Whole genome sequencing of Bulgarian rifampicin resistant Mycobacterium tuberculosis strains

Abstract

Introduction: The transmission of drug-resistant tuberculosis is one of the greatest challenges facing the global tuberculosis control. Aim: The aim of the study was to investigate the resent transmission of rifampicin resistant tuberculosis in Bulgaria and to describe the mutations related to the antimicrobials’ resistance using whole genome sequencing. Materials and methods: As part of an ECDC funded pilot study for evaluation of the systematic use of whole genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) surveillance (EUSeqMyTB), Bulgaria provided 65 rifampicin resistant isolates over a three years’ timeframe (2017-2019) representing 87.5% of the notified rifampicin resistant cases. Drug resistance prediction and relatedness analysis of the resistant isolates was performed in collaboration with San Raffaele Scientific Institute, Milan, Italy. Results: Almost all of the isolates were identified as Euro-American lineage (96.9%); 18.5% of the isolates were found to be resistant to fluoroquinolones, but no mutations conferring resistance to bedaquiline or linezolid could be identified. Less than half (43.3%) of the isolates were clustered (<5 SNPs distance) into a total of seven national SNP-based clusters, while a total of six isolates were found to be part of different cross-border clusters. All clustered cases originated from Bulgaria. Conclusions: WGS has proven to be a reliable tool for surveillance and tracing of recent transmission of tuberculosis and has the potential for resistance prediction for most of the antituberculosis drugs.

Genotypic and phenotypic comparison of drug resistance profiles of clinical multidrug-resistant Mycobacterium tuberculosis isolates using whole genome sequencing in Latvia

“…Overall match between phenotypic DST and WGS-based genotypic DST results for ofloxacin was 93.7% in this study; a full concordance was reported in other studies [ 11 , 30 ]. All ofloxacin/fluoroquinolones-resistant strains belonged to sublineages 2.2.1 and 4.3.3.…”

“…For injectables variable concordance results for phenotypic and genotypic DST were identified, being high for streptomycin (95.4%), and considerably lower for amikacin (82.5%), kanamycin (85.4%), and capreomycin (81.0%). In contrary, in other studies, a full concordance between phenotypic and genotypic DST results for amikacin was reported [ 11 , 30 ]. Here, all Mtb isolates which had the r.1401a > g RAV in rrs gene were characterized as phenotypically cross-resistant either to amikacin and capreomycin, or amikacin, kanamycin and capreomycin; this observation is in agreement with other studies [ 6 , 9 , 42 ].…”

“…For the isoniazid and rifampicin, WGS-based molecular drug resistance tests reach 91.3–97.5% sensitivity and 93.6–99.0% specificity [ 8 , 9 ]. On the other hand, according to the literature data, the genotype-phenotype correlation remains low for pyrazinamide, ethambutol, ethionamide, and fluoroquinolones [ 6 , 10 , 11 ]. Thus, simultaneous phenotypic and genotypic drug resistance analysis of Mtb isolates is of a great importance.…”