title: Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France.
abstract: 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.
  
  
  
  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).
  
  
  
  The most predominant spoligotyping clusters were SIT53/T1 (n = 346, 15.3%) > SIT50/H3 (n = 166, 7.35%) > SIT42/LAM9 (n = 125, 5.5%) > SIT1/Beijing (n = 72, 3.2%) > 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<0.001). Extra-pulmonary TB was more common among female patients while pulmonary TB predominated among men (p-value<0.001; 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<0.001). 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]).
  
  
  
  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.
authors.affiliation: Laboratoire de bactériologie, Centre hospitalier Lyon-Sud, Pierre-Bénite, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Pichat
authors.affiliation: WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, France.
authors.forename: David
authors.initials: D
authors.lastname: Couvin
authors.affiliation: Laboratoire de bactériologie, Centre hospitalier Lyon-Sud, Pierre-Bénite, France.|Laboratoire de Biométrie et Biologie Évolutive, CNRS-UMR 5558, Université Lyon 1, Villeurbanne, France.
authors.forename: Gérard
authors.initials: G
authors.lastname: Carret
authors.affiliation: Laboratoire de bactériologie, Centre hospitalier Lyon-Sud, Pierre-Bénite, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Frédénucci
authors.affiliation: Service des mycobactéries, Laboratoire Biomnis, Lyon, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Jacomo
authors.affiliation: Laboratoire de bactériologie, CHU de Saint-Étienne Nord, Saint-Étienne, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Carricajo
authors.affiliation: Laboratoire de bactériologie, CHU de Grenoble, Grenoble, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Boisset
authors.affiliation: Laboratoire de bactériologie, Centre hospitalier Lyon-Sud, Pierre-Bénite, France.|Centre Internationl de Recherche en Infectiologie, INSERM U1111, Université Lyon 1, Lyon, France.
authors.forename: Oana
authors.initials: O
authors.lastname: Dumitrescu
authors.affiliation: Laboratoire de bactériologie, Centre hospitalier Lyon-Sud, Pierre-Bénite, France.|Laboratoire de Biométrie et Biologie Évolutive, CNRS-UMR 5558, Université Lyon 1, Villeurbanne, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Flandrois
authors.affiliation: Laboratoire de bactériologie, Centre hospitalier Lyon-Sud, Pierre-Bénite, France.|Centre Internationl de Recherche en Infectiologie, INSERM U1111, Université Lyon 1, Lyon, France.
authors.forename: Gérard
authors.initials: G
authors.lastname: Lina
authors.affiliation: WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, France.
authors.forename: Nalin
authors.initials: N
authors.lastname: Rastogi
mesh_terms: D000328:Adult; D015373:Bacterial Typing Techniques; D004352:Drug Resistance, Microbial; D005260:Female; D005602:France / Q000453:epidemiology; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology*; D055815:Young Adult