Introduction. According to the World Health Organization, the Kyrgyz Republic is among the 18 countries
with a high prevalence of multidrug-resistant tuberculosis. The molecular epidemiology of tuberculosis infection, including
genetic diversity, markers of molecular drug resistance, and transmission routes of Mycobacterium tuberculosis complex
strains in the Kyrgyz Republic, remain poorly understood. Whole genome sequencing (WGS) has been used to
determine the molecular genetic structure of the strains circulating in the country. Purpose of the study. The purpose of
the study was to describe the molecular genetic characteristics of strains of the Mycobacterium tuberculosis complex
based on the whole genome sequensing. Materials and methods.Whole genome sequencing was carried out at the National
Reference Laboratory of the National Center for Phthysiology under the supervision of the SNRL, Borstel, Germany.
475 MTBС isolates were tested in 2018 and 2019. Sequencing was performed according to the manufacturer's instructions
on the MySeq platform, Illumina, USA. The MTBSeq protocol was used for comparative genomic analysis and the online
tools “EvolView and PhyResSe” to perform graphical representation and screen for mutations mediating resistance to
antituberculous drugs. Stata/IC version 16.1 was used for statistical analysis.Results. Using WGS, showed that the MTBC population structure in the Kyrgyz Republic mainly consists of three phylogenetic
lineages (L). These lines are L2 (Beijing), L3 (Delhi/CAS) and L4 (Euro-American) as classified by Coll, Mc-
Nerney and Niemann, Merker. The L2 strains were predominant (74.1%, 352/475), while the L3 and L4 strains accounted
for 0.8% (4/475) and 25.1% (119/475), respectively. Next, we classified the L2 and L4 strains into several MTBC sublineages.
The Beijing Central Asia (n=225), Beijing Central Asia outbreak (n=75) and Beijing Europe/Russian W148
Outbreak (n=28) subline strains are the most common strains compared to the other L2 subline strains and the L4 subline
strains. Conclusions. Using WGS, have shown that pulmonary tuberculosis in the Kyrgyz Republic is mainly caused by
L2 (Beijing) strains. Drug resistance is also associated with L2 strains, highlighting the important role of L2 strains in
the epidemiology of tuberculosis in the country. Overall, our results provide a better understanding of the molecular epidemiology
of tuberculosis in the Kyrgyz Republic and require additional molecular epidemiological studies to elucidate
the dynamics of tuberculosis in the country and, therefore, control it.