Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB

Abstract

Drug resistance (DR) remains a major challenge for tuberculosis (TB) control. Whole-genome sequencing (WGS) provides the highest genetic resolution for genotypic drug-susceptibility tests (DST). We compared DST profiles of 60 Mycobacterium tuberculosis isolates which were drug resistant according to agar proportion tests (one poly DR-TB, 34 multidrug-resistant TB and 25 extensively drug-resistant TB). We additionally performed minimum inhibitory concentration (MIC) tests using Sensititre MYCOTBI plates (MYCOTB) and a WGS-based DST. Agreement between WGS-based DST and MYCOTB was high for all drugs except ethambutol (65%) and ethionamide (62%). Isolates harboring the -15 c/t inhA promoter mutation had a significantly lower MIC for isoniazid than did isolates with the katG Ser315Thr mutation (p < 0.001). Similar patterns were seen for ethambutol (embB Gly406Asp vs. embB Met306Ile), streptomycin (gid Gly73Ala vs. rpsL Lys43Arg), moxifloxacin (gyrA Ala90Val vs. gyrA Asp94Gly) and rifabutin (rpoB Asp435Phe/Tyr/Val vs. rpoB Ser450Leu). For genotypic heteroresistance, isolates with lower proportion of mapped read tended to has lower MIC of anti-TB drugs than those with higher proportion. These results emphasize the high applicability of WGS for determination of DR-TB and the association of particular mutations with MIC levels.

Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy

“…Genomics is undeniably the most accurate tool with the highest resolution power for the study and analysis of MTB at both diagnostic and epidemiological levels ( 16 – 19 ). MTB is a slow-growing microorganism, and it takes 2 to 3 weeks to achieve results from cultures; thus, it is key to perform WGS directly from the clinical sample.…”

Detection of Pyrazinamide Heteroresistance in Mycobacterium tuberculosis

“…The detection of subpopulations at frequencies at 1% might be complicated and too expensive for routine use at present ( 32 ). Moreover, the data provided by WGS might be bioinformatically complex ( 6 , 33 ). PZA resistance also occurs by other mechanisms than single nucleotide polymorphism, such as insertions and deletions, which may be more difficult to detect by current WGS pipelines.…”

Towards equitable access to public health pathogen genomics in the Western Pacific

“…The utility of genomics for other infectious disease has been well documented, [14] , [15] , [16] , [17] and the opportunity to harness progress made toward equitable access to genomics due to COVID-19 will directly impact other public health disease control programs such as the global threat of antimicrobial resistance.…”