Whole-genome sequencing-based analyses of drug-resistant Mycobacterium tuberculosis from Taiwan

Abstract

Drug-resistant tuberculosis (DR-TB) posed challenges to global TB control. Whole-genome sequencing (WGS) is recommended for predicting drug resistance to guide DR-TB treatment and management. Nevertheless, data are lacking in Taiwan. Phenotypic drug susceptibility testing (DST) of 12 anti-TB drugs was performed for 200 Mycobacterium tuberculosis isolates. WGS was performed using the Illumina platform. Drug resistance profiles and lineages were predicted in silico using the Total Genotyping Solution for TB (TGS-TB). Using the phenotypic DST results as a reference, WGS-based prediction demonstrated high concordance rates of isoniazid (95.0%), rifampicin (RIF) (98.0%), pyrazinamide (98.5%) and fluoroquinolones (FQs) (99.5%) and 96.0% to 99.5% for second-line injectable drugs (SLIDs); whereas, lower concordance rates of ethambutol (87.5%), streptomycin (88.0%) and ethionamide (84.0%). Furthermore, minimum inhibitory concentrations confirmed that RIF rpoB S450L, FQs gyrA D94G and SLIDs rrs a1401g conferred high resistance levels. Besides, we identified lineage-associated mutations in lineage 1 (rpoB H445Y and fabG1 c-15t) and predominant lineage 2 (rpoB S450L and rpsL K43R). The WGS-based prediction of drug resistance is highly concordant with phenotypic DST results and can provide comprehensive genetic information to guide DR-TB precision therapies in Taiwan.

Mutations in the promoter region of methionine transporter gene metM (Rv3253c) confer para -aminosalicylic acid (PAS) resistance in Mycobacterium tuberculosis

“…Clinical trials have been conducted to identify the most appropriate PAS-containing regimens for patients with MDR-TB or XDR-TB ( 15 , 16 ). In the current clinical research, WGS is increasingly employed in lieu of traditional susceptibility methods to diagnose second-line drug resistance in TB ( 17 – 19 ). However, PAS resistance based solely on WGS is challenging, as some PAS resistance mechanisms remain unidentified.…”

Lineage classification and antitubercular drug resistance surveillance of Mycobacterium tuberculosis by whole-genome sequencing in Southern India

“…An isolate with rpoB_p.His445Leu mutation, which was tested as susceptible at rifampicin critical concentration of 1.00 µg/mL showed resistance at a lower rifampicin concentration of 0.5 µg/mL and prolonged incubation ( 10 ). Isolate with the rpoB_Leu430Pro mutation were reported to exhibit MICs ≤ 1 µg/mL ( 54 ). An isolate with rpoB_p.Ser441Leu mutation was also reported to have a MIC of 0.25 µg/mL ( 55 ).…”

“…katG_p.Ser315Thr was the most frequently identified mutation among the isoniazid-resistant isolates in our study, and high phenotypic concordance was observed in isolates having katG_p.Ser315Thr mutation alone or coexisting with other isoniazid DR variants. The majority of the isolates with only katG_p.Ser315Thr mutation showed MICs ≥ 0.5 µg/mL and a small proportion of isolates exhibited MIC <0.1 µg/mL ( 54 ). Other previously reported low-frequency missense mutations such as katG_p.Ser315Asn and katG_p.Asp419His were also observed at a low frequency in our study with a phenotypic concordance of 66.7% and 100%, respectively ( 59 ).…”

Pangenome-wide association study reveals selective absence of CRISPR genes (Rv2816c-19c) in drug-resistantMycobacterium tuberculosis

“…From existing reports with corresponding NCBI-BioProjects PRJNA879962, PRJEB41116, PRJEB32684, PRJNA379070, and PRJEB29435, Mtb WGS data (n=2601) from India, China, Pakistan, and Zambia were downloaded from the SRA-NCBI database using fasterq-dump v2.11.3 of the SRA Toolkit (NCBI) (19–23). Megahit assembler v1.2.9.…”