Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France

Autor: Jean-Pierre Flandrois, Isabelle Fredenucci, Sandrine Boisset, Nalin Rastogi, Véronique Jacomo, Oana Dumitrescu, Catherine Pichat, David Couvin, Gérard Carret, Anne Carricajo, Gerard Lina
Přispěvatelé: Laboratoire de Bactériologie et des Mycobactéries, Hospices Civils de Lyon (HCL)-Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Unité de la Tuberculose et des Mycobactéries - WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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), Eurofins Biomnis, CHU de Saint-Étienne Hôpital Nord (Saint Etienne), Laboratoire de Bactériologie, Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), 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), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-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 Claude Bernard Lyon 1 (UCBL), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), 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)
Jazyk: angličtina
Rok vydání: 2016
Předmět:
0301 basic medicine
Bacterial Diseases
Male
Pathology
Drug Resistance
lcsh:Medicine
Geographical Locations
Microbial
Medicine and Health Sciences
Ethnicities
French People
lcsh:Science
Phylogeny
Data Management
Molecular Epidemiology
Multidisciplinary
biology
Phylogenetic tree
Geography
Phylogenetic Analysis
Drug Resistance
Microbial
Middle Aged
3. Good health
Bacterial Typing Techniques
Europe
Actinobacteria
Phylogenetics
Phylogeography
Infectious Diseases
Mycobacterium tuberculosis complex
Biogeography
[SDV.IMM]Life Sciences [q-bio]/Immunology
Female
France
Research Article
Adult
medicine.medical_specialty
Computer and Information Sciences
Genotyping
Genotype
Research and Analysis Methods
Mycobacterium tuberculosis
03 medical and health sciences
Young Adult
Genetic variation
medicine
Genetics
Humans
Tuberculosis
Evolutionary Systematics
Molecular Biology Techniques
Molecular Biology
Taxonomy
Genetic diversity
Evolutionary Biology
Molecular Biology Assays and Analysis Techniques
Molecular epidemiology
Population Biology
Bacteria
Ecology and Environmental Sciences
lcsh:R
Organisms
Biology and Life Sciences
Genetic Variation
biology.organism_classification
Tropical Diseases
[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
030104 developmental biology
Genetic epidemiology
Evolutionary biology
People and Places
Earth Sciences
Population Groupings
lcsh:Q
Population Genetics
Zdroj: PLoS ONE
PLoS ONE, Public Library of Science, 2016, 11 (4), pp.e0153580. ⟨10.1371/journal.pone.0153580⟩
PLoS ONE, 2016, 11 (4), pp.e0153580. ⟨10.1371/journal.pone.0153580⟩
PLoS ONE, Vol 11, Iss 4, p e0153580 (2016)
ISSN: 1932-6203
Popis: International audience; BACKGROUND: The present work relates to identification and a deep molecular characterization of circulating Mycobacterium tuberculosis complex (MTBC) strains in the Rhône-Alpes region, France from 2000 to 2010. It aimed to provide with a first snapshot of MTBC genetic diversity in conjunction with bacterial drug resistance, type of disease and available demographic and epidemiologic characteristics over an eleven-year period, in the south-east of France. METHODS: Mycobacterium tuberculosis complex (MTBC) strains isolated in the Rhône-Alpes region, France (n = 2257, 1 isolate per patient) between 2000 and 2010 were analyzed by spoligotyping. MIRU-VNTR typing was applied on n = 1698 strains (with full results available for 974 strains). The data obtained were compared with the SITVIT2 database, followed by detailed genotyping, phylogenetic, and epidemiologic analyses in correlation with anonymized data on available demographic, and epidemiologic characteristics, and location of disease (pulmonary or extrapulmonary TB). RESULTS: The most predominant spoligotyping clusters were SIT53/T1 (n = 346, 15.3%) \textgreater SIT50/H3 (n = 166, 7.35%) \textgreater SIT42/LAM9 (n = 125, 5.5%) \textgreater SIT1/Beijing (n = 72, 3.2%) \textgreater SIT47/H1 (n = 71, 3.1%). Evolutionary-recent strains belonging to the Principal Genetic Group (PGG) 2/3, or Euro-American lineages (T, LAM, Haarlem, X, S) were predominant and represented 1768 or 78.33% of all isolates. For strains having drug resistance information (n = 1119), any drug resistance accounted for 14.83% cases vs. 1.52% for multidrug resistance (MDR); and was significantly more associated with age group 21-40 years (p-value\textless0.001). Extra-pulmonary TB was more common among female patients while pulmonary TB predominated among men (p-value\textless0.001; OR = 2.16 95%CI [1.69; 2.77]). Also, BOV and CAS lineages were significantly well represented in patients affected by extra-pulmonary TB (p-value\textless0.001). The origin was known for 927/2257 patients: 376 (40.6%) being French-born vs. 551 (59.4%) Foreign-born. French patients were significantly older (mean age: 58.42 yrs 95%CI [56.04; 60.80]) than Foreign-born patients (mean age: 42.38 yrs. 95%CI [40.75; 44.0]). CONCLUSION: The study underlined the importance of imported TB cases on the genetic diversity and epidemiologic characteristics of circulating MTBC strains in Rhône-Alpes region, France over a large time-period. It helps better understand intricate relationships between certain lineages and geographic origin of the patients, and pinpoints genotypic and phylogenetic specificities of prevailing MTBC strains. Lastly, it also demonstrated a slow decline in isolation of M. africanum lineage in this region between 2000 and 2010.
Databáze: OpenAIRE
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