Identification of genetic determinants of bedaquiline resistance in Mycobacterium tuberculosis in Ural region, Russia.

Collecting data on rare Mycobacterium tuberculosis (Mtb) clinical isolates with resistance to the new anti-tuberculosis drug bedaquiline is an important task for improving antimicrobial susceptibility testing methods. Nanopore whole genome sequencing, the proportion method on Middlebrook 7H11 medium, and BACTEC MGIT 960 assays were used to analyze genotypic and phenotypic resistance to bedaquiline. We found four mutations: atpE I66M, atpE А63Р, Rv0678 А36Т, and Rv0678 S53P in five isolates with different levels of phenotypic bedaquiline resistance. IMPORTANCE: Bedaquiline (BDQ) is a new anti-tuberculosis drug. The phenotypic and genotypic data describing the mechanism of drug resistance are critical for the design of rapid and accurate diagnostic tests. We consider that our work, which describes genotypic and phenotypic resistance to BDQ, can contribute to the standardization of drug susceptibility testing.

Molecular characteristics of Mycobacterium tuberculosis in the "closed" Russian town with limited population migration.

The aim of this study was to perform a molecular characterization of Mycobacterium tuberculosis strains circulating in one of the "closed" Russian cities under conditions of the limited population migration and high HIV coinfection rate. We analyzed 109 M. tuberculosis isolates recovered from TB patients in the Novouralsk municipality in the Ural area of Russia; 38.5% were from HIV coinfected TB patients and 19.3% patients were former prison inmates. The Beijing genotype was predominant (78.9%) while 57.8% and 17.4% of isolates belonged to the Beijing B0/W148 and Beijing 94-32-clusters, respectively. An atypical allele of the QUB26 VNTR locus (2 repeat units) was detected in 11 of 63 Beijing B0/W148 isolates. The non-Beijing isolates were subdivided into nine spoligotypes of the four genetic families (Ural, LAM, Haarlem, T), SIT35/Ural being the largest group (n = 9; 8.3%). Multidrug resistance (MDR) was detected in 63.6% and 83.7% of isolates from newly diagnosed and previously treated patients, respectively. Almost all isolates of the B0/W148-cluster were MDR (92.1%) compared to the Beijing 94-32-cluster (47.4%). No association was found between HIV status of patients and MDR-TB or particular genetic cluster. A combined contact and molecular investigation confirmed three family foci; in two of them, Ural SIT35 and Beijing B0/W148 strains were transmitted from HIV-infected sons to their fathers. To conclude, M. tuberculosis population in Novouralsk features an exceptionally high prevalence of the strongly MDR Beijing B0/W148-cluster and emergence of the B0/W148 substrain with unusual QUB26 allele. This situation was likely synergistically shaped by the limited population migration, high prevalence of the HIV coinfection and high proportion of the former prisoners. The existing organizational approaches to prevent TB transmission are insufficient and require a serious revision.