title: A first assessment of the genetic diversity of Mycobacterium tuberculosis complex in Cambodia.
abstract: BACKGROUND
  Cambodia is among the 22 high-burden TB countries, and has one of the highest rates of TB in South-East Asia. This study aimed to describe the genetic diversity among clinical Mycobacterium tuberculosis complex (MTC) isolates collected in Cambodia and to relate these findings to genetic diversity data from neighboring countries.
  
  
  METHODS
  We characterized by 24 VNTR loci genotyping and spoligotyping 105 Mycobacterium tuberculosis clinical isolates collected between 2007 and 2008 in the region of Phnom-Penh, Cambodia, enriched in multidrug-resistant (MDR) isolates (n = 33).
  
  
  RESULTS
  Classical spoligotyping confirmed that the East-African Indian (EAI) lineage is highly prevalent in this area (60%-68% respectively in whole sample and among non-MDR isolates). Beijing lineage is also largely represented (30% in whole sample, 21% among non-MDR isolates, OR = 4.51, CI 95% [1.77, 11.51]) whereas CAS lineage was absent. The 24 loci MIRU-VNTR typing scheme distinguished 90 patterns with only 13 multi-isolates clusters covering 28 isolates. The clustering of EAI strains could be achieved with only 8 VNTR combined with spoligotyping, which could serve as a performing, easy and cheap genotyping standard for this family. Extended spoligotyping suggested relatedness of some unclassified "T1 ancestors" or "Manu" isolates with modern strains and provided finer resolution.
  
  
  CONCLUSIONS
  The genetic diversity of MTC in Cambodia is driven by the EAI and the Beijing families. We validate the usefulness of the extended spoligotyping format in combination with 8 VNTR for EAI isolates in this region.
authors.affiliation: Institut de Génétique et Microbiologie, UMR8621 CNRS-Université Paris-Sud 11, UniverSud, Infection Genetics Emerging Pathogens Evolution (IGEPE) Team, Bât, 400, F-91405 Orsay-Cedex, France.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.forename: Seiha
authors.initials: S
authors.lastname: Heng
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Le Moullec
authors.forename: Guislaine
authors.initials: G
authors.lastname: Refregier
authors.forename: Brigitte
authors.initials: B
authors.lastname: Gicquel
authors.forename: Christophe
authors.initials: C
authors.lastname: Sola
authors.forename: Bertrand
authors.initials: B
authors.lastname: Guillard
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D015373:Bacterial Typing Techniques; D002160:Cambodia / Q000453:epidemiology; D002648:Child; D016000:Cluster Analysis; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D058889:Molecular Typing; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D014376:Tuberculosis / Q000453:epidemiology* / Q000382:microbiology*; D055815:Young Adult