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1. Taxonomic and phenotypic analysis of bifidobacteria isolated from IBD patients as potential probiotic strains

Author

Sabine Bosselaar, Lucile Dhelin, Ellena Dautel, Marie Titecat, Stéphanie Duthoy, Marie Stelmaszczyk, Nathan Delory, Madeleine De Sousa Violante, François Machuron, Hassina Ait-Abderrahim, Pierre Desreumaux, Benoit Foligné, and Céline Monnet

Subjects
Bifidobacteria, Inflammatory Bowel Diseases, Microbiota, Culturomics, Functional characterization, Microbiology, QR1-502
Abstract

Abstract Background Inflammatory Bowel Diseases (IBD) are a major public health issue with unclear aetiology. Changes in the composition and functionality of the intestinal microbiota are associated with these pathologies, including the depletion of strict anaerobes such as Feacalibacterium prausnitzii. Less evidence is observed for depletion in other anaerobes, among which bifidobacteria. This study characterized the taxonomic and functional diversity of bifidobacteria isolated from the human intestinal microbiota in active and non-active IBD patients by a culturomics approach and evaluated if these bifidobacteria might be used as probiotics for gut health. Results A total of 341 bifidobacteria were isolated from the intestinal microbiota of IBD patients (52 Crohn’s disease and 26 ulcerative colitis patients), with a high proportion of Bifidobacterium dentium strains (28% of isolated bifidobacteria). In ulcerative colitis, the major species identified was B. dentium (39% of isolated bifidobacteria), in active and non-active ulcerative colitis. In Crohn’s disease, B. adolescentis was the major species isolated from non-active patients (40%), while similar amounts of B. dentium and B. adolescentis were found in active Crohn’s disease patients. The relative abundance of B. dentium was increased with age, both in Crohn’s disease and ulcerative colitis and active and non-active IBD patients. Antibacterial capacities of bifidobacteria isolated from non-active ulcerative colitis against Escherichia coli LF82 and Salmonella enterica ATCC 14028 were observed more often compared to strains isolated from active ulcerative colitis. Finally, B. longum were retained as strains with the highest probiotic potential as they were the major strains presenting exopolysaccharide synthesis, antibacterial activity, and anti-inflammatory capacities. Antimicrobial activity and EPS synthesis were further correlated to the presence of antimicrobial and EPS gene clusters by in silico analysis. Conclusions Different bifidobacterial taxonomic profiles were identified in the microbiota of IBD patients. The most abundant species were B. dentium, mainly associated to the microbiota of ulcerative colitis patients and B. adolescentis, in the intestinal microbiota of Crohn’s disease patients. Additionally, the relative abundance of B. dentium significantly increased with age. Furthermore, this study evidenced that bifidobacteria with probiotic potential (antipathogenic activity, exopolysaccharide production and anti-inflammatory activity), especially B. longum strains, can be isolated from the intestinal microbiota of both active and non-active Crohn’s disease and ulcerative colitis patients.

Published
2024
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2. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

Author

Jean Claude Semuto Ngabonziza, Chloé Loiseau, Michael Marceau, Agathe Jouet, Fabrizio Menardo, Oren Tzfadia, Rudy Antoine, Esdras Belamo Niyigena, Wim Mulders, Kristina Fissette, Maren Diels, Cyril Gaudin, Stéphanie Duthoy, Willy Ssengooba, Emmanuel André, Michel K. Kaswa, Yves Mucyo Habimana, Daniela Brites, Dissou Affolabi, Jean Baptiste Mazarati, Bouke Catherine de Jong, Leen Rigouts, Sebastien Gagneux, Conor Joseph Meehan, and Philip Supply

Subjects
Science
Abstract

The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to be evolved from a common progenitor in Africa. Here, the authors identify two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage further supporting an East African origin for the MTBC.

Published
2020
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3. Drug-Resistant Tuberculosis, Lebanon, 2016 – 2017

Author

Salam El Achkar, Christine Demanche, Marwan Osman, Rayane Rafei, Mohamad Bachar Ismail, Hiam Yaacoub, Claire Pinçon, Stéphanie Duthoy, Frédérique De Matos, Cyril Gaudin, Alberto Trovato, Daniela M. Cirillo, Monzer Hamze, and Philip Supply

Subjects
Tuberculosis, TB, MDR, XDR, drug resistance, survey, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

In a 12-month nationwide study on the prevalence of drug-resistant tuberculosis (TB) in Lebanon, we identified 3 multidrug-resistant cases and 3 extensively drug-resistant TB cases in refugees, migrants, and 1 Lebanon resident. Enhanced diagnostics, particularly in major destinations for refugees, asylum seekers, and migrant workers, can inform treatment decisions and may help prevent the spread of drug-resistant TB.

Published
2019
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4. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna.

Author

Natacha Nikolic, Stéphanie Duthoy, Antoine Destombes, Nathalie Bodin, Wendy West, Alexis Puech, and Jérôme Bourjea

Subjects
Medicine, Science
Abstract

Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87-90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24-27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species-Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.

Published
2015
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5. Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs

Author

Cyril Gaudin, Stefan Niemann, Alice Ferré, Stéphanie Duthoy, Vanessa Mathys, Yannick Laurent, Emmanuel André, Elisa Tagliani, Bouke C. de Jong, Philip Supply, Andrea M. Cabibbe, Silke Feuerriegel, Caroline Allix-Béguec, Nelly Badalato, Sandy Contreras, Michel K. Kaswa, Leen Rigouts, Agathe Jouet, Daniela Maria Cirillo, Maren Diels, Institute of Tropical Medicine [Antwerp] (ITM), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Universiteit Antwerpen [Antwerpen], 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), Genoscreen [Lille], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Forschungszentrum Borstel - Research Center Borstel, German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), National Tuberculosis Program [Kinshasa], IRCCS Ospedale San Raffaele [Milan, Italy], Maladies bactériennes = Bacterial diseases [Bruxelles], Sciensano [Bruxelles], 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, Parts of this work have been supported by the European Union PathoNGen-Trace project (FP7-278864) and by the World Health Organization (for the TB drug resistance survey conducted in the Democratic Republic of the Congo). B.C. de Jong and L. Rigouts were supported by European Research Council starting grant 'INTERRUPTB' (grant agreement 311725)., European Project: 278864,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PATHONGEN-TRACE(2012), European Project: 311725,EC:FP7:ERC,ERC-2012-StG_20111109,INTERRUPTB(2013), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], Universiteit Antwerpen = University of Antwerpen [Antwerpen], Noel, Anne-Laure, Next Generation Genome Based High Resolution Tracing of Pathogens - PATHONGEN-TRACE - - EC:FP7:HEALTH2012-01-01 - 2016-06-30 - 278864 - VALID, and Estimating the effective reproductive rate of M. tuberculosis from changes in molecular clustering rates, to measure the impact of public health interventions on TB transmission - INTERRUPTB - - EC:FP7:ERC2013-01-01 - 2017-12-31 - 311725 - VALID

Subjects
0301 basic medicine, Pulmonary and Respiratory Medicine, 030106 microbiology, Respiratory System, Antitubercular Agents, Drug resistance, Microbial Sensitivity Tests, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Deep sequencing, Mycobacterium, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Tuberculosis, Multidrug-Resistant, medicine, Humans, Tuberculosis, Deeplex Myc-TB may enable fast, Ethambutol, Genetics, Whole genome sequencing, Science & Technology, biology, business.industry, High-Throughput Nucleotide Sequencing, Original Articles, Mycobacterium tuberculosis, Pyrazinamide, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Mycobacterium tuberculosis complex, Pharmaceutical Preparations, Pulmonary Infections and Tuberculosis, Mutation, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Ethionamide, tailored tuberculosis treatment, Human medicine, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, business, Life Sciences & Biomedicine, Rifampicin, medicine.drug
Abstract

Conventional molecular tests for detecting Mycobacterium tuberculosis complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole-genome sequencing (WGS) typically requires culture. Here, we evaluated the Deeplex Myc-TB targeted deep-sequencing assay for prediction of resistance to 13 anti-tuberculous drugs/drug classes, directly applicable on sputum. With MTBC DNA tests, the limit of detection was 100–1000 genome copies for fixed resistance mutations. Deeplex Myc-TB captured in silico 97.1–99.3% of resistance phenotypes correctly predicted by WGS from 3651 MTBC genomes. On 429 isolates, the assay predicted 92.2% of 2369 first- and second-line phenotypes, with a sensitivity of 95.3% and a specificity of 97.4%. 56 out of 69 (81.2%) residual discrepancies with phenotypic results involved pyrazinamide, ethambutol and ethionamide, and low-level rifampicin or isoniazid resistance mutations, all notoriously prone to phenotypic testing variability. Only two out of 91 (2.2%) resistance phenotypes undetected by Deeplex Myc-TB had known resistance-associated mutations by WGS analysis outside Deeplex Myc-TB targets. Phenotype predictions from Deeplex Myc-TB analysis directly on 109 sputa from a Djibouti survey matched those of MTBSeq/PhyResSE/Mykrobe, fed with WGS data from subsequent cultures, with a sensitivity of 93.5/98.5/93.1% and a specificity of 98.5/97.2/95.3%, respectively. Most residual discordances involved gene deletions/indels and 3–12% heteroresistant calls undetected by WGS analysis or natural pyrazinamide resistance of globally rare “Mycobacterium canettii” strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 out of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free. Deeplex Myc-TB may enable fast, tailored tuberculosis treatment., The novel Deeplex Myc-TB molecular assay shows a high degree of accuracy for extensive prediction of susceptibility and resistance to 13 anti-tuberculous drugs, directly achievable without culture, which may enable fast, tailored tuberculosis treatment https://bit.ly/3bAvcAt

Published
2020
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6. Z oonotic tuberculosis in humans assessed by next-generation sequencing: an 18-month nationwide study in Lebanon

Author

Claire Pinçon, Cyril Gaudin, Marwan Osman, Philip Supply, Christine Demanche, Mohamad Bachar Ismail, Monzer Hamze, Rayane Rafei, Salam El Achkar, Stéphanie Duthoy, Frédérique De Matos, Hiam Yaacoub, Biodiversité et fonctionnement du sol (BIOSOL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), 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), Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), Laboratoire Microbiologie Santé et Environnement - LMSE [Tripoli, Lebanon] (Faculté de Santé Publique), Université Libanaise-Ecole Doctorale des Sciences et de Technologie [Tripoli, Lebanon], Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Genoscreen, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre AZM pour la Recherche en Biotechnologie et ses Applications, Université Libanaise, 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), Centre d’Infection et d’Immunité de Lille (CIIL) - U1019 - UMR 8204 (CIIL), 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 National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie / Nantes - Angers (CRCNA), Centre hospitalier universitaire de Nantes (CHU Nantes)-Faculté de Médecine d'Angers-Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Centre National de la Recherche Scientifique (CNRS)-Hôpital Laennec-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôtel-Dieu de Nantes, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), and Santé publique : épidémiologie et qualité des soins-EA 2694 (CERIM)

Subjects
Pulmonary and Respiratory Medicine, 0303 health sciences, International call, Tuberculosis, 030306 microbiology, business.industry, 030231 tropical medicine, MEDLINE, medicine.disease, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Environmental health, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Income country, Medicine, business, Bit (key), ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The World Health Organization (WHO) and other international organisations, including the Food and Agriculture Organization of the United Nations, the World Organisation for Animal Health and the International Union Against Tuberculosis and Lung Disease recently called for formally assessing and (re)prioritising the burden of zoonotic tuberculosis (TB) in people, due to Mycobacterium bovis [1, 2]. Its global contribution to human TB, otherwise principally caused by Mycobacterium tuberculosis, might be underestimated [2]. Nationally representative prevalence data are virtually non-existent on continents with the highest presumed burdens, i.e. in Africa and Asia [3]. In addition to causing hard-to-diagnose extrapulmonary TB more frequently, M. bovis is naturally resistant to pyrazinamide [4], a crucial drug for the standard short-course anti-TB therapy. Due to reliability issues, phenotypic susceptibility to pyrazinamide is often not tested [5]. The most commonly used phenotypic and molecular diagnostics, including the WHO-endorsed GeneXpert MTB/RIF test (Cepheid, Sunnyvale, CA, USA), do not differentiate M. bovis from M. tuberculosis [1]. Thus, M. bovis-infected patients may receive inadequate treatment, risking poorer outcomes [6]. Underdiagnosis in people also implies the existence of undetected animal and food sources and zoonotic risks escaping common TB control measures [1, 2]. In Europe, patients with M. bovis infection are often African-or southern Mediterranean-born, suggesting regional endemicity [6, 7]. We determined the prevalence of M. bovis-caused TB in a survey including all TB patients reported to the national TB programme over an 18-month period in Lebanon. In addition to its national population and >1.5 million Syrian and Palestinian refugees, this Mediterranean country hosts large numbers of migrant workers from Africa and Asia [8]. Many are from Ethiopia [8], where proportions of extrapulmonary TB and M. bovis-caused disease among TB patients apparently culminate, reaching ∼30% [9] and 15-30% (in focal studies; [10]), respectively. We used a novel targeted next-generation sequencing-based assay for extensive drug resistance detection, including resistance to pyrazinamide, and genotypic differentiation between M. bovis and M. tuberculosis [11]. This survey was approved by the Azm Center/Lebanese University ethical committee (document CE-EDST-3-2016). Clinical samples were collected from all 1104 different TB patients with presumption of pulmonary or extrapulmonary TB, based on the presence of symptoms and prior tuberculin skin testing or radiological examination in local hospitals for a number of patients, and reported to all national anti-TB centres between June 1, 2016 and November 31, 2017. All of these 1104 patients were tested by at least one of the following assays: solid (Lowenstein-Jensen) and/or liquid (BBL MGIT; Beckton Dickinson, Franklin Lakes, NJ, USA) culturing, GeneXpert MTB/RIF on sputum, and Anyplex MTB/NTM Real-time (Seegene, Seoul, Republic of Korea) on sputum or culture on solid or liquid medium. Out of these 1104, 417 were confirmed as TB positive by GeneXpert and/or Anyplex. Among these 417 patients, 354 were culture positive. Among the 354 corresponding patients, 325 were new TB patients, 22 had a previous TB history, while TB history information was unavailable for seven patients. Available DNA extracts, obtained from 348 out of 354 primary cultures by using MasterPure™ DNA Purification Kit (Epicentre, Illumina, Madison, WI, USA), were subjected to targeted sequencing, more @ERSpublications In response to recent international calls, this study reveals the nationally representative prevalence of zoonotic tuberculosis in people in a non-high income country, highlighting the need for appropriate diagnostics and treatment of these patients http://bit.ly/2l3ydDh

Published
2019
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7. Drug-Resistant Tuberculosis, Lebanon, 2016 - 2017

Author

Claire Pinçon, Monzer Hamze, Marwan Osman, Alberto Trovato, Philip Supply, Cyril Gaudin, Christine Demanche, Mohamad Bachar Ismail, Rayane Rafei, Salam El Achkar, Daniela Maria Cirillo, Hiam Yaacoub, Frédérique De Matos, Stéphanie Duthoy, CHU Lille, CNRS, Inserm, Institut Pasteur de Lille, Université de Lille, Centre d'Infection et d'Immunité de Lille (CIIL) - U1019 - UMR 9017, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], METRICS : Evaluation des technologies de santé et des pratiques médicales - ULR 2694, University of Tripoli - University Al Fateh, Evaluation des technologies de santé et des pratiques médicales - ULR 2694 [METRICS], Genoscreen [Lille], IRCCS Istituto Nazionale dei Tumori [Milano], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), 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), Université Libanaise, IRCCS San Raffaele Scientific Institute [Milan, Italie], 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), and Supply, Philip

Subjects
Male, Epidemiology, Antitubercular Agents, lcsh:Medicine, Drug resistance, Minisatellite Repeats, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Bacterial, Tuberculosis, Multidrug-Resistant, MDR, 030212 general & internal medicine, DNA sequencing, Lebanon, bacteria, Drug-Resistant Tuberculosis, Lebanon, 2016–2017, health care economics and organizations, Dispatch, food and beverages, TB, Tuberculosis, XDR, antimicrobial resistance, asylum seekers, drug resistance, migrant workers, refugees, survey, tuberculosis and other mycobacteria, whole-genome sequencing, Middle Aged, 3. Good health, Infectious Diseases, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, population characteristics, Female, Microbiology (medical), Adult, Genotype, Refugee, 030231 tropical medicine, education, Microbial Sensitivity Tests, History, 21st Century, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Young Adult, Antibiotic resistance, Environmental health, medicine, Humans, lcsh:RC109-216, business.industry, Drug resistant tuberculosis, Migrant workers, lcsh:R, fungi, Mycobacterium tuberculosis, medicine.disease, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Genes, Bacterial, Mutation, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Treatment decision making, business
Abstract

International audience; In a 12-month nationwide study on the prevalence of drug-resistant tuberculosis (TB) in Lebanon, we identified 3 multidrug-resistant cases and 3 extensively drug-resistant TB cases in refugees, migrants, and 1 Lebanon resident. Enhanced diagnostics, particularly in major destinations for refugees, asylum seekers, and migrant workers, can inform treatment decisions and may help prevent the spread of drug-resistant TB.

Published
2019
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8. High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries

Author

André Gilles, Christophe Délye, Emese Meglécz, Valérie Le Corre, Stéphanie Ferreira, Pierre-Jean G. Malé, Hélène Blanquart, Thibaut Malausa, Brigitte Lung-Escarmant, Vincent Dubut, Caroline Costedoat, Thomas Guillemaud, Jean-François Martin, Philippe Castagnone-Sereno, Philippe Gauthier, Nicolas Feau, Stéphanie Duthoy, Nicolas Pech, Pascal Frey, Laurent Hazard, Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), Aix Marseille Université (AMU), Genoscreen, Biodiversité, Gènes et Communautés, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-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), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), FLAveur, VIsion et Comportement du consommateur (FLAVIC), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Institut National de la Recherche Agronomique ( INRA ), Aix Marseille Université ( AMU ), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Centre de Biologie pour la Gestion des Populations ( CBGP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut Sophia Agrobiotech [Sophia Antipolis] ( ISA ), Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Institut National de la Recherche Agronomique ( INRA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
0106 biological sciences, enriched library, taxonomie, [SDV]Life Sciences [q-bio], marqueur génétique, Computational biology, Biology, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, 03 medical and health sciences, taxonomy, pcr, Genetics, Animals, Multiplex, Genomic library, Taxonomic rank, Microsatellite enrichment, Ecology, Evolution, Behavior and Systematics, Gene Library, 030304 developmental biology, 0303 health sciences, [ SDV ] Life Sciences [q-bio], microsatellite isolation, High-Throughput Nucleotide Sequencing, DNA, Bees, pyroséquençage, banque d'adn, Molecular Typing, pyrosequencing, genotyping, marqueur microsatellite, Genetic marker, primer design, génotypage, Pyrosequencing, Microsatellite, next-generation sequencing, genetic marker, microsatellite repeats, Biotechnology
Abstract

Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11 497 to 34 483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms.

Published
2011
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9. The complete mitochondrial genome sequence of the pathogenic yeast Candida ( Torulopsis ) glabrata

Author

Christiane Bouchier, Romain Koszul, Patrick Wincker, Bernard Dujon, Lionel Frangeul, Stéphanie Duthoy, Agnès Thierry, Alain Malpertuy, Christophe Hennequin, Stéphane Ferris, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Institut Pasteur [Paris], Génomique (Plate-Forme) - Genomics Platform, 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), Laboratoire de parasitologie et de mycologie médicales [CHU Amiens], CHU Amiens-Picardie, This work is supported by CNRS GDR 2354., Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Subjects
MESH: Sequence Analysis, DNA, Transcription, Genetic, MESH: Introns, [SDV]Life Sciences [q-bio], Candida glabrata, MESH: Base Sequence, Biochemistry, Genome, MESH: Membrane Transport Proteins, MESH: Gene Order, MESH: Mitochondrial Proton-Translocating ATPases, MESH: Saccharomyces cerevisiae Proteins, RNA, Transfer, Structural Biology, Gene Order, MESH: Candida glabrata, 2. Zero hunger, Genetics, Adenosine Triphosphatases, 0303 health sciences, MESH: DNA, Ribosomal, MESH: Codon, MESH: Mitochondrial Proteins, Cytochromes b, Mitochondrial Proton-Translocating ATPases, MESH: Cytochromes b, MESH: Ribosomal Proteins, Mitochondrial DNA, Mitochondria, Genetic Code, MESH: Genome, Fungal, MESH: Fungal Proteins, MESH: Membrane Proteins, Genome, Fungal, Ribosomal Proteins, Saccharomyces cerevisiae Proteins, RNase P, MESH: Mitochondria, Molecular Sequence Data, Biophysics, DNA sequence, Biology, DNA, Ribosomal, Ribonuclease P, Electron Transport Complex IV, Fungal Proteins, Mitochondrial Proteins, 03 medical and health sciences, Complete sequence, MESH: Electron Transport Complex IV, Ribosomal protein, MESH: Adenosine Triphosphatases, Group I catalytic intron, Codon, Molecular Biology, Gene, 030304 developmental biology, MESH: Molecular Sequence Data, Base Sequence, 030306 microbiology, MESH: Transcription, Genetic, RNA, Membrane Proteins, Membrane Transport Proteins, MESH: Ribonuclease P, Cell Biology, Sequence Analysis, DNA, Ribosomal RNA, MESH: RNA, Transfer, Molecular biology, MESH: Genetic Code, Introns
Abstract

We report here the complete sequence of the mito- chondrial (mt) genome of the pathogenic yeast Candida glabra- ta. This 20 kb mt genome is the smallest among sequenced hemiascomycetous yeasts. Despite its compaction,the mt ge- nome contains the genes encoding the apocytochrome b (COB),three subunits of ATP synthetase ( ATP6, 8 and 9), three subunits of cytochrome oxidase (COX1, 2 and 3),the ribosomal protein VAR1,23 tRNAs,small and large ribosomal RNAs and the RNA subunit of RNase P. Three group I introns each with an intronic open reading frame are present in the COX1 gene. This sequence is available under accession number AJ511533. , 2002 Federation of European Biochemical Societies. Pub- lished by Elsevier Science B.V. All rights reserved.

Published
2003
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