Whole genome sequencing of drug resistance Mycobacterium tuberculosis from extra-pulmonary sites.

This study aimed to determinate characteristics of drug resistance Mycobacterium tuberculosis from patients with extra-pulmonary tuberculosis (EPTB). Patients were retrospectively studied from January 2020 to December 2021. All the isolates were cultured, tested drug susceptibility, and detected the gene mutation using whole genome sequencing. The correlations of whole genome sequencing, pattern of DR, patients' distribution, and transmission were analyzed. 111 DR-EPTB isolates included pre-XDR-TB (53.2%), MDR-TB (29.7%), and poly-DR-TB (12.6%). The resistant drugs were INH followed by RFP and SM. The genotypes of 111 strains were lineage 2 and lineage 4. KatG _p.Ser315Thr was main gene mutation for resistance to INH; rpsL _p.Lys43Arg for SM, rpoB _p.Ser450Leu for rifampicin, embB _p.Met306Val for ethambutol, gyrA _p.Asp94Gly for FQs, and pncA _p.Thr76Pro for PZA. The residence was a significant risk factor for cluster transmission by patients and phenotypic DR types of strains for lineage 2 transmission. In the local area of southwest China INH, rifampicin and SM were main drugs in patients with DR-EPTB. KatG _p.Ser315, rpoB _p.Ser450Leu, and rpsL _p.Lys43Arg were main gene mutations. Phenotypic DR types and residence were main risk of transmission.