A first assessment of the genetic diversity of Mycobacterium tuberculosis complex in Cambodia

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).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, CI95% [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.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.Tuberculosis (TB) as caused by Mycobacterium tuberculosis complex (MTC) is one of the most important public health problems in the world. In 2008, WHO estimated 9.4 million incident cases of TB, 11.1 million prevalent cases, 1.3 million deaths among HIV-negative people and an additional 0.52 million TB deaths among HIV-positive people [1]. The largest number of new TB cases occurs in the South-East Asian Region, that accounted for 34% of incident cases in 2006 [2].Cambodia is among the 22 high-burden TB countries, and has one of the highest rates of TB in South-East Asia [3]. The population of Cambodia is 13.4 million (Population Census of 2008). The new sputum smear positivity rate for Cambodia is estimated to be 220/100,000 inhabitants whereas the TB i