A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic

Abstract

Background: Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resistance mutations. Methods: We conducted Illumina sequencing of 211 Beijing genotype M. tuberculosis isolates to facilitate the detection of genomic features that may promote acquisition of drug resistance and restore fitness in highly resistant atypical Beijing forms. Phylogenetic and comparative genomic analysis was done to determine changes that are unique to the resistant strains that also transmit well. Minimum inhibitory concentration (MIC) determination for streptomycin and bedaquiline was done for a limited number of isolates to demonstrate a difference in MIC between isolates with and without certain variants. Results: Phylogenetic analysis confirmed that two clades of atypical Beijing strains have independently developed resistance to virtually all the potent drugs included in standard (pre-bedaquiline) drug-resistant TB treatment regimens. We show that undetected drug resistance in a progenitor strain was likely instrumental in this resistance acquisition. In this cohort, ethionamide (ethA A381P) resistance would be missed in first-line drug-susceptible isolates, and streptomycin (gidB L79S) resistance may be missed due to an MIC close to the critical concentration. Subsequent inadequate treatment historically led to amplification of resistance and facilitated spread of the strains. Bedaquiline resistance was found in a small number of isolates, despite lack of exposure to the drug. The highly resistant clades also carry inhA promoter mutations, which arose after ethA and katG mutations. In these isolates, inhA promoter mutations do not alter drug resistance, suggesting a possible alternative role. Conclusion:The presence of the ethA mutation in otherwise susceptible isolates from ethionamide-naïve patients demonstrates that known exposure is not an adequate indicator of drug susceptibility. Similarly, it is demonstrated that bedaquiline resistance can occur without exposure to the drug. Inappropriate treatment regimens, due to missed resistance, leads to amplification of resistance, and transmission. We put these results into the context of current WHO treatment regimens, underscoring the risks of treatment without knowledge of the full drug resistance profile.

Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis

“… 8 , 10 , 11 , 13 , 21 – 23 , 26 – 58 Additionally, a technical report published by WHO was identified and included ( figure 1 ). 19 QUADAS-2 assessment of the clinical studies showed that the risk of bias was unclear for 19 (68%) of 28 studies 19 , 22 , 23 , 26 , 29 , 30 , 32 , 33 , 39 , 44 , 46 – 49 , 52 , 53 , 55 , 56 , 58 due to a possible absence of masked interpretation of mutations; risk of bias was high for 11 studies 23 , 27 , 28 , 32 , 35 , 40 , 43 , 44 , 47 , 48 , 53 that used a phenotypic DST method not approved by WHO ( appendix 1 pp 3–7). According to the QUADAS-2 assessment, the level of concern regarding applicability was classified as high for six (21%) of the 28 clinical studies 23 , 35 , 45 , 48 , 49 , 51 because they did not report on both atpE and Rv0678 genes.…”

Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2

“…(4) Liu et al [27] provided 44 SNPs specific to Modern Beijing strains. (5) South African strain of Asia Ancestral 1 (AA1SA) [35]. (6) Mestre et al [19] Bmyc scheme is based on the presence/absence pattern of SNPs in genes involved in replication, recombination and repair.…”

Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis

“…Reports describing the presence of bedaquiline and clofazimine resistance in southern Africa (defined as the countries of the Southern African Development Community) have been scarce. 12 , 13 In this study, we present genotypic and phenotypic data for M tuberculosis isolates with RAVs identified from our clinical report 11 and other unpublished (to date) cohort studies at the Africa Health Research Institute, and report a more extensive microbiological investigation of bedaquiline and clofazimine MICs to investigate the extent of cross-resistance. To better understand the phylogenetic and geographical distribution of bedaquiline and clofazimine RAVs in southern Africa, we then analysed a comprehensive collection of our own and publicly available whole-genome sequencing data.…”