Drug resistance characterization and whole genome sequencing of extensively drug-resistant (XDR) and pre-XDR M.tuberculosis from TB patients in Kazakhstan

Kazakhstan is among the countries with a high incidence rate of drug-resistant TB, especially MDR TB. This study collected 161 drug-resistant <italic>M.tuberculosis</italic> and selected 7 XDR and 42 pre-XDR isolates for whole genome sequencing (WGS). Drug susceptibility testing of <italic>M.tuberculosis</italic> for the 1 and 2 lines anti-TB drugs was done by the BACTEC-MGIT 960 system. Spoligotyping was performed using the MeltPro® McSpoligotyping Test Kit, Zeesan. WGS was performed on the HiSeq (Illumina, USA) platform. Among seven XDR isolates, six were resistant to isoniazid (H) and rifampin (R), any of fluoroquinolones (levofloxacin- Lfx, moxifloxacin- Mfx) and to linezolid (Lzd). Only one case identified the same resistance with additional resistance to bedaquiline (Bdq). All seven XDR <italic>M.tuberculosis</italic> related to W-Beijing genotype (East Asian lineage). Among 42 pre-XDR <italic>M.tuberculosis</italic> clinical isolates, 23 (54.8%) were multidrug-resistant (MDR) plus resistant to Lfx+Mfx, 18 (42.8%) – MDR plus resistant to Mfx and one (2.4%) – MDR plus resistant to Lfx. Two cases showed resistance to Lfx+Mfx+Cfx+Dlm (delamanid). Genotyping pre-XDR clinical isolates identified 39 (98.5%) W-Beijing genotypes. Genomic drug resistance analysis with TB Profiler, CASTB, etc. databases is in progress. Drug resistance in pre-XDR-TB and XDR-TB is a significant challenge for TB treatment in Kazakhstan. Further studies are needed to study mutations in genes associated with drug resistance and to understand the impact of using WGS on drug resistance TB diagnostics. This study was funded by a grant from Nazarbayev University under Collaborative Research Program №11022021CRP1511, U.K.