MESH: Bacterial Proteins, Phylogeny, 2. Zero hunger, 0303 health sciences, biology, Strain (chemistry), 2404 Microbiology, MESH: Feces, MESH: Galliformes, 3. Good health, Infectious Diseases, medicine.anatomical_structure, Ducks, MESH: Whole Genome Sequencing, Genomic Islands, Listeria, Immunology, Virulence, 610 Medicine & health, Spleen, Microbiology, 03 medical and health sciences, Listeria monocytogenes, Bacterial Proteins, medicine, Animals, Humans, Internalin, Serotyping, Gene, 10082 Institute of Food Safety and Hygiene, 030304 developmental biology, 2403 Immunology, MESH: Humans, Whole Genome Sequencing, 030306 microbiology, Bird Diseases, MESH: Serotyping, 2725 Infectious Diseases, biology.organism_classification, Pathogenicity island, Molecular Pathogenesis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, virulence, L. innocua, MESH: Listeriosis, 570 Life sciences, Parasitology, Genome, Bacterial, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Listeria innocua is considered a nonpathogenic Listeria species. Natural atypical hemolytic L. innocua isolates have been reported but have not been characterized in detail. Here, we report the genomic and functional characterization of representative isolates from the two known natural hemolytic L. innocua clades. Whole-genome sequencing confirmed the presence of Listeria pathogenicity islands (LIPI) characteristic of Listeria monocytogenes species. Functional assays showed that LIPI-1 and inlA genes are transcribed, and the corresponding gene products are expressed and functional. Using in vitro and in vivo assays, we show that atypical hemolytic L. innocua is virulent, can actively cross the intestinal epithelium, and spreads systemi-cally to the liver and spleen, albeit to a lesser degree than the reference L. monocy-togenes EGDe strain. Although human exposure to hemolytic L. innocua is likely rare, these findings are important for food safety and public health. The presence of viru-lence traits in some L. innocua clades supports the existence of a common virulent ancestor of L. monocytogenes and L. innocua.
Published: 2019

25. More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

Author: Gordon Dougan, Ana Elena Pérez-Cobas, Christophe Rusniok, Sandra Reuter, Carmen Buchrieser, Jasmin Demirtas, Shivani Pasricha, Elizabeth L. Hartland, Gunnar N. Schroeder, Gad Frankel, S. Jarraud, Sonia Mondino, Laura Gomez-Valero, Johannes Crumbach, Monica Rolando, Stéphane Descorps-Declère, Danielle Carson, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Medical Research Council Centre for Molecular Bacteriology and Infection [Londres, Royaume-Uni] (MRC CMBI), Imperial College London, Department of Life Sciences, The Peter Doherty Institute for Infection and Immunity [Melbourne], University of Melbourne-The Royal Melbourne Hospital, The Wellcome Trust Sanger Institute [Cambridge], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Monash University [Clayton], Centre for Innate Immunity and Infectious Diseases [Clayton] (CiiiD), Hudson Institute of Medical Research [Clayton], Centre National de Référence des Légionelles (CNR), Pathogenèse des légionelles- Legionella pathogenesis (LegioPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Wellcome-Wolfson Institute For Experimental Medicine [Belfast] (WWIEM), School of Medicine, Dentistry and Biomedical Sciences [Belfast], Queen's University [Belfast] (QUB)-Queen's University [Belfast] (QUB), Work in the C.B. laboratory is financed by the Institut Pasteur, the Agence Nationale de la Recherche Grant ANR-10-LABX-62-IBEID, and the Fondation pour la Recherche Médicale Grant DEQ20120323697., We thank Tim P. Stinear for critical reading of the manuscript and helpful comments, and we acknowledge the receipt of 53 different Legionella strains from the Collection of the Institut Pasteur., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Rolando, Monica [0000-0002-3710-0115], Apollo - University of Cambridge Repository, HOFFMANN, Isabelle, and Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID
Subjects: Intracellular Space, MESH: Intracellular Space/microbiology, co-evolution, Legionella pneumophila, Genome, protozoa, human pathogen, MESH: Computational Biology/methods, MESH: Bacterial Secretion Systems/genetics, MESH: Phylogeny, Bacterial Secretion Systems, Phylogeny, virulence 29 30, MESH: Evolution, Molecular, Genetics, 0303 health sciences, Multidisciplinary, biology, Effector, Genomics, Phenotype, MESH: Genomics/methods, Horizontal gene transfer, coevolution, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], horizontal gene transfer, MESH: Protein Domains, MESH: Bacterial Proteins/chemistry, Legionella, Protein domain, MESH: Bacterial Proteins/genetics, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, Protein Domains, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Gene, MESH: Legionella/classification, 030304 developmental biology, Legionellosis, MESH: Humans, 030306 microbiology, Computational Biology, MESH: Genome, Bacterial, biology.organism_classification, MESH: Legionellosis/microbiology, MESH: Legionella/physiology, Genome, Bacterial
Abstract: The genus Legionella comprises 65 species, among which Legionella pneumophila is a human pathogen causing severe pneumonia. To understand the evolution of an environmental to an accidental human pathogen, we have functionally analyzed 80 Legionella genomes spanning 58 species. Uniquely, an immense repository of 18,000 secreted proteins encoding 137 different eukaryotic-like domains and over 200 eukaryotic-like proteins is paired with a highly conserved type IV secretion system (T4SS). Specifically, we show that eukaryotic Rho- and Rab-GTPase domains are found nearly exclusively in eukaryotes and Legionella . Translocation assays for selected Rab-GTPase proteins revealed that they are indeed T4SS secreted substrates. Furthermore, F-box, U-box, and SET domains were present in >70% of all species, suggesting that manipulation of host signal transduction, protein turnover, and chromatin modification pathways are fundamental intracellular replication strategies for legionellae. In contrast, the Sec-7 domain was restricted to L. pneumophila and seven other species, indicating effector repertoire tailoring within different amoebae. Functional screening of 47 species revealed 60% were competent for intracellular replication in THP-1 cells, but interestingly, this phenotype was associated with diverse effector assemblages. These data, combined with evolutionary analysis, indicate that the capacity to infect eukaryotic cells has been acquired independently many times within the genus and that a highly conserved yet versatile T4SS secretes an exceptional number of different proteins shaped by interdomain gene transfer. Furthermore, we revealed the surprising extent to which legionellae have coopted genes and thus cellular functions from their eukaryotic hosts, providing an understanding of how dynamic reshuffling and gene acquisition have led to the emergence of major human pathogens.
Published: 2019

26. Fitness restoration of a genetically tractable Enterococcus faecalis V583 derivative to study decoration-related phenotypes of the enterococcal polysaccharide antigen

Author: Sylviane Furlan, Lionel Rigottier-Gois, Renata C. Matos, Benoît Doublet, Pascale Serror, Sean Kennedy, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), We are grateful for excellent assistance from Mathilde Bauducel, Jérôme Pottier, and Bernard Cayron of IERP Unit (INRA Jouy-en-Josas) and from Christine Longin and Martine Letheule of MIMA2 (INRA Jouy-en-Josas) and from Isabelle Foubert (INRA Nouzilly). We are grateful to Sébastien Nouaille for providing strain VE14037. We also thank Stéphane Mesnage for stimulating discussion and Cristel Archambaud and Francis Repoila for critical reading of the manuscript., Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: Molecular Biology and Physiology, MESH: Larva/microbiology, [SDV]Life Sciences [q-bio], MESH: Virulence, Moths, MESH: Genome, Bacterial, Genome, MESH: Moths/microbiology, Mice, Plasmid, epa variable region, MESH: Polysaccharides, Bacterial/genetics, Enterococcus faecalis, MESH: Animals, Genetics, Animal biology, 0303 health sciences, biology, Virulence, MESH: Polymorphism, Single Nucleotide, Polysaccharides, Bacterial, host adaptation, growth fitness, genome and SNP analyses, platform strain, MESH: Genetic Fitness, QR1-502, Phenotype, Larva, Host adaptation, MESH: Bacterial Proteins/genetics, MESH: Whole Genome Sequencing, Research Article, Virulence Factors, MESH: Enterococcus faecalis/pathogenicity, Locus (genetics), MESH: Phenotype, Polymorphism, Single Nucleotide, Microbiology, 03 medical and health sciences, Bacterial Proteins, Genetic variation, Biologie animale, MESH: Virulence Factors/genetics, Animals, Point Mutation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Mice, Molecular Biology, Gene, MESH: Point Mutation, 030304 developmental biology, Whole Genome Sequencing, MESH: Enterococcus faecalis/genetics, 030306 microbiology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genetic Fitness, Genome, Bacterial
Abstract: E. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle., Commensal and generally harmless in healthy individuals, Enterococcus faecalis causes opportunistic infections in immunocompromised patients. Plasmid-cured E. faecalis strain VE14089, derived from sequenced reference strain V583, is widely used for functional studies due to its improved genetic amenability. Although strain VE14089 has no major DNA rearrangements, with the exception of an ∼20-kb integrated region of pTEF1 plasmid, the strain presented significant growth differences from the V583 reference strain of our collection (renamed VE14002). In the present study, genome sequencing of strain VE14089 identified additional point mutations. Excision of the integrated pTEF1 plasmid region and sequential restoration of wild-type alleles showing nonsilent mutations were performed to obtain the VE18379 reference-derivative strain. Recovery of the growth ability of the restored VE18379 strain at a level similar to that seen with the reference strain points to GreA and Spx as bacterial fitness determinants. Virulence potential in Galleria mellonella and intestinal colonization in mouse demonstrated host adaptation of the VE18379 strain equivalent to VE14002 host adaptation. We further demonstrated that deletion of the 16.8-kb variable region of the epa locus recapitulates the key role of Epa decoration in host adaptation, providing a genetic system to study the role of specific epa-variable regions in host adaptation independently of other genetic variations. IMPORTANCE E. faecalis strain VE14089 was derived from V583 cured of its plasmids. Although VE14089 had no major DNA rearrangements, it presented significant growth and host adaptation differences from the reference strain V583 of our collection. To construct a strain with better fitness, we sequenced the genome of VE14089, identified single nucleotide polymorphisms (SNPs), and repaired the genes that could account for these changes. Using this reference-derivative strain, we provide a novel genetic system to understand the role of the variable region of epa in the enterococcal lifestyle.
Published: 2019

27. Neisseria meningitidisSerogroup X in Sub-Saharan Africa

Author: Alain Agnememel, Muhamed-Kheir Taha, Eva Hong, Viginia Nuñez-Samudio, Dario Giorgini, Ala-Eddine Deghmane, Institut Pasteur [Paris], This work was supported by the Institut Pasteur and by funding from the Fondation Total including a fellowship to A.A. This study made use of the Neisseria Multilocus Sequence Typing website (http://pubmlst.org/neisseria/), developed by Keith Jolley and sited at the University of Oxford, and the dynamic imaging facilities of Imagopole at the Institut Pasteur, Paris. The development of this site has been funded by the Wellcome Trust and European Union. This study also made use of the Meningitis Research Foundation Meningococcus Genome Library (http://www.meningitis.org/research/genome) developed by Public Health England, the Wellcome Trust Sanger Institute, and the University of Oxford., and Institut Pasteur [Paris] (IP)
Subjects: sub-Saharan Africa, 0301 basic medicine, Serotype, Neisseria meningitidis Serogroup X in Sub-Saharan Africa, Epidemiology, Gene Expression, lcsh:Medicine, MESH: Virulence, Neisseria meningitidis, MESH: Genome, Bacterial, medicine.disease_cause, Mice, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genes, Reporter, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, bacteria, Luciferases, MESH: High-Throughput Nucleotide Sequencing, Phylogeny, Mice, Inbred BALB C, Optical Imaging, MESH: Meningitis, Meningococcal, Dispatch, meningococci, High-Throughput Nucleotide Sequencing, meningitis, Europe, Infectious Diseases, whole-genome sequencing, Microbiology (medical), MESH: Operon, MESH: Gene Expression, Sub saharan, MESH: Mice, Transgenic, 030106 microbiology, MESH: Mice, Inbred BALB C, Virulence, Mice, Transgenic, Meningitis, Meningococcal, Biology, Serogroup, Meningococcal disease, MESH: Neisseria meningitidis, Neisseria meningitidis serogroup X, lcsh:Infectious and parasitic diseases, Microbiology, 03 medical and health sciences, Optical imaging, Operon, parasitic diseases, medicine, Animals, Humans, emergence, lcsh:RC109-216, MESH: Africa South of the Sahara, serogroup X, Serotyping, MESH: Mice, Africa South of the Sahara, Whole genome sequencing, MESH: Optical Imaging, MESH: Humans, MESH: Clone Cells, MESH: Genes, Reporter, lcsh:R, MESH: Serotyping, Genetic Variation, MESH: Serogroup, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virology, Clone Cells, virulence, Disease Models, Animal, MESH: Luciferases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Europe, MESH: Disease Models, Animal, Genome, Bacterial
Abstract: International audience; The epidemiology of meningococcal disease varies by geography and time. Whole-genome sequencing of Neisseria meningitidis serogroup X isolates from sub-Saharan Africa and Europe showed that serogroup X emergence in sub-Saharan Africa resulted from expansion of particular variants within clonal complex 181. Virulence of these isolates in experimental mouse models was high.
Published: 2016

28. RD5-mediated lack of PE_PGRS and PPE-MPTR export in BCG vaccine strains results in strong reduction of antigenic repertoire but little impact on protection

Author: Louis S. Ates, Merel P.M. Damen, Roland Brosch, Daria Bottai, Wafa Frigui, Fadel Sayes, Laleh Majlessi, Wilbert Bitter, Marcel A. Behr, Roy Ummels, Jeroen W. J. van Heijst, Pathogénomique mycobactérienne intégrée - Integrated Mycobacterial Pathogenomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Amsterdam [Amsterdam] (UvA), Vrije Universiteit Amsterdam [Amsterdam] (VU), VU University Medical Center [Amsterdam], University of Pisa - Università di Pisa, McGill University Health Center [Montreal] (MUHC), LSA and RB acknowledge the support in part by grants of the Agence national de la Recherche ANR-14-JAMR-001-02, ANR-10-LABX-62-IBEID, and ANR-16-CE35-0009, the Fondation pour la Recherche Médicale FRM (DEQ20130326471) and the European Union's Horizon 2020 Research and Innovation Program grant TBVAC2020 643381. LSA and JWJvH are supported by the Netherlands Organisation for Scientific Research (Vidi grant 91717305 to JWJvH)., VU University medical center, Medical Microbiology and Infection Prevention, AII - Infectious diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE35-0009,TBemerg,Naissance d'un tueur: facteurs génétiques et adaptations métaboliques impliquées dans l'émergence des bacilles tuberculeux épidémiques(2016), Experimental Immunology, AIMMS, and Molecular Microbiology
Subjects: MESH: Mycobacterium tuberculosis, Pathology and Laboratory Medicine, MESH: Genome, Bacterial, Biochemistry, Mice, Animal Cells, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Microbial Physiology, MESH: Animals, Bacterial Physiology, Biology (General), Immune Response, MESH: Bacterial Proteins, 3. Good health, Actinobacteria, Multigene Family, MESH: Membrane Proteins, Cellular Types, Tuberculosis, QH301-705.5, Virulence Factors, Immune Cells, Immunology, Virulence, Microbiology, Mycobacterium tuberculosis, 03 medical and health sciences, Antigen, SDG 3 - Good Health and Well-being, Bacterial Proteins, Genetics, Secretion, Molecular Biology, Blood Cells, Bacteria, Organisms, Biology and Life Sciences, Protein Secretion, Proteins, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Mice, Inbred C57BL, 030104 developmental biology, MESH: Multigene Family, Parasitology, Immunologic diseases. Allergy, Physiological Processes, BCG vaccine, MESH: Female, 0301 basic medicine, Physiology, Secretion Systems, MESH: Virulence, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, White Blood Cells, Immune Physiology, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Medicine and Health Sciences, MESH: Tuberculosis, Tuberculosis Vaccines, MESH: Bacterial Secretion Systems, Bacterial Secretion Systems, Mice, Inbred BALB C, Vaccines, Immune System Proteins, biology, T Cells, Protein Transport, Infectious Diseases, Cell Processes, Female, Pathogens, Tuberculosis vaccines, Research Article, Infectious Disease Control, MESH: Mice, Inbred BALB C, Immune system, MESH: Mice, Inbred C57BL, Virology, medicine, Animals, Antigens, MESH: Mice, Antigens, Bacterial, Membrane Proteins, Bacteriology, Cell Biology, RC581-607, biology.organism_classification, MESH: Tuberculosis Vaccines, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Genome, Bacterial, MESH: Antigens, Bacterial
Abstract: Tuberculosis is the deadliest infectious disease worldwide. Although the BCG vaccine is widely used, it does not efficiently protect against pulmonary tuberculosis and an improved tuberculosis vaccine is therefore urgently needed. Mycobacterium tuberculosis uses different ESX/Type VII secretion (T7S) systems to transport proteins important for virulence and host immune responses. We recently reported that secretion of T7S substrates belonging to the mycobacteria-specific Pro-Glu (PE) and Pro-Pro-Glu (PPE) proteins of the PGRS (polymorphic GC-rich sequences) and MPTR (major polymorphic tandem repeat) subfamilies required both a functional ESX-5 system and a functional PPE38/71 protein for secretion. Inactivation of ppe38/71 and the resulting loss of PE_PGRS/PPE-MPTR secretion were linked to increased virulence of M. tuberculosis strains. Here, we show that a predicted total of 89 PE_PGRS/PPE-MPTR surface proteins are not exported by certain animal-adapted strains of the M. tuberculosis complex including M. bovis. This Δppe38/71-associated secretion defect therefore also occurs in the M. bovis-derived tuberculosis vaccine BCG and could be partially restored by introduction of the M. tuberculosis ppe38-locus. Epitope mapping of the PPE-MPTR protein PPE10, further allowed us to monitor T-cell responses in splenocytes from BCG/M. tuberculosis immunized mice, confirming the dependence of PPE10-specific immune-induction on ESX-5/PPE38-mediated secretion. Restoration of PE_PGRS/PPE-MPTR secretion in recombinant BCG neither altered global antigenic presentation or activation of innate immune cells, nor protective efficacy in two different mouse vaccination-infection models. This unexpected finding stimulates a reassessment of the immunomodulatory properties of PE_PGRS/PPE-MPTR proteins, some of which are contained in vaccine formulations currently in clinical evaluation., Author summary One of the major findings of the pioneering Mycobacterium tuberculosis H37Rv genome sequencing project was the identification of the highly abundant PE and PPE proteins, named after their N-terminal motifs Pro–Glu (PE) or Pro–Pro–Glu (PPE). Within the 20 years of research since then, many claims were made that PE/PPE proteins, including the two large subgroups encoded by repetitive sequences with very high GC content (PE_PGRS and PPE-MPTR families), are exported to the bacterial surface or beyond, and show broad immunomodulatory impact on host-pathogen interaction. We thus screened strains from different branches of the M. tuberculosis complex, including the attenuated Mycobacterium bovis BCG vaccine strains, for their capacity to export PE_PGRS/PPE-MPTR proteins. Strikingly, we found that BCG strains were unable to export the plethora of PE_PGRS/PPE-MPTR proteins due to the absence of the region of difference RD5, which in M. tuberculosis encodes PPE38, required for PE_PGRS/PPE-MPTR export. Surprisingly, the restoration of PE_PGRS/PPE-MPTR export by genetic complementation in recombinant BCG did not result in immunomodulatory changes or altered protection in mouse models. Our results thus put into perspective the numerous reports on virulence-associated immunomodulatory impact of individual PE_PGRS and PPE-MPTR proteins and open novel questions on their biological function(s).
Published: 2018

29. Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

Author: Kathryn E. Holt, Stephen Baker, François-Xavier Weill, Nicholas R. Thomson, Oxford University Clinical Research Unit [Ho Chi Minh City] (OUCRU), University of Oxford [Oxford], University of Cambridge [UK] (CAM), The Wellcome Trust Sanger Institute [Cambridge], London School of Hygiene and Tropical Medicine (LSHTM), Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris], University of Melbourne, S.B. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (100087/Z/12/Z). K.E.H. is a Viertel Foundation of Australia Senior Medical Research Fellow and HHMI-Gates International Research Scholar. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., University of Oxford, Institut Pasteur [Paris] (IP), Baker, Stephen [0000-0003-1308-5755], Thomson, Nicholas [0000-0002-4432-8505], Weill, François-Xavier [0000-0001-9941-5799], Holt, Kathryn E [0000-0003-3949-2471], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Methicillin-Resistant Staphylococcus aureus, 030106 microbiology, Sexually Transmitted Diseases, Genomics, Computational biology, Review, MESH: Methicillin-Resistant Staphylococcus aureus, Biology, MESH: Genome, Bacterial, Evolution, Molecular, Foodborne Diseases, 03 medical and health sciences, Antibiotic resistance, MESH: Anti-Bacterial Agents, Drug Resistance, Bacterial, MESH: Drug Resistance, Bacterial, Spatial evolution, Humans, MESH: Foodborne Diseases, MESH: Evolution, Molecular, Multidisciplinary, MESH: Humans, Bacteria, Whole Genome Sequencing, MESH: Genomics, Antimicrobial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Community-Acquired Infections, MESH: Bacteria, 030104 developmental biology, MESH: Community-Acquired Infections, MESH: Whole Genome Sequencing, Genome, Bacterial, MESH: Sexually Transmitted Diseases
Abstract: International audience; Whole-genome sequencing (WGS) has been vital for revealing the rapid temporal and spatial evolution of antimicrobial resistance (AMR) in bacterial pathogens. Some antimicrobial-resistant pathogens have outpaced us, with untreatable infections appearing in hospitals and the community. However, WGS has additionally provided us with enough knowledge to initiate countermeasures. Although we cannot stop bacterial adaptation, the predictability of many evolutionary processes in AMR bacteria offers us an opportunity to channel them using new control strategies. Furthermore, by using WGS for coordinating surveillance and to create a more fundamental understanding of the outcome of antimicrobial treatment and AMR mechanisms, we can use current and future antimicrobials more effectively and aim to extend their longevity.
Published: 2018

30. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira

Author: Haritha Adhikarla, Elsio A. Wunder, Ariel E. Mechaly, Sameet Mehta, Zheng Wang, Luciane Santos, Vimla Bisht, Peter Diggle, Gerald Murray, Ben Adler, Francesc Lopez, Jeffrey P. Townsend, Eduardo Groisman, Mathieu Picardeau, Alejandro Buschiazzo, Albert I. Ko, Yale School of Public Health (YSPH), Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Yale Centre for Genome Analysis (YCGA), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Lancaster University, Monash University [Clayton], Yale School of Medicine [New Haven, Connecticut] (YSM), Biologie des Spirochètes / Biology of Spirochetes, Institut Pasteur [Paris] (IP), Département de Microbiologie - Department of Microbiology, This work was supported by grants from the National Institutes of Health (U01 AI0038752, R01 AI052473, R01 TW009504), Institut Pasteur (ACIP # A11-2010 and PTR #407), ANII Program Alianzas (ALI_1_2014_1_4982) and Program Fondo Sectorial Innovagro (FSA_1_2013_1_12557)., Fundação Oswaldo Cruz (FIOCRUZ), Yale University School of Medicine, and Institut Pasteur [Paris]
Subjects: MESH: Signal Transduction, 0301 basic medicine, Microbiology (medical), MESH: Mutation, Operon, [SDV]Life Sciences [q-bio], Immunology, lcsh:QR1-502, Virulence, MESH: Virulence, MESH: Genome, Bacterial, MESH: Leptospira, Microbiology, lcsh:Microbiology, 03 medical and health sciences, hybrid response regulator, Leptospira, Gene duplication, MESH: Bacterial Proteins, Gene, MESH: Evolution, Molecular, MESH: Microbial Viability, Genetics, Regulation of gene expression, MESH: Gene Expression Regulation, Bacterial, MESH: Humans, biology, MESH: Transcription, Genetic, Histidine kinase, gene duplication, MESH: Models, Biological, pathogenic, MESH: Leptospirosis, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, virulence, Response regulator, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Infectious Diseases, two-component system, bacteria, branched signaling, MESH: Whole Genome Sequencing, hybrid histidine kinase
Abstract: International audience; Leptospirosis is an emerging zoonotic disease with more than 1 million cases annually. Currently there is lack of evidence for signaling pathways involved during the infection process of Leptospira. In our comprehensive genomic analysis of 20 Leptospira spp. we identified seven pathogen-specific Two-Component System (TCS) proteins. Disruption of two these TCS genes in pathogenic Leptospira strain resulted in loss-of-virulence in a hamster model of leptospirosis. Corresponding genes lvrA and lvrB (leptospira virulence regulator) are juxtaposed in an operon and are predicted to encode a hybrid histidine kinase and a hybrid response regulator, respectively. Transcriptome analysis of lvr mutant strains with disruption of one (lvrB) or both genes (lvrA/B) revealed global transcriptional regulation of 850 differentially expressed genes. Phosphotransfer assays demonstrated that LvrA phosphorylates LvrB and predicted further signaling downstream to one or more DNA-binding response regulators, suggesting that it is a branched pathway. Phylogenetic analyses indicated that lvrA and lvrB evolved independently within different ecological lineages in Leptospira via gene duplication. This study uncovers a novel-signaling pathway that regulates virulence in pathogenic Leptospira (Lvr), providing a framework to understand the molecular bases of regulation in this life-threatening bacterium.
Published: 2018

31. History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology

Author: Mart Krupovic, Patrick Forterre, Yoshizumi Ishino, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Kyushu University [Fukuoka], Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), P.F. is supported by an ERC grant from the European Union's Seventh Framework Program (FP/2007-2013)/Project., This perspective paper stemmed from discussions during Y.I.'s stay in P.F.'s laboratory thanks to the generous support from the program of visiting researchers in Institut Pasteur and the two-country exchange program of the Japan Society for the Promotion of Science (JSPS)., We apologize to the researchers whose work was not cited due to space limitations., Institut Pasteur [Paris] (IP), and Kyushu University
Subjects: 0301 basic medicine, MESH: Gene Editing, MESH: CRISPR-Cas Systems, [SDV]Life Sciences [q-bio], 030106 microbiology, Computational biology, Biology, MESH: Genome, Bacterial, Microbiology, Genome, 03 medical and health sciences, Genome editing, repeated sequence, Escherichia coli, CRISPR, genome editing, Humans, Clustered Regularly Interspaced Short Palindromic Repeats, casposon, Repeated sequence, Molecular Biology, Gene, Sequence (medicine), Comparative genomics, Gene Editing, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, Bacteria, MESH: Escherichia coli, MESH: Genomics, Genomics, History, 20th Century, Archaea, MESH: Bacteria, MESH: Archaea, MESH: Clustered Regularly Interspaced Short Palindromic Repeats, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: History, 20th Century, Minireview, Mobile genetic elements, CRISPR-Cas Systems, Genome, Bacterial
Abstract: Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in the Escherichia coli genome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparative genomics, structural biology, and advanced biochemistry could then work hand in hand, not only culminating in the explosion of genome editing tools based on CRISPR-Cas9 and other class II CRISPR-Cas systems but also providing insights into the origin and evolution of this system from mobile genetic elements denoted casposons. To celebrate the 30th anniversary of the discovery of CRISPR, this minireview briefly discusses the fascinating history of CRISPR-Cas systems, from the original observation of an enigmatic sequence in E. coli to genome editing in humans.
Published: 2018

32. Universal and idiosyncratic characteristic lengths in bacterial genomes

Author: Olivier Rivoire, Ivan Junier, Paul Frémont, Génomique et Évolution des Microorganismes (TIMC-IMAG-GEM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, MESH: Chromosomes, Bacterial, MESH: Sequence Analysis, DNA, Characteristic length, Base pair, Biophysics, Bacterial genome size, MESH: Genome, Bacterial, Synteny, Genome, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, MESH: Base Composition, Structural Biology, Kuhn length, Quantitative Biology - Genomics, Molecular Biology, MESH: Evolution, Molecular, Genomics (q-bio.GN), Base Composition, Bacteria, Circular bacterial chromosome, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MESH: Synteny, Sequence Analysis, DNA, Cell Biology, Chromosomes, Bacterial, MESH: Bacteria, 030104 developmental biology, Evolutionary biology, FOS: Biological sciences, Genome, Bacterial, 030217 neurology & neurosurgery, GC-content
Abstract: International audience; In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a physics standpoint, in vitro DNA has thus a characteristic length of 300 base pairs (bp), the Kuhn length of the molecule beyond which correlations in its orientations are typically lost. From a biology standpoint, in vivo DNA has a characteristic length of 1000 bp, the typical length of genes. Since bacteria live in very different physico-chemical conditions and since their genomes lack translational invariance, whether larger, universal characteristic lengths exist is a non-trivial question. Here, we examine this problem by leveraging the large number of fully sequenced genomes available in public databases. By analyzing GC content correlations and the evolutionary conservation of gene contexts (synteny) in hundreds of bacterial chromosomes, we conclude that a fundamental characteristic length around 10-20 kb can be defined. This characteristic length reflects elementary structures involved in the coordination of gene expression, which are present all along the genome of nearly all bacteria. Technically, reaching this conclusion required us to implement methods that are insensitive to the presence of large idiosyncratic genomic features, which may co-exist along these fundamental universal structures.
Published: 2018

33. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Author: Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, Enzyme complex, MESH: Genome, Archaeal, LUCA, [SDV]Life Sciences [q-bio], MESH: Genome, Bacterial, Genome, Corrections, chemistry.chemical_compound, Genome, Archaeal, MESH: Multienzyme Complexes/genetics, methanogens, Phylogeny, MESH: Phylogeny, Genetics, Carbon Monoxide, Multidisciplinary, Last universal ancestor, Carbon fixation, Acetyl-CoA, MESH: Carbon Cycle, Aldehyde Oxidoreductases, Biological Evolution, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PNAS Plus, MESH: Bacteria/enzymology, Wood–Ljungdahl pathway, Wood-Ljungdahl pathway, MESH: Aldehyde Oxidoreductases/metabolism, Carbon monoxide dehydrogenase, 030106 microbiology, MESH: Bacteria/genetics, Acetate-CoA Ligase, Bacterial genome size, Biology, MESH: Biological Evolution, MESH: Aldehyde Oxidoreductases/genetics, Carbon Cycle, 03 medical and health sciences, MESH: Carbon Monoxide/metabolism, Multienzyme Complexes, MESH: Archaea/genetics, evolution, MESH: Acetate-CoA Ligase/metabolism, MESH: Multienzyme Complexes/metabolism, MESH: Archaea/enzymology, Bacteria, MESH: Acetate-CoA Ligase/genetics, Archaea, acetogens, 030104 developmental biology, chemistry, biology.protein, Genome, Bacterial
Abstract: Erratum in : Correction for Adam et al., Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. [Proc Natl Acad Sci U S A. 2018]; International audience; Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of un-cultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
Published: 2018

34. Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota

Author: Romain Koszul, Théo Foutel-Rodier, Agnès Thierry, Martial Marbouty, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Sorbonne Université (SU), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, MESH: Sequence Analysis, DNA, Base pair, Assembly, Computational biology, Biology, MESH: Genome, Bacterial, Genome, Human gut, DNA sequencing, MESH: Gastrointestinal Microbiome, 03 medical and health sciences, 0302 clinical medicine, Plasmid, Meta Hi-C, Metagenomics binning, MESH: Animals, Microbiome, Gene, MESH: High-Throughput Nucleotide Sequencing, Meta3C, Contig, MESH: Metagenome, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Metagenomics, MESH: Metagenomics, 030217 neurology & neurosurgery
Abstract: International audience; Microbial species thrive in very diverse environments and play fundamental roles in their equilibrium and dynamics. Metagenomics consists in extracting, sequencing, and studying the DNA present in ecosystems to better understand their regulation. Ideally, the maximal amount of information would be gathered from the full sequences of the genomes, episomes, and phages present in the microbial communities. Current high-throughput DNA sequencing produces reads ranging in size from a few dozen base pairs for the most commonly used technologies to several kb for emerging single-molecule real-time sequencing techniques. Although valuable information can be extracted from processing these DNA sequences into contigs, reconstructing full genomes remains a difficult task. Clustering contigs according to their similarities or read coverage covariations gives some insights on these genomes, but remains limited as viral sequences, or recent horizontal gene transfers, often differ from their host genomes. We recently developed meta3C, a proximity ligation approach that bins contigs in a sequence-independent way by quantifying and exploiting their tridimensional collisions frequencies in vivo. This technique has demonstrated a great potential to reconstruct genomes as well as to assign plasmids and phages to their hosts. It nevertheless requires a specific processing of the microbial samples before sequencing, which has to be carefully planned.
Published: 2018

35. Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017

Author: Sofie Gillesberg Lassen, Alexandre Leclercq, Alexandra Moura, Eva Møller Nielsen, Steen Ethelberg, Stine Thielke, Luise Müller, Marc Lecuit, Jette Kjeldgaard, T. Jensen, Mylène M. Maury, Mathieu Tourdjman, Marie-Pierre Donguy, Susanne Schjørring, Statens Serum Institut [Copenhagen], Danish Veterinary and Food Administration, Centre collaborateur de l'OMS Listeria - Biologie des Infections (CCOMS), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Référence Listeria - Biologie des Infections (CNRL), Technical University of Denmark [Lyngby] (DTU), Santé publique France, Direction Générale de l'Alimentation (DGAL), Ministère de l'agriculture, de l'agroalimentaire et de la forêt, Biologie des Infections - Biology of Infection, Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Institut des Maladies Génétiques Imagine [Paris], Part of this work was supported by the European Union’s Horizon 2020 research and innovation program through COMPARE under grant agreement No. 643476., We thank the Danish Clinical Microbiological Laboratories for rapid referral of isolates and support of the surveillance system. In addition, we thank the physicians and other health personnel for supplying clinical information, Marie Walther, Charlotte Munkstrup, Louise La Barbera Kastberg, for their assistance in interviewing patients. Furthermore, we thank Christian Vråby Pedersen and Anette Holm (SSI), Anne Mette Seyfarth (DFVA) the French National reference center technicians, and the PIBnet platform (Institut Pasteur) for excellent technical expertise in performing whole-genome sequencing. We also thank the staff at the DFVA Laboratory in Ringsted, Denmark and the regional food inspection units for collecting the environment and product samples, European Project: 643476,H2020,H2020-PHC-2014-single-stage,COMPARE(2014), Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)
Subjects: Male, 0301 basic medicine, food-borne infections, MESH: Salmon, MESH: Sequence Analysis, DNA, Epidemiology, Denmark, MESH: Emigration and Immigration, [SDV]Life Sciences [q-bio], MESH: Genome, Bacterial, MESH: Listeria monocytogenes, Genome, Disease Outbreaks, Foodborne Diseases, MESH: Aged, 80 and over, listeriosis, Salmon, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Animals, MESH: Disease Outbreaks, media_common, cold-smoked salmon, Aged, 80 and over, MESH: Aged, Molecular Epidemiology, whole genome sequencing, MESH: Middle Aged, Cross-border outbreak, Emigration and Immigration, Middle Aged, 3. Good health, Smoked salmon, Geography, MESH: Multilocus Sequence Typing, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, surveillance, Female, France, MESH: Whole Genome Sequencing, Rapid Communication, Adult, 030106 microbiology, Zoology, Disease cluster, 03 medical and health sciences, food, Virology, Animals, Humans, media_common.cataloged_instance, MESH: Molecular Epidemiology, European union, MESH: Foodborne Diseases, Aged, Whole genome sequencing, MESH: Denmark, MESH: Humans, Molecular epidemiology, Public Health, Environmental and Occupational Health, Outbreak, MESH: Adult, Sequence Analysis, DNA, Listeria monocytogenes, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, food.food, MESH: Male, MESH: France, Smoked fish, 030104 developmental biology, MESH: Listeriosis, MESH: Female, Genome, Bacterial, WGS, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Multilocus Sequence Typing
Abstract: International audience; In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human isolate from 2016 within the same cgMLST cluster as the Danish isolates (L2-SL8-ST8-CT771). The salmon product came from a third European Union country. WGS can rapidly link human cases and food isolates across Europe.
Published: 2017

36. Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: a reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group

Author: Tatiana Vallaeys, Dominique Clermont, Alexis Criscuolo, Cécile Wandersman, Catherine Dauga, Josef Deutscher, Eugene Christo-Foroux, Elie Dassa, Valentin Loux, Olivier Chesneau, Aurélien Livernois, Chloé Hot, Institut Pasteur [Paris], Université de Montpellier (UM), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Expression Génétique Microbienne (EGM (UMR_8261 / FRE_3630)), Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), International Group of Data Analysis (IGDA), Collection de l'Institut Pasteur (CIP), This work is dedicated to the memory of Pr. Cécile Wandersman and was in part supported by the ANR 12-BSV3-022/2012/2014. A.L. was an Interreg SUDOE 'ENERMASS' fellowship recipient. All authors are indebted to Dr. Nicolas Berthet for critically reading the manuscript before publication., ANR-05-PADD-0012,PRODDIG,Promotion du Développement Durable par les Indications Géographiques(2005), Institut Pasteur [Paris] (IP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut de biologie physico-chimique (IBPC), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie physico-chimique (IBPC)
Subjects: 0301 basic medicine, MESH: Sequence Analysis, DNA, Operon, Staphylococcus, [SDV]Life Sciences [q-bio], Oxidase-positive Staphylococcus, MESH: Base Sequence, medicine.disease_cause, MESH: Genome, Bacterial, Applied Microbiology and Biotechnology, Genome, MESH: Terpenes, MESH: High-Throughput Nucleotide Sequencing, Genetics, biology, MESH: Novobiocin, High-Throughput Nucleotide Sequencing, MESH: Sigma Factor, MESH: Staphylococcus, MESH: Mevalonic Acid, Phosphoenolpyruvate:carbohydrate phosphotransferase systems, Phenotype, MESH: ATP-Binding Cassette Transporters, Oxidoreductases, Novobiocin, 030106 microbiology, Virulence, Mevalonic Acid, Sigma Factor, Two-component regulatory systems, MESH: Phosphoenolpyruvate Sugar Phosphotransferase System, MESH: Phenotype, Microbiology, 03 medical and health sciences, Drug Resistance, Bacterial, MESH: Drug Resistance, Bacterial, Staphylococcus sciuri, medicine, Humans, MESH: Oxidoreductases, prokaryote complete genome, Phosphoenolpyruvate Sugar Phosphotransferase System, Iron transport, Gene, Ecology, Evolution, Behavior and Systematics, Whole genome sequencing, Bacillaceae, MESH: Humans, Base Sequence, Terpenes, Mevalonate, Sequence Analysis, DNA, biology.organism_classification, ATP-Binding Cassette Transporters, ATP-binding cassette systems, Genome, Bacterial
Abstract: Accepted Manuscript :3-7-2017; Staphylococcus sciuri is considered to be one of the most ancestral species in the natura history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. In this current study, the genome analysis of S. sciuri ATCC 29059 provided the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depicted the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.
Published: 2017

37. Insights on the Emergence of Mycobacterium tuberculosis from the Analysis of Mycobacterium kansasii

Author: Joyce Wang, Eduardo P. C. Rocha, Marcel A. Behr, Frédéric J. Veyrier, Jost Enninga, Roxane Simeone, Ken Dewar, Roland Brosch, Fiona McIntosh, Nicolas Radomski, McGill University = Université McGill [Montréal, Canada], McGill International Tuberculosis Centre (TB), McGill University and Genome Quebec Innovation Centre, Pathogénomique mycobactérienne intégrée, Institut Pasteur [Paris] (IP), Dynamique des Interactions Hôte-Pathogène - Dynamics of Host-Pathogen Interactions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), J.W. was supported by a PhD studentship award from the Fonds de la Recherche en Sante du Quebec (FRSQ) where M.B. is a Chercheur National. M.B. acknowledges the support of an operating grant from the Canadian Institutes for Health Research, MOP-97813. R.B. acknowledges the support by the Fondation pour la Recherche Médicale FRM no. DEQ20130326471. J.E. was supported by an ERC starting grant (Rupteffects, number 261166), and both J.E. and R.B are members of the LabEx consortium IBEID at the Institut Pasteur., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 261166,EC:FP7:ERC,ERC-2010-StG_20091118,RUPTEFFECTS(2011), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Tuberculosis, MESH: Mycobacterium tuberculosis, mycobacteria, [SDV]Life Sciences [q-bio], Virulence, comparative genomics, MESH: Virulence, MESH: Genome, Bacterial, MESH: Phenotype, phylogeny, Microbiology, Mycobacterium tuberculosis, Evolution, Molecular, Plasmid, MESH: Mice, Inbred C57BL, Genetics, medicine, Animals, MESH: Animals, MESH: Phylogeny, Pathogen, Ecology, Evolution, Behavior and Systematics, MESH: Evolution, Molecular, Mycobacterium kansasii, Comparative genomics, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, MESH: Genomics, Genomics, medicine.disease, biology.organism_classification, bacterial infections and mycoses, 3. Good health, Mice, Inbred C57BL, Phenotype, Female, MESH: Mycobacterium kansasii, MESH: Female, Genome, Bacterial, Mycobacterium, Research Article
Abstract: International audience; By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium tuberculosis. Yet, although both organisms cause pulmonary disease, M. tuberculosis is a global health menace, whereas M. kansasii is an opportunistic pathogen. To illuminate the differences between these organisms, we have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478) and conducted side-by-side in vitro and in vivo investigations of these two organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise comparisons reveal conserved and discordant genes and genomic regions. A notable example of genomic conservation is the virulence locus ESX-1, which is intact and functional in the low-virulence M. kansasii, potentially mediating phagosomal disruption. Differences between these organisms include a decreased predicted metabolic capacity, an increased proportion of toxin-antitoxin genes, and the acquisition of M. tuberculosis-specific genes in the pathogen since their common ancestor. Consistent with their distinct epidemiologic profiles, following infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3 weeks. Together, these data suggest that M. kansasii can serve as an image of the environmental ancestor of M. tuberculosis before its emergence as a professional pathogen, and can be used as a model organism to study the switch from an environmental opportunistic pathogen to a professional host-restricted pathogen.
Published: 2015

38. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

Author: Sabine Rüsch-Gerdes, Hans P eter Beck, Vladyslav Nikolayevskyy, Irina Kontsevaya, Petras Stakenas, Kadri Toit, Shinji Maeda, Eman Aleksic, Marie Ballif, Stefano Mona, Troels Lillebaek, Maryline Bonnet, Caroline Allix-Béguec, Sophie Lecher, Robin M. Warren, Isdore Chola Shamputa, Francesca Barletta, Isolina Campos-Herrero, Wei wei Jiao, Thomas Kohl, Suzanne M. Crowe, Ewa Augustynowicz-Kopeć, Solomon Ghebremichael, Branislava Savic, Francis Varaine, Dragana Vuković, Camille Blin, Annick Antierens, Li Hwei Sng, Maryse Fauville-Dufaux, Céline Wahl, Thierry Wirth, Stefan Niemann, Eve Willery, Helen Cox, Valeriu Crudu, Emanuele Borroni, Sebastien Gagneux, Philip Supply, Sven Hoffner, Adong Shen, Stobdan Kalon, Michael Rasmussen, Francis Drobniewski, Igor Mokrousov, Michael G. B. Blum, Madeleine Hanekom, Sofía Samper, Matthias Merker, Clifton E. Barry, Nicolas Duforet-Frebourg, Roland Diel, Nalin Rastogi, Daniela Maria Cirillo, Elisabeth Sanchez-Padilla, Molecular Mycobacteriology, Research Center Borstel - Leibniz Lung Center [Germany], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), National Reference Center for Mycobacteria, Institut Pasteur de Saint-Pétersbourg, Réseau International des Instituts Pasteur (RIIP), Centre for Biomedical Research, Burnet Institute [Melbourne, Victoria], genoscreen, GenoScreen, Medical Department, Médecins sans Frontières [Genève] (MSF), Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Institute of Social and Preventive Medicine, Universität Bern [Bern] (UNIBE), Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit–Tuberculosis, Instituto de Medicina Tropical 'Alexander von Humboldt' (IMT AvH), Universidad Peruana Cayetano Heredia (UPCH)-Universidad Peruana Cayetano Heredia (UPCH), Medical Parasitology and Infection Biology [Basel, Suisse] (MPI), Swiss Tropical and Public Health Institute [Basel], Laboratoire de Recherche en Informatique d'Amiens (LaRIA), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Epicentre [Paris] [Médecins Sans Frontières], Emerging Bacterial Pathogen Unit, San Raffaele Scientific Institute, hospital Universitario de Gran Canaria Dr Negrin, Macfarlane Burnet Institute for Medical Research, Laboratoire Jean Alexandre Dieudonné (LJAD), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), PHE National Mycobacterial Reference Laboratory and Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, Division of Infectious Diseases, Imperial College London, Centre national de Référence et Laboratoire Tuberculose et Mycobactéries = National Reference Centre of Tuberculosis and Mycobacteria [Brussels] (CNR), Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), MRC National Institute for Medical Research, Department of Preparedness, Swedish Institute for Infectious Disease Control, Faculty of Medicine and Health Sciences, stellen, Key Laboratory of Major Diseases in Children, Beijing Children's Hospital affiliated to Capital Medical University-Beijing Pediatric Research Institute-Chine - Ministry of Education, Samara Oblast TB Service, Research institute of Tuberculosis, Anti-tuberculosis Association, Institut Pasteur de la Guadeloupe, LAboratoire de Recherche en Mécanique Appliquée (LARMAUR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Microbiology Unit, Tropical Diseases Research Centre [Zambia] (TDRC), Alcatel-Thalès III-V lab (III-V Lab), THALES [France]-ALCATEL, Central Tuberculosis Laboratory, Singapore General Hospital, Medecins Sans Frontieres (Medecins Sans Frontieres), Médecins Sans Frontières, DTU Fotonik - Department of Photonics Engineering, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), molecular biology and human genetics, Stell, Molecular Mycobacteriology Group, National Reference Center for Mycobacyeria, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), We acknowledge J. Peh for her assistance and support in the study andI. Comas for statistical advice. Parts of this work have been supported by grantsfrom the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement 278864 in the framework of the European UnionPathoNGenTrace project and grant agreement 223681 in the framework of theTB-PAN-NET project. We also thank Action Transversale du Muséum Nationald’Histoire Naturelle ‘Les Microorganismes, Acteurs Clés dans les Ecosystèmes’for financial support, European Project: 223681,EC:FP7:HEALTH,FP7-HEALTH-2007-B,TB PAN-NET(2009), European Project: 278864,FP7/2007- 2013, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Universität Bern [Bern], Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), THALES-ALCATEL, and Technical University of Denmark [Lyngby] (DTU)
Subjects: Tuberculosis, Lineage (genetic), MESH: Mutation, MESH: Mycobacterium tuberculosis, Genotype, MESH: Biological Evolution, MESH: Global Health, Biology, MESH: Genome, Bacterial, Global Health, Genetic analysis, Mycobacterium tuberculosis, MESH: Genotype, Evolution, Molecular, Phylogenetics, Tuberculosis, Multidrug-Resistant, Genetics, Global health, medicine, Humans, MESH: Phylogeny, MESH: Evolution, Molecular, MESH: Tuberculosis, Multidrug-Resistant, Phylogeny, MESH: Humans, Ecology, Population size, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biological Evolution, 3. Good health, Mycobacterium tuberculosis/classification/genetics/isolation & purification, Evolutionary biology, Mutation, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Tuberculosis, Multidrug-Resistant/epidemiology/microbiology, Genome, Bacterial, purl.org/pe-repo/ocde/ford#1.06.07 [https]
Abstract: International audience; Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.
Published: 2015
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39. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

Author: Du, C, Gryganskyi, G, Tschaplinski, R, Misztal, C, Wu, A, Desirò, I, Vande Pol, I, Du, R, Zienkiewicz, R, Zienkiewicz, G, Tisserant, R, Splivallo, G, Hainaut, R, Henrissat, R, Ohm, R., Kuo, G, Yan, G., Lipzen, G, Nolan, G, LaButti, G, Barry, G, Goldstein, G, Labbe, R., Schadt, R, Tuskan, G., Grigoriev, G, Martin, R, Vilgalys, R., Bonito, G., Du, J., Gryganskyi, A., Du, K., Tschaplinski, T., Misztal, K., Wu, S., Desirò, A., Vande Pol, N., Du, Z., Zienkiewicz, A., Zienkiewicz, K., Morin, E., Tisserant, E., Splivallo, R., Hainaut, M., Henrissat, B., Kuo, A., Yan, J., Lipzen, A., Nolan, M., LaButti, K., Barry, K., Goldstein, A., Labbé, J., Schadt, C., Grigoriev, I., Martin, F., Duke University [Durham], BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, University of California [Berkeley], University of California, Arizona State University [Tempe] (ASU), Deparment of Plant, Soil and Microbial Sciences, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Goethe-University Frankfurt am Main, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Utrecht University [Utrecht], Genomic Science Program, U.S. Department of Energy, Office of Science - Biological and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area at Oak Ridge National Laboratory, U.S. Department of Energy DE-AC05- 00OR22725, DOE Joint Genome Institute by the JGI Community sequencing program 570, Office of Science of the US Department of Energy DE-AC02-05CH11231, EU Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE) ANR-11-LABX-0002-01, Joint Genome Institute (JGI), Northwest Institute for Nonferrous Metal Research (NIN), Laboratorio de Turbulencia, Universidad de Santiago de Chile [Santiago] (USACH), UT-Battelle, LLC, Centre d'études de chimie métallurgique (CECM), Centre National de la Recherche Scientifique (CNRS), Kansas State University, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Center for Human Genetics, University of Leuven School of Medicine, SCHOOL of MEDICINE [Louvain], Université Catholique de Louvain (UCL)-Université Catholique de Louvain (UCL), DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Sub Molecular Microbiology, Molecular Microbiology, Joint Genome Institute ( JGI ), Northwest Institute for Nonferrous Metal Research, Oak Ridge National Laboratory, Duke university [Durham], Centre d'études de chimie métallurgique ( CECM ), Centre National de la Recherche Scientifique ( CNRS ), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), UNIVERSITY of LEUVEN SCHOOL of MEDICINE, Institute of Northern Engineering, 455 Duckering Bldg, Lawrence Berkeley National Laboratory [Berkeley] ( LBNL ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), University of California [Berkeley] (UC Berkeley), and University of California (UC)
Subjects: Burkholderiaceae, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH : Symbiosis, MESH: Base Sequence, MESH: Genome, Bacterial, 2.2 Factors relating to physical environment, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, LAND PLANTS, 2.2 Factors relating to the physical environment, MESH : Metagenome, MESH: Animals, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, Phylogeny, MESH: Lipid Metabolism, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Symbiosis, Endosymbiosis, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Bacterial, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], FATTY-ACID BIOSYNTHESIS, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Fungal, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Infection, Evolution, 030106 microbiology, MESH : Genome, Bacterial, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology, GENE-TRANSFER, 03 medical and health sciences, MESH : Burkholderiaceae, Botany, MESH : Evolution, Molecular, Ecology, Evolution, Behavior and Systematics, Comparative genomics, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, MESH : Genome, Fungal, Molecular, ENDOBACTERIA, MESH: Burkholderiaceae, DNA, 15. Life on land, Lipid Metabolism, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, INTRACELLULAR BACTERIA, 030104 developmental biology, MESH: Mortierella, Metagenome, MESH : Sequence Analysis, DNA, 0301 basic medicine, MESH: Sequence Analysis, DNA, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH: Carbohydrate Metabolism, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genome, GUT MICROBIOME, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, ARBUSCULAR MYCORRHIZAL FUNGI, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Mortierella, MESH : Lipid Metabolism, MESH: Evolution, Molecular, 2. Zero hunger, Genetics, biology, Ecology, Fungal genetics, MESH : Carbohydrate Metabolism, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], ESCHERICHIA-COLI, Carbohydrate Metabolism, Sequence Analysis, Metabolic Networks and Pathways, CANDIDATUS GLOMERIBACTER GIGASPORARUM, Bacterial genome size, Symbiosis, Behavior and Systematics, Lipid biosynthesis, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Evolutionary Biology, Base Sequence, MESH : Metabolic Networks and Pathways, MESH : Phylogeny, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [ SDV.SP.PHARMA ] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH: Metagenome, biology.organism_classification, MESH: Metabolic Networks and Pathways, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH : Base Sequence, BICOLOR S238N, MESH : Animals, MESH : Mortierella, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: International audience; Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.
Published: 2017

40. Correction: Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

Author: Christophe Rusniok, Carmen Buchrieser, Leonor Sánchez-Busó, Julian Parkhill, Sophia David, Timothy G. Harrison, Pekka Marttinen, Simon R. Harris, The Wellcome Trust Sanger Institute [Cambridge], Public Health England [London], Helsinki Institute for Information Technology (HIIT), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Aalto University, Aalto University, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This study was funded by the Wellcome Trust (https://wellcome.ac.uk) grant number 098051 to JP and the Agence Nationale de Research (http://www.agence-nationale-recherche.fr) grant number ANR-10-LABX-62-IBEID to CB., We thank the library-generation, sequencing and informatics teams at the Wellcome Trust Sanger Institute for their assistance. We are also grateful to Jukka Corander for his help with the hierBAPS analysis., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Sánchez-Busó, Leonor [0000-0002-4162-0228], Harris, Simon R [0000-0003-1512-6194], Buchrieser, Carmen [0000-0003-3477-9190], Parkhill, Julian [0000-0002-7069-5958], Apollo - University of Cambridge Repository, Aalto University-University of Helsinki, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Wellcome Trust Sanger Institute, Department of Computer Science, Institut Pasteur Paris, Public Health England, and Aalto-yliopisto
Subjects: 0301 basic medicine, Lipopolysaccharides, Cancer Research, [SDV]Life Sciences [q-bio], Cell Membranes, MESH: Legionnaires' Disease, Outer membrane proteins, Pathology and Laboratory Medicine, MESH: Genome, Bacterial, Genome, Legionella pneumophila, Biochemistry, MESH: Recombinant Proteins, Database and Informatics Methods, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine and Health Sciences, Genomic library, MESH: Phylogeny, Homologous Recombination, Genetics (clinical), MESH: Evolution, Molecular, Phylogeny, Data Management, Species diversity, Genetics, education.field_of_study, Phylogenetic analysis, Genomics, Genomic Databases, Recombinant Proteins, Bacterial Pathogens, Nucleic acids, Phylogenetics, Medical Microbiology, Genomic libraries, Cellular Structures and Organelles, Legionnaires' Disease, Recombination, Research Article, Bacterial Outer Membrane Proteins, Computer and Information Sciences, lcsh:QH426-470, DNA recombination, 030106 microbiology, Population, Legionella, Biology, Research and Analysis Methods, Microbiology, MESH: Homologous Recombination, Evolution, Molecular, 03 medical and health sciences, Evolutionary Systematics, staffpaper, education, Molecular Biology, Gene, Microbial Pathogens, Ecology, Evolution, Behavior and Systematics, Taxonomy, ta113, Evolutionary Biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Biology and life sciences, Bacteria, MESH: Bacterial Outer Membrane Proteins, Organisms, Proteins, Membrane Proteins, Computational Biology, Correction, pathogens, DNA, Cell Biology, biology.organism_classification, Genome Analysis, MESH: Legionella pneumophila, lcsh:Genetics, 030104 developmental biology, Biological Databases, MESH: Lipopolysaccharides, Homologous recombination, Genome, Bacterial
Abstract: Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires’ disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) of diversity within several major disease-associated sequence types (STs) of L. pneumophila. This suggests that recombination represents a potentially important force shaping adaptation and virulence. Despite this, little is known about the biological effects of recombination in L. pneumophila, particularly with regards to homologous recombination (whereby genes are replaced with alternative allelic variants). Using newly available population genomic data, we have disentangled events arising from homologous and non-homologous recombination in six major disease-associated STs of L. pneumophila (subsp. pneumophila), and subsequently performed a detailed characterisation of the dynamics and impact of homologous recombination. We identified genomic “hotspots” of homologous recombination that include regions containing outer membrane proteins, the lipopolysaccharide (LPS) region and Dot/Icm effectors, which provide interesting clues to the selection pressures faced by L. pneumophila. Inference of the origin of the recombined regions showed that isolates have most frequently imported DNA from isolates belonging to their own clade, but also occasionally from other major clades of the same subspecies. This supports the hypothesis that the possibility for horizontal exchange of new adaptations between major clades of the subspecies may have been a critical factor in the recent emergence of several clinically important STs from diverse genomic backgrounds. However, acquisition of recombined regions from another subspecies, L. pneumophila subsp. fraseri, was rarely observed, suggesting the existence of a recombination barrier and/or the possibility of ongoing speciation between the two subspecies. Finally, we suggest that multi-fragment recombination may occur in L. pneumophila, whereby multiple non-contiguous segments that originate from the same molecule of donor DNA are imported into a recipient genome during a single episode of recombination., Author summary Legionella pneumophila is an environmental bacterium that causes Legionnaires’ disease, a serious and potentially fatal pneumonia. Previous studies have shown that members of this species undergo a process called recombination, whereby DNA is imported from another bacterial cell into the recipient genome. The imported DNA can either replace an equivalent segment of the genome (homologous recombination) or can comprise novel genes that are new to the recipient genome (non-homologous recombination). Whilst recombination plays an undoubtedly important role in L. pneumophila evolution, accounting for more than 96% of the diversity observed within some lineages, little is known about its biological impact. In this study, we performed a detailed characterisation of the dynamics and effect of homologous recombination on L. pneumophila evolution in six clinically important lineages of L. pneumophila. We identified “hotspot” regions of the genome in which an excess of homologous recombination events was observed, which provided important clues to the selection pressures faced by L. pneumophila. By determining the donors of the recombined regions, we also revealed that recombination has occurred most frequently between isolates from the same clade, but also occurred between isolates from different major clades. This demonstrates the possibility of new adaptations arising in one lineage and being transferred to another distantly related lineage, which we predict has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds.
Published: 2017

41. Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

Author: Marbouty, Martial, Baudry, Lyam, Cournac, Axel, Koszul, Romain, Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This research was supported by funding from the European Research Council (ERC) under the 7th Framework Program (FP7/2007-2013)/ERC grant agreement 260822 (to R.K.)., European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, mammal, Genome, Viral, MESH: Genome, Bacterial, Microbiology, MESH: Gastrointestinal Microbiome, Mice, Hi-C, phage, Animals, Bacteriophages, MESH: Animals, MESH: Bacteriophages, MESH: Mice, Research Articles, mouse, virome, metagenomics, contact genomics, meta3C, Bacteria, SciAdv r-articles, MESH: Male, Gastrointestinal Microbiome, MESH: Bacteria, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, genome assembly, proximity ligation, MESH: Genome, Viral, Genome, Bacterial, Research Article
Abstract: Two proximity ligation approaches are used to probe the gut’s phage-bacteria infection network using Meta3C and GRAAL scaffolding., The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.
Published: 2017

42. The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system

Author: Sahr, Tobias, Rusniok, Christophe, Impens, Francis, Oliva, Giulia, Sismeiro, Odile, Coppée, Jean-Yves, Buchrieser, Carmen, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Work in the CB laboratory is financed by the Institut Pasteur, the Institut Carnot-Pasteur MI, the French Region Ile de France (DIM Malinf), the grant n°ANR-10-LABX-62-IBEID, the Fondation pour la Recherche Médicale (FRM) grant N° DEQ20120323697 and the Pasteur-Weizmann consortium « The roles of non-coding RNAs in regulation of microbial life styles and virulence ». The Transcriptome and EpiGenome Platform is a member of the France Génomique consortium (ANR10-NBS-09-08). FI received financial support from a Pasteur-Roux Fellowship The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris], Biologie des Bactéries intracellulaires, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Bidault, Floran, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, and Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID
Subjects: MESH: Feedback, Physiological, [SDV]Life Sciences [q-bio], Gene Expression, LEGIONNAIRES-DISEASE, Electrophoretic Mobility Shift Assay, MESH: Legionnaires' Disease, Restriction Fragment Mapping, MESH: Base Sequence, MESH: Virulence, Pathology and Laboratory Medicine, MESH: Genome, Bacterial, Biochemistry, Pentose Phosphate Pathway, Tandem Mass Spectrometry, Medicine and Health Sciences, MESH: Bacterial Proteins, MESH: Evolution, Molecular, GENE-EXPRESSION, Oligonucleotide Array Sequence Analysis, Feedback, Physiological, MESH: Gene Expression Regulation, Bacterial, Virulence, Messenger RNA, GLYCOGEN BIOSYNTHESIS, Bacterial Pathogens, [SDV] Life Sciences [q-bio], Nucleic acids, Legionella Pneumophila, ESCHERICHIA-COLI, Medical Microbiology, MESH: Repressor Proteins, Host-Pathogen Interactions, MESH: Glycolysis, POSTTRANSCRIPTIONAL REGULATION, Legionnaires' Disease, Pathogens, MESSENGER-RNA, Glycolysis, Protein Binding, Research Article, MESH: Operon, MESH: Mutation, lcsh:QH426-470, DNA transcription, AUTOINDUCER SYNTHASE LQSA, Legionella, INTRACELLULAR REPLICATION, Research and Analysis Methods, Biosynthesis, Microbiology, Evolution, Molecular, MESH: Gene Expression Profiling, TRANSCRIPTION TERMINATION, Bacterial Proteins, Gene Types, Operon, Genetics, Humans, MESH: Protein Binding, MESH: Blotting, Northern, Gene Regulation, RNA, Messenger, Molecular Biology Techniques, Operons, PATHOGEN-HOST INTERACTIONS, Microbial Pathogens, Molecular Biology, MESH: Pentose Phosphate Pathway, MESH: RNA, Messenger, MESH: Humans, Base Sequence, Bacteria, Gene Expression Profiling, Gene Mapping, MESH: Host-Pathogen Interactions, Organisms, Biology and Life Sciences, MESH: Tandem Mass Spectrometry, Gene Expression Regulation, Bacterial, DNA, Blotting, Northern, MESH: Legionella pneumophila, Repressor Proteins, lcsh:Genetics, Riboswitch, Mutation, MESH: Oligonucleotide Array Sequence Analysis, Regulator Genes, RNA, Genome, Bacterial, MESH: Riboswitch
Abstract: The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA co-immunoprecipitation followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs. Further analyses revealed that CsrA exhibits a dual regulatory role in virulence as it affects the expression of the regulators FleQ, LqsR, LetE and RpoS but it also directly regulates the timely expression of over 40 Dot/Icm substrates. CsrA controls its own expression and the stringent response through a regulatory feedback loop as evidenced by its binding to RelA-mRNA and links it to quorum sensing and motility. CsrA is a central player in the carbon, amino acid, fatty acid metabolism and energy transfer and directly affects the biosynthesis of cofactors, vitamins and secondary metabolites. We describe the first L. pneumophila riboswitch, a thiamine pyrophosphate riboswitch whose regulatory impact is fine-tuned by CsrA, and identified a unique regulatory mode of CsrA, the active stabilization of RNA anti-terminator conformations inside a coding sequence preventing Rho-dependent termination of the gap operon through transcriptional polarity effects. This allows L. pneumophila to regulate the pentose phosphate pathway and the glycolysis combined or individually although they share genes in a single operon. Thus the L. pneumophila genome has evolved to acclimate at least five different modes of regulation by CsrA giving it a truly unique position in its life cycle., Author summary The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen. Here, we have used deep sequencing of RNA enriched by co-immunoprecipitation with epitope-tagged CsrA to identify CsrA-associated transcripts at the genome level. We found 479 mRNAs or non-coding RNAs to be targets of CsrA. Among those major regulators including FleQ, the regulator of flagella expression, LqsR, the regulator of quorum sensing and RpoS implicated in stress response were identified. The expression of over 40 type IV secreted effector proteins important for intracellular survival and virulence are under the control of CsrA. Combined with transcriptomics, whole shotgun proteomics of a wild type and a CsrA mutant strain and functional analyses of several CsrA-targeted RNAs we identified the first riboswitch in L. pneumophila, a thiamine pyrophosphate riboswitch, and discovered a new mode of regulation by CsrA that allows L. pneumophila to regulate the pentose phosphate pathway and the glycolysis combined or individually although they share genes in a single operon. Our results further underline the indispensable role of CsrA in the life cycle of L. pneumophila and provide new insights into its regulatory roles and mechanisms.
Published: 2017

43. Whole-Genome Characterization of Epidemic Neisseria meningitidis Serogroup C and Resurgence of Serogroup W, Niger, 2015

Author: Cecilia B, Kretz, Adam C, Retchless, Fati, Sidikou, Bassira, Issaka, Sani, Ousmane, Stephanie, Schwartz, Ashley H, Tate, Assimawè, Pana, Berthe-Marie, Njanpop-Lafourcade, Innocent, Nzeyimana, Ricardo Obama, Nse, Ala-Eddine, Deghmane, Eva, Hong, Ola Brønstad, Brynildsrud, Ryan T, Novak, Sarah A, Meyer, Odile Ouwe Missi, Oukem-Boyer, Olivier, Ronveaux, Dominique A, Caugant, Muhamed-Kheir, Taha, Xin, Wang, Goumbi, Kadade, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), World Health Organization [Niamey], Agence de Médecine Préventive, Institut Pasteur [Paris] (IP), Norwegian Institute of Public Health [Oslo] (NIPH), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), This work was funded by CDC., Members of the Niger Response Team who contributed to this study: Jennifer D. Thomas, Fang Hu, Brian H. Harcourt, Melissa J. Whaley, How-Yi Chang, Laurel Thompson Jenkins, Susanna E. Schmink (CDC), Didier Mounkoro, Oubote Abodji (Agence de Médecine Préventive), Jibir Zanguina, Aichatou Moussa, Mariama Sambo (CERMES), and Maman Zaneidou and Goumbi Kadade (Direction de la Surveillance et de la Riposte aux Epidémies)., and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, MESH: Neisseria meningitidis, Serogroup C/genetics, MESH: Meningitis, Meningococcal/microbiology, MESH: Sequence Analysis, DNA, Epidemiology, MESH: Neisseria meningitidis, Serogroup C/isolation & purification, lcsh:Medicine, MESH: Antigens, Bacterial/genetics, Neisseria meningitidis, Serogroup C, Neisseria meningitidis, Meningococcal meningitis, MESH: Genome, Bacterial, Genome, Communicable Diseases, Emerging, meningitis belt, MESH: Drug Resistance, Bacterial/genetics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Communicable Diseases, Emerging, Niger, MESH: Genetic Variation, bacteria, MESH: Phylogeny, Phylogeny, Phylogenetic tree, MESH: Molecular Typing, Epidemic season, Neisseria meningitidis serogroup C, 3. Good health, Infectious Diseases, whole-genome sequencing, MESH: Neisseria meningitidis/genetics, Microbiology (medical), DNA, Bacterial, Whole-Genome Characterization of Epidemic Neisseria meningitidis Serogroup C and Resurging Serogroup W, Niger, 2015, MESH: Meningitis, Meningococcal/epidemiology, Biology, Meningitis, Meningococcal, lcsh:Infectious and parasitic diseases, Microbiology, 03 medical and health sciences, Genetic Evolution, Drug Resistance, Bacterial, parasitic diseases, Humans, lcsh:RC109-216, Serotyping, Epidemics, MESH: Epidemics, Antigens, Bacterial, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, Research, lcsh:R, MESH: Niger/epidemiology, Outbreak, Genetic Variation, MESH: Serotyping, Sequence Analysis, DNA, Virology, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Typing, 030104 developmental biology, MESH: Neisseria meningitidis/isolation & purification, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Genome, Bacterial
Abstract: International audience; In 2015, Niger reported the largest epidemic of Neisseria meningitidis serogroup C (NmC) meningitis in sub-Saharan Africa. The NmC epidemic coincided with serogroup W (NmW) cases during the epidemic season, resulting in a total of 9,367 meningococcal cases through June 2015. To clarify the phylogenetic association, genetic evolution, and antibiotic determinants of the meningococcal strains in Niger, we sequenced the genomes of 102 isolates from this epidemic, comprising 81 NmC and 21 NmW isolates. The genomes of 82 isolates were completed, and all 102 were included in the analysis. All NmC isolates had sequence type 10217, which caused the outbreaks in Nigeria during 2013-2014 and for which a clonal complex has not yet been defined. The NmC isolates from Niger were substantially different from other NmC isolates collected globally. All NmW isolates belonged to clonal complex 11 and were closely related to the isolates causing recent outbreaks in Africa.
Published: 2016

44. Characterization of meningococcal carriage isolates from Greece by whole genome sequencing: Implications for 4CMenB vaccine implementation

Author: Holly B. Bratcher, Muhamed-Kheir Taha, Athanasia Xirogianni, Konstantinos Kesanopoulos, Georgina Tzanakaki, Martin C. J. Maiden, Anastasia Papandreou, Eva Hong, National Meningitis Reference Laboratory, National School of Public Health Athens, Department of Zoology [Oxford], University of Oxford [Oxford], Infections Bactériennes Invasives, Institut Pasteur [Paris], Funding for this study was provided by GlaxoSmithKline Biologicals SA., University of Oxford, and Institut Pasteur [Paris] (IP)
Subjects: Male, 0301 basic medicine, Physiology, Glycobiology, Neisseria meningitidis, Serogroup B, Pathology and Laboratory Medicine, MESH: Genome, Bacterial, medicine.disease_cause, Biochemistry, MESH: Meningococcal Vaccines, Serology, Database and Informatics Methods, Antigen Encapsulation, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Immune Physiology, Medicine and Health Sciences, MESH: Genetic Variation, Drug Delivery System Preparation, MESH: High-Throughput Nucleotide Sequencing, Vaccines, education.field_of_study, Immune System Proteins, Multidisciplinary, Greece, Pharmaceutics, Neisseria meningitidis, MESH: Meningitis, Meningococcal, High-Throughput Nucleotide Sequencing, Antigenic Variation, Bacterial Pathogens, 3. Good health, Infectious Diseases, Medical Microbiology, Medicine, Female, Pathogens, Neisseria, Sequence Analysis, Research Article, Infectious Disease Control, Bioinformatics, Science, Immunology, 030106 microbiology, Population, Sequence Databases, Meningococcal Vaccines, Meningitis, Meningococcal, Biology, Research and Analysis Methods, Microbiology, Herd immunity, 03 medical and health sciences, Antigen, Polysaccharides, MESH: Neisseria meningitidis, Serogroup B, Antigenic variation, medicine, Humans, Typing, Antigens, education, Microbial Pathogens, DNA sequence analysis, MESH: Humans, Bacteria, Pharmaceutical Processing Technology, Organisms, Genetic Variation, Biology and Life Sciences, Proteins, Virology, MESH: Male, Biological Databases, Carriage, MESH: Greece, Conjugate Vaccines, MESH: Genome-Wide Association Study, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, MESH: Female, Genome, Bacterial, Neisseria Meningitidis, Genome-Wide Association Study
Abstract: International audience; Herd protection, resulting from the interruption of transmission and asymptomatic carriage, is an important element of the effectiveness of vaccines against the meningococcus. Whilst this has been well established for conjugate polysaccharide vaccines directed against the meningococcal capsule, two uncertainties surround the potential herd protection provided by the novel protein-based vaccines that are used in place of serogroup B (MenB) polysaccharide vaccines (i) the strain coverage of such vaccines against carried meningococci, which are highly diverse; and (ii) the generation of a protective immune response in the mucosa. These considerations are essential for realistic estimates of cost-effectiveness of new MenB vaccines. Here the first of these questions is addressed by the whole genome sequence (WGS) analysis of meningococci isolated from healthy military recruits and university students in Greece. The study included a total of 71 MenB isolates obtained from 1420 oropharyngeal single swab samples collected from military recruits and university students on voluntary basis, aged 18-26 years. In addition to WGS analysis to identify genetic lineage and vaccine antigen genes, including the Bexsero Antigen Sequence Type (BAST), the isolates were examined with the serological Meningococcal antigen Typing System (MATS) assay. Comparison of these data demonstrated that the carried meningococcal population was highly diverse with 38% of the carriage isolates showed expression of antigens matching those included in the 4CMenB vaccine. Our data may suggest a limited potential herd immunity to be expected and be driven by an impact on a subset of carriage isolates.
Published: 2018

45. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

Author: Wafa Frigui, Fadel Sayes, Camille Locht, Gregory Salvignol, Varun Khanna, Eve Willery, Danielle Walker, Anne-Sophie Debrie, Philip Supply, Michael Marceau, Timothy P. Stinear, Alessandro Cascioferro, Roland Brosch, Sylvain Brisse, Michael A. Quail, Stephen D. Bentley, Michel Fabre, Sophie Mangenot, Laurence Fiette, Claudine Médigue, Stéphane Cruveiller, Carine Rouanet, Claude Leclerc, Alexandre Pawlik, Julien Tap, Torsten Seemann, Laleh Majlessi, Christiane Bouchier, Roxane Simeone, Laurence Ma, David Roche, Cecile Parmentier, Valérie Barbe, Mickael Orgeur, Julian Parkhill, Eva C. Boritsch, Alexis Criscuolo, Maria-Cristina Gutierrez, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Pathogénomique mycobactérienne intégrée, Institut Pasteur [Paris] (IP), Régulation Immunitaire et Vaccinologie, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Histopathologie humaine et Modèles animaux, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), HIA Percy, Mécanismes moléculaires de la pathogénie microbienne, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Wellcome Trust Sanger Institute [Cambridge], Génomique (Plate-Forme) - Genomics Platform, Victorian Bioinformatics Consortium [Clayton], Monash University [Clayton], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Mécanismes moléculaires de la pathogenèse bactérienne, Département Infection et Epidémiologie - Department of Infection and Epidemiology, University of Melbourne, The work was supported in part by the Institut Pasteur (PTR 314 and PTR 383), European Community's Framework Programme 7 grant 260872, Wellcome Trust grant 098051 and Genoscope collaborative grant 114., European Project: 260872,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MM4TB(2011), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: MESH: Sequence Analysis, DNA, MESH: Mycobacterium tuberculosis, Tuberculosis, MESH: Spleen, [SDV]Life Sciences [q-bio], MESH: Mice, Inbred BALB C, Virulence, Genomics, MESH: Virulence, MESH: Base Sequence, MESH: Genome, Bacterial, Genome, DNA sequencing, Mycobacterium tuberculosis, 03 medical and health sciences, Genetic variation, Genetics, medicine, MESH: Species Specificity, MESH: Animals, MESH: Lung, MESH: Mice, 030304 developmental biology, 0303 health sciences, MESH: Molecular Sequence Data, biology, 030306 microbiology, MESH: Adaptation, Biological, MESH: Genomics, MESH: Polymorphism, Single Nucleotide, biology.organism_classification, medicine.disease, MESH: Cluster Analysis, 3. Good health, MESH: Inverted Repeat Sequences, Mycobacterium
Abstract: International audience; Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5× coverage), 454/Roche (13-18× coverage) and/or Illumina DNA sequencing (45-105× coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.
Published: 2013

46. Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

Author: Mikael Koutero, Noam Stern-Ginossar, J. R. Mellin, Daniel Dar, Pascale Cossart, Rotem Sorek, Maya Shamir, Weizmann Institute of Science [Rehovot, Israël], Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Israel Science Foundation [1303/12], Israel Science Foundation (I-CORE) [1796/12], Human Frontier Science Program [RGP0011/2013], Abisch-Frenkel, European Project: 260432,EC:FP7:ERC,ERC-2010-StG_20091118,PROKRNA(2011), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), ProdInra, Migration, and Prokaryotic RNomics: Unravelling the RNA-mediated regulatory layers - PROKRNA - - EC:FP7:ERC2011-01-01 - 2016-06-30 - 260432 - VALID
Subjects: 0301 basic medicine, Riboswitch, [SDV]Life Sciences [q-bio], MESH: Listeria monocytogenes, MESH: Genome, Bacterial, Ribosome, Gene expression, Enterococcus faecalis, MESH: Sequence Analysis, RNA, messenger-rna structure, 3' Untranslated Regions, bacillus-subtilis, MESH: High-Throughput Nucleotide Sequencing, Regulation of gene expression, transcriptional attenuation mechanism, MESH: Gene Expression Regulation, Bacterial, Multidisciplinary, Human microbiome, High-Throughput Nucleotide Sequencing, controls gene-expression, MESH: 3' Untranslated Regions, Anti-Bacterial Agents, [SDV] Life Sciences [q-bio], Bacillus subtilis, MESH: Enterococcus faecalis, 030106 microbiology, Computational biology, Biology, MESH: Gastrointestinal Microbiome, Bacterial genetics, Microbiology, 03 medical and health sciences, MESH: Transcription Termination, Genetic, MESH: Anti-Bacterial Agents, Drug Resistance, Bacterial, MESH: Drug Resistance, Bacterial, Humans, MESH: Humans, Sequence Analysis, RNA, RNA, Gene Expression Regulation, Bacterial, MESH: Bacillus subtilis, biology.organism_classification, Listeria monocytogenes, Gastrointestinal Microbiome, 030104 developmental biology, Transcription Termination, Genetic, MESH: Genome-Wide Association Study, synthetic biology, listeria-monocytogenes, Ribosomes, MESH: Ribosomes, Genome, Bacterial, Bacteria, Genome-Wide Association Study, MESH: Riboswitch
Abstract: How bacteria switch between tracks Bacterial riboswitches prevent the formation of full-length messenger RNA, and hence proteins, via transcriptional termination in response to metabolites. However, identifying riboswitches within the genome has previously required comparative analysis, which may miss species- and environmentally specific responses. Dar et al. developed a method called term-seq to document all riboswitches in a bacterial genome, as well as their metabolite counterparts (see the Perspective by Sommer and Suess). The method revealed a role for pathogenic bacterial riboswitches in antibiotic resistance. Thus, transcription may be one way pathogens fend off antibiotic attack. Science , this issue p. 10.1126/science.aad9822 ; see also p. 144
Published: 2016

47. The potential of whole genome NGS for infectious disease diagnosis

Author: Marc Eloit, Marc Lecuit, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service des Maladies infectieuses et tropicales [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Découverte de Pathogènes - Pathogen Discovery, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), M Eloit is the founder and CSO of Pathoquest (Paris, France), a spin out of Institut Pasteur dedicated to diagnostic of infectious diseases by NGS. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed., Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP]-Institut des Maladies Génétiques Imagine [Paris]
Subjects: Standardization, [SDV]Life Sciences [q-bio], diagnostic, Computational biology, Genome, Viral, virus, Biology, Bioinformatics, infectious diseases, MESH: Genome, Bacterial, Genome, Communicable Diseases, Deep sequencing, Pathology and Forensic Medicine, Standard procedure, Infectious disease diagnosis, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genetics, Humans, In patient, bacteria, Molecular Biology, MESH: Genome, Microbial, MESH: High-Throughput Nucleotide Sequencing, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Humans, fungus, High-Throughput Nucleotide Sequencing, 3. Good health, Genome, Microbial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, NGS, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Communicable Diseases, Molecular Medicine, Identification (biology), Genome, Fungal, MESH: Genome, Viral, Genome, Bacterial, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Erratum in Corrigendum. [Expert Rev Mol Diagn. 2016]; International audience; Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.
Published: 2015

48. An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains

Author: Marie Elise Caliot, Chantal Le Bouguénec, Christophe Pichon, Patrick Trieu-Cuot, Laurence du Merle, Biologie des Bactéries Pathogènes à Gram-positif, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by Institut Pasteur (PTR165 toC.P.), Agence National de la Recherche for the ERA-NET Pathogenomics project (ANR-06-PATHO-002-03), Postdoctoral fellowship by the French Region Ile-de-France (DIM Malinf to C.P.). Funding for open accesscharge: Institut Pasteur., and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genomic Islands, In silico, MESH: Base Pairing, Virulence, MESH: Host Factor 1 Protein, MESH: Escherichia coli Proteins, MESH: Biofilms, Bacterial genome size, Host Factor 1 Protein, Biology, MESH: Genome, Bacterial, medicine.disease_cause, Regulon, Streptococcus agalactiae, 03 medical and health sciences, MESH: Computer Simulation, Complementary DNA, Escherichia coli, Genetics, medicine, MESH: Genomic Islands, Computer Simulation, RNA, Antisense, RNA, Messenger, MESH: RNA, Antisense, Base Pairing, Gene, MESH: RNA, Messenger, 030304 developmental biology, Antigens, Bacterial, MESH: Gene Expression Regulation, Bacterial, 0303 health sciences, MESH: Escherichia coli, 030306 microbiology, Escherichia coli Proteins, Computational Biology, RNA, Gene Expression Regulation, Bacterial, MESH: Fimbriae Proteins, MESH: Streptococcus agalactiae, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Pathogenicity island, Biofilms, MESH: Regulon, Fimbriae Proteins, Genome, Bacterial, MESH: Antigens, Bacterial
Abstract: International audience; Characterization of small non-coding ribonucleic acids (sRNA) among the large volume of data generated by high-throughput RNA-seq or tiling microarray analyses remains a challenge. Thus, there is still a need for accurate in silico prediction methods to identify sRNAs within a given bacterial species. After years of effort, dedicated software were developed based on comparative genomic analyses or mathematical/statistical models. Although these genomic analyses enabled sRNAs in intergenic regions to be efficiently identified, they all failed to predict antisense sRNA genes (asRNA), i.e. RNA genes located on the DNA strand complementary to that which encodes the protein. The statistical models enabled any genomic region to be analyzed theorically but not efficiently. We present a new model for in silico identification of sRNA and asRNA candidates within an entire bacterial genome. This model was successfully used to analyze the Gram-negative Escherichia coli and Gram-positive Streptococcus agalactiae. In both bacteria, numerous asRNAs are transcribed from the complementary strand of genes located in pathogenicity islands, strongly suggesting that these asRNAs are regulators of the virulence expression. In particular, we characterized an asRNA that acted as an enhancer-like regulator of the type 1 fimbriae production involved in the virulence of extra-intestinal pathogenic E. coli.
Published: 2011

49. Detection of a geographical and endemic cluster of hyper-invasive meningococcal strains

Author: Thierry de Baere, Corinne Ruckly, Sophie Bertrand, Jean-Marc Collard, Muhamed-Kheir Taha, Raymond Vanhoof, Eva Van Meervenne, Françoise Carion, Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP), Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Infections Bactériennes Invasives, Institut Pasteur [Paris] (IP), In Belgium, this work was financed in part by the Federal Public Health Service. This publication made use of the Neisseria Multi Locus Sequence Typing website (http://pubmlst.org/neisseria/) developed by Keith Jolley and Man-Suen Chan and sited at the University of Oxford. The development of this site has been funded by the Wellcome Trust and European Union., and Institut Pasteur [Paris]
Subjects: Male, Serotype, MESH: Geography, Neisseria meningitidis, Serogroup B, MESH: Genome, Bacterial, MESH: Meningococcal Infections, medicine.disease_cause, Disease Outbreaks, MESH: Belgium, Belgium, Genotype, Cluster Analysis, MESH: Disease Outbreaks, MESH: Evolution, Molecular, MESH: Aged, Genetics, Gel electrophoresis, MESH: Microbial Sensitivity Tests, 0303 health sciences, MESH: Middle Aged, Geography, biology, Neisseria meningitidis, Middle Aged, MESH: Infant, Electrophoresis, Gel, Pulsed-Field, MESH: Multilocus Sequence Typing, MESH: Electrophoresis, Gel, Pulsed-Field, Infectious Diseases, MESH: Young Adult, Child, Preschool, Female, Neisseriaceae, Adult, DNA, Bacterial, Adolescent, Immunology, Microbial Sensitivity Tests, Meningococcal disease, Microbiology, Evolution, Molecular, Young Adult, 03 medical and health sciences, MESH: Neisseria meningitidis, Serogroup B, medicine, Humans, Serotyping, Aged, Retrospective Studies, 030304 developmental biology, MESH: Adolescent, MESH: Humans, 030306 microbiology, MESH: Child, Preschool, MESH: Serotyping, Infant, Outbreak, MESH: Adult, MESH: Retrospective Studies, medicine.disease, biology.organism_classification, MESH: Cluster Analysis, MESH: DNA, Bacterial, Virology, MESH: Male, Meningococcal Infections, Multilocus sequence typing, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Female, Genome, Bacterial, Multilocus Sequence Typing
Abstract: International audience; From 2006 to December 2009, 45 out of the 513 strains isolated from patients with invasive meningococcal disease in Belgium, were identified as Neisseria meningitidis serogroup B, non-serotypeable, subtype P1.14 (B:NT:P1.14). Most cases were geographically clustered in the northern part of the country. Multilocus Sequence Typing and antigen gene sequencing combined with Pulsed-Field Gel electrophoresis were used to investigate this cluster. Molecular typing showed that 39 out of these 45 N. meningitidis strains belonged to the clonal complex cc-269. The presence of the same PorA Variable Regions (VR1-VR2: 22, 14), the FetA allele (F5-1) and the highly similar Pulsed-Field Gel Electrophoresis profiles, supported genetic relatedness for 38 out of these 39 isolates. Retrospective analysis of B:NT:P1.22,14 isolates from 1999 onwards suggested that these strains belonging to the cc-269 complex, first emerged in the Belgian province of West-Flanders in 2004. This study showed that the combination of molecular tools with classical methods enabled reliable outbreak detection as well as a cluster identification.
Published: 2011

50. Insertion Sequence-Driven Evolution of Escherichia coli in Chemostats

Author: Christopher McKenzie, Dominique Schneider, Thomas Ferenci, Evelyne Coursange, Joël Gaffé, Ram P. Maharjan, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), and Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)
Subjects: Mutation rate, MESH: Mutation, MESH: Gene Rearrangement, Cell Culture Techniques, Bacterial genome size, Biology, MESH: Genome, Bacterial, medicine.disease_cause, Genome, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Genetic variation, Escherichia coli, Genetics, medicine, MESH: Genetic Variation, Insertion sequence, MESH: Phylogeny, Molecular Biology, MESH: Evolution, Molecular, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Gene Rearrangement, MESH: Cell Culture Techniques, 0303 health sciences, Mutation, MESH: Escherichia coli, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, Gene rearrangement, MESH: DNA Transposable Elements, Genes, Bacterial, DNA Transposable Elements, MESH: Genes, Bacterial, Genome, Bacterial
Abstract: International audience; Insertion sequence (IS) elements are present in almost all bacterial genomes and are mobile enough to provide genomic tools to differentiate closely related isolates. They can be used to estimate genetic diversity and identify fitness-enhancing mutations during evolution experiments. Here, we determined the genomic distribution of eight IS elements in 120 genomes sampled from Escherichia coli populations that evolved in glucose- and phosphate-limited chemostats by comparison to the ancestral pattern. No significant differential transposition of the various IS types was detected across the environments. The phylogenies revealed substantial diversity amongst clones sampled from each chemostat, consistent with the phenotypic diversity within populations. Two IS-related changes were common to independent chemostats, suggesting parallel evolution. One of them corresponded to insertions of IS1 elements within rpoS encoding the master regulator of stress conditions. The other parallel event was an IS5-dependent deletion including mutY involved in DNA repair, thereby providing the molecular mechanism of generation of mutator clones in these evolving populations. These deletions occurred in different co-existing genotypes within single populations and were of various sizes. Moreover, differential locations of IS elements combined with their transpositional activity provided evolved clones with different phenotypic landscapes. Therefore, IS elements strongly influenced the evolutionary processes in continuous E. coli cultures by providing a way to modify both the global regulatory network and the mutation rates of evolving cells.
Published: 2011

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