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102. Evolutionary History of Salmonella Typhi

Author

Roumagnac, Philippe, Weill, François-Xavier, Dolecek, Christiane, Baker, Stephen, Brisse, Sylvain, Chinh, Nguyen Tran, Le, Thi Anh Hong, Acosta, Camilo J., Farrar, Jeremy, Dougan, Gordon, and Achtman, Mark

Published
2006
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103. Emergence and global spread of main clinical clonal complex

Author

Moura, Alexandra, Lefrancq, Noémie, Wirth, Thierry, Leclercq, Alexandre, Borges, Vítor, Gilpin, Brent, Dallman, Timothy J, Frey, Joachim, Franz, Eelco, Nielsen, Eva M, Thomas, Juno, Pightling, Arthur, Howden, Benjamin P, Tarr, Cheryl L, Gerner-Smidt, Peter, Cauchemez, Simon, Salje, Henrik, Brisse, Sylvain, and Lecuit, Marc

Published
2021

104. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

Author

Argimón, Silvia, David, Sophia, Underwood, Anthony, Abrudan, Monica, Wheeler, Nicole E, Kekre, Mihir, Abudahab, Khalil, Yeats, Corin A, Goater, Richard, Taylor, Ben, Harste, Harry, Muddyman, Dawn, Feil, Edward J, Brisse, Sylvain, Holt, Kathryn, Donado-Godoy, Pilar, Ravikumar, KL, Okeke, Iruka N, Carlos, Celia, Aanensen, David M, NIHR Global Health Research Unit on Genomic Surveillance of Anti, and NIHR Global Health Research Unit on Genomic Surveillance

Abstract

BACKGROUND: Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. METHODS: We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR. RESULTS: Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse. CONCLUSIONS: Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.

Published
2021

105. [Letter] Cutaneous diphtheria: 3 case-reports to discuss determinants of re-emergence in resource-rich settings

Author

Levi, Laura, Barbut, Frédéric, Chopin, Dorothée, Rondeau, Paul, Lalande, Valérie, Jolivet, Sarah, Badell, Edgar, Brisse, Sylvain, Lacombe, Karine, Surgers, Laure, Services des Maladies Infectieuses et Tropicales [CHU Saint-Antoine], CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Bactériologie [CHU Saint-Antoine], Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris], Centre national de Référence des Corynebactéries du Complexe Diphtheriae - National Reference Center Corynebacteria of the diphtheriae complex (CNR), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and Gestionnaire, HAL Sorbonne Université 5

Subjects
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Corynebacterium diphtheriae, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, vaccine skepticism, emergence, Diphtheria, complex mixtures, Corynebacterium ulcerans
Abstract

International audience; Diphtheria is a re-emerging disease in resource-rich settings. We here report three cases of cutaneous diphtheria diagnosed and managed in our infectious disease department and discuss the determinants of its re-emergence. Migration, travel and vaccine skepticism are key factors not only for diphtheria re-emergence, but for the future of most preventable diseases.

Published
2021
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106. Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups

Author

Bialek-Davenet, Suzanne, Criscuolo, Alexis, Ailloud, Florent, Passet, Virginie, Jones, Louis, Delannoy-Vieillard, Anne- Sophie, Garin, Benoit, Le Hello, Simon, Arlet, Guillaume, Nicolas-Chanoine, Marie-Helene, Decre, Dominique, and Brisse, Sylvain

Subjects
Bacterial pneumonia -- Comparative analysis, Genomics -- Comparative analysis, Drug resistance in microorganisms -- Comparative analysis, Genomes -- Comparative analysis, Pneumonia -- Comparative analysis, Health
Abstract

Klebsiella pneumoniae is a frequent cause of nosocomial infections and has also emerged as an agent of severe community-acquired infections, including pyogenic liver abscess, pneumonia, and meningitis (1,2). The rise [...]

Published
2014
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109. Evolution of Bordetella pertussis over a 23-year period in France, 1996 to 2018

Author

Bouchez, Valérie, Guillot, Sophie, Landier, Annie, Armatys, Nathalie, Matczak, Soraya, Toubiana, Julie, Brisse, Sylvain, Brieu, Nathalie, Hamdad, Farida, Kempf, Marie, Pailhoriès, Hélène, Jensen, Cécile, Lehours, Philippe, Guiraud, Jennifer, Le Bars, Hervé, Isnard, Christophe, Wilhelm, Nathalie, Le Coustumier, Alain, Delmas, Julien, De Briel, Dominique, Souply, Laurent, Aberrane, Saïd, Coudé, Marie, Garnier, Fabien, Descours, Ghislaine, Jean-Pierre, Hélène, Alauzet, Corentine, Gibaud, Sophie-Anne, Bonacorsi, Stéphane, Brasme, Lucien, Lemée, Ludovic, Koebel, Christelle, Lanotte, Philippe, Bland, Stéphane, Petitprez, Hélène, Raffenot, Didier, Levast, Marion, Doucet-Populaire, Florence, Bourgeois-Nicolaos, Nadège, Burucoa, Christophe, Grattard, Florence, Marque-Juillet, Stéphanie, 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 - National Reference Center for Whooping Cough and other Bordetella infections (CNR), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Département de Pédiatrie et maladies infectieuses [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), Université de Paris (UP), This work was performed with the financial support of the Institut Pasteur and of Santé Publique France., French pertussis microbiology study group: Nathalie Brieu, Farida Hamdad, Marie Kempf, Hélène Pailhoriès, Cécile Jensen, Philippe Lehours, Jennifer Guiraud, Hervé Le Bars, Christophe Isnard, Nathalie Wilhelm, Alain Le Coustumier, Julien Delmas, Dominique De Briel, Laurent Souply, Saïd Aberrane, Marie Coudé, Fabien Garnier, Ghislaine Descours, Hélène Jean-Pierre, Corentine Alauzet, Sophie-Anne Gibaud, Stéphane Bonacorsi, Lucien Brasme, Ludovic Lemée, Christelle Koebel, Philippe Lanotte, Stéphane Bland, Hélène Petitprez, Didier Raffenot, Marion Levast, Florence Doucet-Populaire, Nadège Bourgeois-Nicolaos, Christophe Burucoa, Florence Grattard, Stéphanie Marque-Juillet, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Collège Doctoral, Université Paris Cité (UPCité), and Institut Pasteur [Paris]-Institut Pasteur [Paris]

Subjects
Serotype, Bordetella pertussis, population evolution, Whooping Cough, Epidemiology, [SDV]Life Sciences [q-bio], Fimbria, MESH: Pertussis Toxin, MESH: Virulence Factors, Bordetella, Pertussis toxin, Microbiology, pertactin, MESH: Bordetella pertussis, 03 medical and health sciences, 0302 clinical medicine, Antigen, Virology, MESH: Child, medicine, Humans, Virulence Factors, Bordetella, 030212 general & internal medicine, Child, Whooping cough, 030304 developmental biology, Pertussis Vaccine, vaccine antigen deficiency, 0303 health sciences, Surveillance, MESH: Humans, biology, MESH: Bacterial Outer Membrane Proteins, Public Health, Environmental and Occupational Health, MESH: Whooping Cough, biology.organism_classification, medicine.disease, fimbriae serotype, 3. Good health, respiratory tract diseases, Vaccination, MESH: France, Pertussis Toxin, MESH: Pertussis Vaccine, France, Pertactin, Bacterial Outer Membrane Proteins
Abstract

Background Bordetella pertussis is the main agent of whooping cough. Vaccination with acellular pertussis vaccines has been largely implemented in high-income countries. These vaccines contain 1 to 5 antigens: pertussis toxin (PT), filamentous haemagglutinin (FHA), pertactin (PRN) and/or fimbrial proteins (FIM2 and FIM3). Monitoring the emergence of B. pertussis isolates that might partially escape vaccine-induced immunity is an essential component of public health strategies to control whooping cough. Aim We aimed to investigate temporal trends of fimbriae serotypes and vaccine antigen-expression in B. pertussis over a 23-year period in France (1996–2018). Methods Isolates (n = 2,280) were collected through hospital surveillance, capturing one third of hospitalised paediatric pertussis cases. We assayed PT, FHA and PRN production by Western blot (n = 1,428) and fimbriae production by serotyping (n = 1,058). Molecular events underlying antigen deficiency were investigated by genomic sequencing. Results The proportion of PRN-deficient B. pertussis isolates has increased steadily from 0% (0/38) in 2003 to 48.4% (31/64) in 2018 (chi-squared test for trend, p 481 insertion within the prn gene or a 22 kb genomic inversion involving the prn promoter sequence, indicative of convergent evolution. FIM2-expressing isolates have emerged since 2011 at the expense of FIM3. Conclusions B. pertussis is evolving through the rapid increase of PRN-deficient isolates and a recent shift from FIM3 to FIM2 expression. Excluding PRN, the loss of vaccine antigen expression by circulating B. pertussis isolates is epidemiologically insignificant.

Published
2021
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110. Deliverables of Codes4strains project (Part2)

Author

Hennart Melanie and Brisse Sylvain

Subjects
Klebsiella pneumoniae, genomic classification, strain nomenclature
Abstract

Background One of the main objectives of the PhD project is to develop a novel nomenclature system, potentially applicable to all bacterial pathogens. Here we first focus is on a highly antibiotic resistant bacterial pathogen, K. pneumoniae (Kp), and on a foodborne bacterial pathogen, Escherichia coli (Ec). The aim is to combine two main microbial strain nomenclatures approaches that are currently being used separately. (further details: https://onehealthejp.eu/codes4strains/) Deliverables D-PhD16-3.2: cgLINcodes algorithm defined and implemented on full dataset D-PhD16-4.2: Preprint publication on the cgLIN codes concept and comparison with multi-level single-linkage classifications D-PhD16-4.3: A novel tool to define the population structure of species, called MSTclust D-PhD16-4.4: An inheritance algorithm to provide backwards compatibility of MLSL groups with 7-gene MLST identifiers D-PhD16-4.5: Comparison of the ANI metric with the cgMLST metric D-PhD16-4.6: A novel method to identify recombination in cgMLST profiles D-PhD16-4.7: Integration of MLSL identifiers into the BIGSdb platform to make them publicly available, {"references":["https://doi.org/10.1101/2021.07.26.453808"]}

Published
2021
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111. Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study

Author

Badell Edgar, Alharazi Abdulilah, Criscuolo Alexis, Almoayed Khaled Abdullah Ali, Lefrancq Noémie, Bouchez Valerie, Guglielmini Julien, Hennart Melanie, Carmi-Leroy Annick, Zidane Nora, Pascal-Perrigault Marine, Lebreton Manon, Martini Helena, Salje Henrik, Toubiana Julie, Dureab Fekri, Dhabaan Ghulam, Brisse Sylvain, NCPHL diphtheria outbreak working group, Lefrancq, Noemie [0000-0001-5991-6169], Salje, Henrik [0000-0003-3626-4254], Apollo - University of Cambridge Repository, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP), Centre national de Référence des Corynebactéries du Complexe Diphtheriae - National Reference Center Corynebacteria of the diphtheriae complex (CNR), National Centre of the Public Health Laboratories [Sana'a, Yemen], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ministry of Public Health and Population [Sana'a, Yemen], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Collège Doctoral, Sorbonne Université (SU), Vrije Universiteit Brussel (VUB), University of Cambridge [UK] (CAM), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Akkon University of Human Sciences - Akkon Hochschule für Humanwissenschaften [Berlin, Allemagne], Universität Heidelberg [Heidelberg] = Heidelberg University, University of Toronto, This work was supported financially by institutional funding from the NCPHL (Sana'a, Yemen) and Institut Pasteur. The French National Reference Center for Corynebacteria of the diphtheriae complex received support from Institut Pasteur and Public Health France (Santé publique France, Saint Maurice, France). This work was also supported financially by the French Government Investissement d'Avenir Programme Laboratoire d'Excellence, Integrative Biology of Emerging Infectious Diseases (ANR-10-LABX-62-IBEID)., NCPHL diphtheria outbreak working group (Abdulaziz A Rawah, Mohammed A Aldawla, Ekram M Al­Awdi, Nabila M Al­Moalmy, Huda Z Al­Shami, Ali A Al­Somainy), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Department of Clinical Microbiology, Brussels Heritage Lab, Supporting clinical sciences, Microbiology and Infection Control, Clinical Biology, Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], and Universität Heidelberg [Heidelberg]

Subjects
OHEJP, Yemen/epidemiology, Adult, Corynebacterium diphtheriae/genetics, Yemen, Adolescent, [SDV]Life Sciences [q-bio], genomic epidemiology, Corynebacterium, Diphtheria/epidemiology, Disease Outbreaks, Young Adult, Anti-Infective Agents, Humans, Diphtheria Toxin, Child, Phylogeny, Aged, Aged, 80 and over, Diphtheria Toxin/genetics, Corynebacterium diphtheriae, Infant, Diphtheria, Codes4strains, Genomics, Middle Aged, Cross-Sectional Studies, Child, Preschool
Abstract

Background An outbreak of diphtheria, declared in Yemen in October, 2017, is ongoing. We did a cross-sectional study to investigate the epidemiological, clinical, and microbiological features of the outbreak. Methods Probable cases of diphtheria that were defined clinically and recorded through a weekly electronic diseases early warning system (from 2017, week 22, to 2020, week 17) were used to identify trends of the outbreak (we divided the epidemic into three time periods: May 29, 2017, to June 10, 2018; June 11, 2018, to June 3, 2019; and June 4, 2019, to April 26, 2020). We used the line list of diphtheria reports for governorate-level descriptions. Vaccination coverage was estimated using the 2017 and 2018 annual reports by the national Expanded Programme on Immunization. To confirm cases biologically,Corynebacterium diphtheriaewas isolated and identified from throat swabs using standard microbiological culture and identification procedures. We assessed differences in the temporal and geographical distributions of cases, including between different age groups. For in-depth microbiological analysis,toxgene and species-specificrpoBreal-time PCR, Illumina genomic sequencing, antimicrobial susceptibility analysis (disk diffusion, E-test), and the Elek diphtheria toxin production test were done on confirmed cases. We used genomic data for phylogenetic analyses and to estimate the nucleotide substitution rate. Findings The Yemen diphtheria outbreak affected almost all governorates (provinces), with 5701 probable cases and 330 deaths recorded up to April 26, 2020. We collected clinical data for 888 probable cases with throat swab samples referred for biological confirmation, and genomic data for 42 positive cases, corresponding to 43 isolates (two isolates from one culture were included due to distinct colony morphologies). The median age of patients was 12 years (range 0·2–80). The proportion of cases in children aged 0–4 years was reduced during the second time period, after a vaccination campaign, compared with the first period (19% [95% CI 18–21] in the first periodvs14% [12–15] in the second period, pC diphtheriaephylogenetic sublineages, four of which are genetically related to isolates from Saudi Arabia, Eritrea, and Somalia. Inter-sublineage genomic variations in genes associated with antimicrobial resistance, iron acquisition, and adhesion were observed. The predominant sublineage (30 [70%] of 43 isolates) was resistant to trimethoprim and was associated with unique genomic features, more frequent neck swelling (p=0·0029) and a younger age of patients (p=0·060) compared with the other sublineages. Its evolutionary rate was estimated at 1·67 × 10−6substitutions per site per year, placing its most recent common ancestor in 2015, and indicating silent circulation ofC diphtheriaein Yemen before the outbreak was declared. Interpretation In the Yemen outbreak,C diphtheriaeshows high phylogenetic, genomic, and phenotypic variation. Laboratory capacity and real-time microbiological monitoring of diphtheria outbreaks need to be scaled up to inform case management and transmission control of diphtheria. Catch-up vaccination might have provided some protection to the targeted population (children aged 0–4 years). Funding National Centre of the Public Health Laboratories (Yemen), Institut Pasteur, and the French Government Investissement d'Avenir Programme. Translation For the Arabic translation of the abstract see Supplementary Materials section.

Published
2021
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112. High prevalence of Klebsiella pneumoniae in European food products: a multicentric study comparing culture and molecular detection methods

Author

Rodrigues, Carla, primary, Hauser, Kathrin, additional, Cahill, Niamh, additional, Ligowska-Marzęta, Małgorzata, additional, Centorotola, Gabriella, additional, Cornacchia, Alessandra, additional, Garcia Fierro, Raquel, additional, Haenni, Marisa, additional, Møller Nielsen, Eva, additional, Piveteau, Pascal, additional, Barbier, Elodie, additional, Morris, Dearbháile, additional, Pomilio, Francesco, additional, and Brisse, Sylvain, additional

Published
2021
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114. Spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis

Author

Lefrancq, Noemie, primary, Bouchez, Valerie, additional, Fernandes, Nadia, additional, Barkoff, Alex-Mikael, additional, Bosch, Thijs, additional, Dalby, Tine, additional, Akerlund, Thomas, additional, Fabianova, Katerina, additional, Vestrheim, Didrik F, additional, Fry, Norman K., additional, Gonzalez-Lopez, Juan Jose, additional, Gullsby, Karolina, additional, Habington, Adele, additional, He, Qiushui, additional, Litt, David, additional, Martini, Helena, additional, Pierard, Denis, additional, Stefanelli, Paola, additional, Stegger, Marc K., additional, Zavadilov, Jana, additional, Armatys, Nathalie, additional, Landier, Annie, additional, Guillot, Sophie, additional, Hong, Samuel L, additional, Lemey, Philippe, additional, Parkhill, Julian, additional, Toubiana, Julie, additional, Cauchemez, Simon, additional, Salje, Henrik, additional, and Brisse, Sylvain, additional

Published
2021
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117. Liver abscess caused by infection with community-acquired Klebsiella quasipneumoniae subsp. quasipneumoniae

Author

Breurec, Sebastien, Melot, Benedicte, Hoen, Bruno, Passet, Virginie, Schepers, Kinda, Bastian, Sylvaine, and Brisse, Sylvain

Subjects
Polysaccharides -- Health aspects, Liver diseases -- Health aspects, Liver -- Health aspects, Health
Abstract

The syndrome of pyogenic liver abscess caused by community-acquired Klebsiella pneumoniae (CAKLA) infection has been described mainly in Asia, particularly in Taiwan. Infection is caused by hypervirulent strains of particular [...]

Published
2016
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119. Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Author

Njamkepo, Elisabeth, Fawal, Nizar, Tran-Dien, Alicia, Hawkey, Jane, Strockbine, Nancy, Jenkins, Claire, Talukder, Kaisar A., Bercion, Raymond, Kuleshov, Konstantin, Kolínská, Renáta, Russell, Julie E., Kaftyreva, Lidia, Accou-Demartin, Marie, Karas, Andreas, Vandenberg, Olivier, Mather, Alison E., Mason, Carl J., Page, Andrew J., Ramamurthy, Thandavarayan, Bizet, Chantal, Gamian, Andrzej, Carle, Isabelle, Sow, Amy Gassama, Bouchier, Christiane, Wester, Astrid Louise, Lejay-Collin, Monique, Fonkoua, Marie-Christine, Le Hello, Simon, Blaser, Martin J., Jernberg, Cecilia, Ruckly, Corinne, Mérens, Audrey, Page, Anne-Laure, Aslett, Martin, Roggentin, Peter, Fruth, Angelika, Denamur, Erick, Venkatesan, Malabi, Bercovier, Hervé, Bodhidatta, Ladaporn, Chiou, Chien-Shun, Clermont, Dominique, Colonna, Bianca, Egorova, Svetlana, Pazhani, Gururaja P., Ezernitchi, Analia V., Guigon, Ghislaine, Harris, Simon R., Izumiya, Hidemasa, Korzeniowska-Kowal, Agnieszka, Lutyńska, Anna, Gouali, Malika, Grimont, Francine, Langendorf, Céline, Marejková, Monika, Peterson, Lorea A.M., Perez-Perez, Guillermo, Ngandjio, Antoinette, Podkolzin, Alexander, Souche, Erika, Makarova, Mariia, Shipulin, German A., Ye, Changyun, Žemličková, Helena, Herpay, Mária, Grimont, Patrick A. D., Parkhill, Julian, Sansonetti, Philippe, Holt, Kathryn E., Brisse, Sylvain, Thomson, Nicholas R., and Weill, François-Xavier

Published
2016
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122. One Health or Three? Transmission modelling ofKlebsiellaisolates reveals ecological barriers to transmission between humans, animals and the environment

Author

Thorpe, Harry, primary, Booton, Ross, additional, Kallonen, Teemu, additional, Gibbon, Marjorie J., additional, Couto, Natacha, additional, Passet, Virginie, additional, Fernandez, Juan Sebastian Lopez, additional, Rodrigues, Carla, additional, Matthews, Louise, additional, Mitchell, Sonia, additional, Reeve, Richard, additional, David, Sophia, additional, Merla, Cristina, additional, Corbella, Marta, additional, Ferrari, Carolina, additional, Comandatore, Francesco, additional, Marone, Piero, additional, Brisse, Sylvain, additional, Sassera, Davide, additional, Corander, Jukka, additional, and Feil, Edward J., additional

Published
2021
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124. Association between the COVID-19 pandemic and pertussis in France using multiple nationwide data sources

Author

Matczak, Soraya, primary, Levy, Corinne, additional, Fortas, Camille, additional, Cohen, Jérémie F., additional, Béchet, Stéphane, additional, El Belghiti, Fatima Aït, additional, Guillot, Sophie, additional, Trombert-Paolantoni, Sabine, additional, Jacomo, Véronique, additional, Savitch, Yann, additional, Paireau, Juliette, additional, Brisse, Sylvain, additional, Guiso, Nicole, additional, Lévy-Bruhl, Daniel, additional, Cohen, Robert, additional, and Toubiana, Julie, additional

Published
2021
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129. Evolution and population structure of Salmonella enterica serovar Newport

Author

Sangal, Vartul, Harbottle, Heather, Mazzoni, Camila J., Helmuth, Reiner, Guerra, Beatriz, Didelot, Xavier, Paglietti, Bianca, Rabsch, Wolfgang, Brisse, Sylvain, Weill, Francois-Xavier, Roumagnac, Philippe, and Achtman, Mark

Subjects
Salmonella -- Genetic aspects, Salmonella -- Physiological aspects, Evolution -- Research, Biological sciences
Abstract

Salmonellosis caused by Salmonella enterica serovar Newport is a major global public health concern, particularly because S. Newport isolates that are resistant to multiple drugs (MDR), including third-generation cephalosporins (MDR-AmpC phenotype), have been commonly isolated from food animals. We analyzed 384 S. Newport isolates from various sources by a multilocus sequence typing (MLST) scheme to study the evolution and population structure of the serovar. These were compared to the population structure of S. enterica serovars Enteritidis, Kentucky, Paratyphi B, and Typhimurium. Our S. Newport collection fell into three lineages, Newport-I, Newport-II, and Newport-III, each of which contained multiple sequence types (STs). Newport-I has only a few STs, unlike Newport-II or Newport-III, and has possibly emerged recently. Newport-I is more prevalent among humans in Europe than in North America, whereas Newport-II is preferentially associated with animals. Two STs of Newport-II encompassed all MDR-AmpC isolates, suggesting recent global spread after the acquisition of the [bla.sub.CMY-2] gene. In contrast, most Newport-III isolates were from humans in North America and were pansusceptible to antibiotics. Newport was intermediate in population structure to the other serovars, which varied from a single monophyletic lineage in S. Enteritidis or S. Typhimurium to four discrete lineages within S. Paratyphi B. Both mutation and homologous recombination are responsible for diversification within each of these lineages, but the relative frequencies differed with the lineage. We conclude that serovars of S. enterica provide a variety of different population structures. doi: 10.1128/JB.00969-10

Published
2010

131. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

Author

Argimón, Silvia, primary, David, Sophia, additional, Underwood, Anthony, additional, Abrudan, Monica, additional, Wheeler, Nicole E., additional, Kekre, Mihir, additional, Abudahab, Khalil, additional, Yeats, Corin A., additional, Goater, Richard, additional, Taylor, Ben, additional, Harste, Harry, additional, Muddyman, Dawn, additional, Feil, Edward J., additional, Brisse, Sylvain, additional, Holt, Kathryn, additional, Donado-Godoy, Pilar, additional, Ravikumar, KL, additional, Okeke, Iruka N., additional, Carlos, Celia, additional, and Aanensen, David M., additional

Published
2021
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133. Characterization of Klebsiella pneumoniae isolated from patients suspected of pulmonary or bubonic plague during the Madagascar epidemic in 2017

Author

Rakotondra, Andriniaina, primary, Andrianonimiadana, Lova, additional, Rahajandraibe, Soloandry, additional, Razafimahatratra, Solohery, additional, Andrianaivoarimanana, Voahangy, additional, Rahelinirina, Soanandrasana, additional, Crucitti, Tania, additional, Brisse, Sylvain, additional, Jeannoda, Victor, additional, Rajerison, Minoarisoa, additional, and Collard, Jean-Marc, additional

Published
2021
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134. 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, and Brisse, Sylvain

Subjects
TAXONOMY, MICROBIAL ecology, POPULATION biology, MICROEVOLUTION, CLUSTER analysis (Statistics)
Abstract

Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication 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 threat Klebsiella pneumoniae as 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 (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (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 barcode 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. [ABSTRACT FROM AUTHOR]

Published
2022
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135. D-additional task 1 - Klebsiella MALDI TypeR: a web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry

Author

Bridel, Sébastien, Watts, Stephen W., Judd, Louise M., Harshegyi, Taylor, Passet, Virginie, Rodrigues, Carla, Holt, Kathryn E., and Brisse, Sylvain

Abstract

MotivationKlebsiellaspecies are increasingly multidrug resistant pathogens affecting human and animal health and are widely distributed in the environment. Among these, theKlebsiella pneumoniaespecies complex (KpSC), which includes seven phylogroups, is an important cause of community and hospital infections. In addition, theKlebsiella oxytocaspecies complex (KoSC) also causes hospital infections and antibiotic-associated haemorrhagic colitis. The unsuitability of widely used clinical microbiology methods to distinguish species within each of these species complexes leads to high rates of misidentifications that are masking the true clinical significance and potential epidemiological specificities of individual species.ResultsWe developed a web-based tool,KlebsiellaMALDI TypeR, a platform-independent and user-friendly application that enables uploading raw data from MALDI-TOF mass spectrometer to identifyKlebsiellaisolates at the species complex and phylogroup levels. The tool is based on a database of previously identified biomarkers that are specific for either the species complex, individual phylogroups, or related phylogroups, and is available athttps://maldityper.pasteur.fr.

Published
2020

136. Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing

Author

Salerno, Anna, Deletoile, Alexis, Lefevre, Martine, Ciznar, Ivan, Krovacek, Karel, Grimont, Patrick, and Brisse, Sylvain

Subjects
Enterobacter -- Genetic aspects, Enterobacter -- Analysis, Enterobacteriaceae -- Genetic aspects, Enterobacteriaceae -- Analysis, Phylogeny -- Analysis, Polymerase chain reaction -- Usage, Biological sciences
Abstract

Plesiomonas shigelloides is an emerging pathogen that is widespread in the aquatic environment and is responsible for intestinal diseases and extraintestinal infections in humans and other animals. Virtually nothing is known about its genetic diversity, population structure, and evolution, which severely limits epidemiological control. We addressed these questions by developing a multilocus sequence typing (MLST) system based on five genes (fusA, leuS, pyrG, recG, and rpoB) and analyzing 77 epidemiologically unrelated strains from several countries and several ecological sources. The phylogenetic position of P. shigelloides within family Enterobacteriaceae was precisely defined by phylogenetic analysis of the same gene portions in other family members. Within P. shigelloides, high levels of nucleotide diversity (average percentage of nucleotide differences between strains, 1.49%) and genotypic diversity (64 distinct sequence types; Simpson's index, 99.7%) were found, with no salient internal phylogenetic structure. We estimated that homologous recombination in housekeeping genes affects P. shigelloides alleles and nucleotides 7 and 77 times more frequently than mutation, respectively. These ratios are similar to those observed in the naturally transformable species Streptococcus pneumoniae with a high rate of recombination. In contrast, recombination within Salmonella enterica, Escherichia coli, and Yersinia enterocolitica was much less frequent. P. shigelloides thus stands out among members of the Enterobacteriaceae. Its high rate of recombination results in a lack of association between genomic background and O and H antigenic factors, as observed for the 51 serotypes found in our sample. Given its robustness and discriminatory power, we recommend MLST as a reference method for population biology studies and epidemiological tracking of P. shigelloides strains.

Published
2007

137. Multilocus sequence typing of Lactobacillus casei reveals a clonal population structure with low levels of homologous recombination

Author

Diancourt, Laure, Passet, Virginie, Chervaux, Christian, Garault, Peggy, Smokvina, Tamara, and Brisse, Sylvain

Subjects
Lactobacillus -- Research, Lactobacillus -- Genetic aspects, Nucleotide sequencing -- Research, Biological sciences
Abstract

Research study is conducted to develop multilocus sequence typing (MLST) scheme for Lactobacillus casei and to initiate characterization of the population structure of this species. Clear evidence for homologous recombination is found during the diversification of Lactobacillus casei clones.

Published
2007

138. Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak

Author

Schuffenecker, Isabelle, Iteman, Isabelle, Michault, Alain, Murri, Severine, Frangeul, Lionel, Vaney, Marie-Christine, Lavenir, Rachel, Pardigon, Nathalie, Reynes, Jean-Marc, Pettinelli, Francois, Biscornet, Leon, Diancourt, Laure, Michel, Stephanie, Duquerroy, Stephane, Guigon, Ghislaine, Frenkiel, Marie-Pascale, Brehin, Anne-Claire, Cubito, Nadege, Despres, Philippe, Kunst, Frank, Rey, Felix A., Zeller, Herve, and Brisse, Sylvain

Subjects
RNA viruses -- Research, RNA virus infections -- Development and progression
Abstract

ABSTRACT Background A chikungunya virus outbreak of unprecedented magnitude is currently ongoing in Indian Ocean territories. In Reunion Island, this alphavirus has already infected about one-third of the human population. [...]

Published
2006

139. Leakiness at the human-animal interface in Southeast Asia and implications for the spread of antibiotic resistance

Author

Nadimpalli, Maya L., primary, Stegger, Marc, additional, Viau, Roberto, additional, Yith, Vuthy, additional, de Lauzanne, Agathe, additional, Sem, Nita, additional, Borand, Laurence, additional, Huynh, Bich-tram, additional, Brisse, Sylvain, additional, Passet, Virginie, additional, Overballe-Petersen, Søren, additional, Aziz, Maliha, additional, Gouali, Malika, additional, Jacobs, Jan, additional, Phe, Thong, additional, Hungate, Bruce A., additional, Leshyk, Victor O., additional, Pickering, Amy J., additional, Gravey, François, additional, Liu, Cindy M., additional, Johnson, Timothy J., additional, Hello, Simon Le, additional, and Price, Lance B., additional

Published
2021
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140. High-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones

Author

Jamet, Anne, primary, Guglielmini, Julien, additional, Brancotte, Bryan, additional, Coureuil, Mathieu, additional, Euphrasie, Daniel, additional, Meyer, Julie, additional, Roux, Johanna, additional, Barnier, Jean-Philippe, additional, Bille, Emmanuelle, additional, Ferroni, Agnès, additional, Magny, Jean-François, additional, Bôle-Feysot, Christine, additional, Charbit, Alain, additional, Nassif, Xavier, additional, and Brisse, Sylvain, additional

Published
2021
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141. Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population in Norway: a cross-sectional study of risk factors and bacterial genomic diversity

Author

Raffelsberger, Niclas, primary, Hetland, Marit Andrea Klokkhammer, additional, Svendsen, Kristian, additional, Småbrekke, Lars, additional, Löhr, Iren H., additional, Andreassen, Lotte Leonore Eivindsdatter, additional, Brisse, Sylvain, additional, Holt, Kathryn E., additional, Sundsfjord, Arnfinn, additional, Samuelsen, Ørjan, additional, and Gravningen, Kirsten, additional

Published
2021
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142. Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae

Author

Batisti Biffignandi, Gherard, primary, Gibbon, Marjorie J, additional, Corbella, Marta, additional, Thorpe, Harry A, additional, Merla, Cristina, additional, Castelli, Michele, additional, Kallonen, Teemu, additional, Pegrum, Katie, additional, Brisse, Sylvain, additional, Corander, Jukka, additional, Marone, Piero, additional, Feil, Edward J, additional, and Sassera, Davide, additional

Published
2021
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143. Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity

Author

Raffelsberger, Niclas, primary, Hetland, Marit Andrea Klokkhammer, additional, Svendsen, Kristian, additional, Småbrekke, Lars, additional, Löhr, Iren Høyland, additional, Andreassen, Lotte Leonore Eivindsdatter, additional, Brisse, Sylvain, additional, Holt, Kathryn E., additional, Sundsfjord, Arnfinn, additional, Samuelsen, Ørjan, additional, and Gravningen, Kirsten, additional

Published
2021
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144. Impact of Vaccine Schedule Change on Pertussis Epidemiology in France: A Modelling and Serological Study

Author

Paireau, Juliette, primary, Guillot, Sophie, additional, Aït El Belghiti, Fatima, additional, Matczak, Soraya, additional, Trombert-Paolantoni, Sabine, additional, Jacomo, Véronique, additional, Taha, Muhamed-Kheir, additional, Salje, Henrik, additional, Brisse, Sylvain, additional, Lévy-Bruhl, Daniel, additional, Cauchemez, Simon, additional, and Toubiana, Julie, additional

Published
2021
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