Phenotypic drug resistance and genome sequencing based identified mutations linked to resistance in Mycobacterium tuberculosis isolated from extrapulmonary clinical specimens

Globally, drug-resistant tuberculosis (DR-TB) is responsible for 13% of mortality attributable to antimicrobial resistance. In Ethiopia, extrapulmonary tuberculosis (EPTB) is a significant public health challenge, and drug resistance (DR) in EPTB is often overlooked. In a cross-sectional study conducted between August 2022 and October 2023, we aimed to explore the magnitude of phenotypic drug resistance and identify genetic mutations linked to resistance using 189 Mycobacterium tuberculosis (MTB) isolates cultured from extrapulmonary clinical specimens. Additionally, we assessed the agreement between phenotypic and whole genome sequencing (WGS) based genotypic drug resistance detection. We performed phenotypic drug sensitivity testing (pDST) using the liquid culture BD BACTEC™ MGIT™ 960 system and WGS using Illumina NextSeq500/550. The genomic data analysis pipelines MTBSeq and TBProfiler were used to predict drug resistance-conferring mutations. The agreement between the pDST and WGS based drug resistances was analyzed using SPSS version 29.0. Our study results showed that the prevalence of any forms of phenotypic resistance to at least one anti-TB drug was 16.9% (95%: CI, 11.9% – 23.1%). Isoniazid-resistant rifampicin-susceptible-TB (Hr-TB) accounted for 2.6% (95%: CI, 0.9% − 6.1%) and multi-drug-resistant TB (MDR-TB) accounted for 4.2% (95%CI: 1.8% − 8.2%). The prevalence of MDR-TB was 2.4% (95%CI: 0.6% − 5.9%) among newly diagnosed and, 21.1% (95%CI: 6.1% − 45.6%) among previously treated cases. More rifampicin-resistances were detected using WGS (8.75%) than the pDST (4.2%). We identified a putative compensatory mutation for rifampicin resistance (rpoBSer450Leu, rpoC Asp747Ala) and a previously unreported mutations on the hotspot rifampicin resistance determining region (rpoB_p. Asn438Thr). There were 3.75% rifampicin mono-resistant-TB (RMR-TB) cases detected through WGS and represented nearly half of the total RR/MDR-TB cases. Mutations conferring rifampicin resistance-interim (rpoB.Ser450Ala) represented most of these RMR-TB. Changes in ethA genes associated with ethionamide resistance were the most common second-line resistance among MDR-TB isolates. There was a substantial to strong agreement between the pDST and WGS for the detection of resistance to first line anti TB drugs. In conclusion, MDR-TB, Hr-TB, and interim-RMR-TB are public health challenges in the realm of EPTB in Ethiopia. Given, most RMR-TB were detected as borderline RR-TB and were missed by both pDST and the rapid molecular diagnostics currently in place, integrating NGS into the national guidelines is highly relevant. This would help for comprehensive detection of mutations including rare and novel mutations missed by the conventional approaches and planning tailored therapy. Investigation of the role of the identified compensatory mutation and the new mutation we reported on the target gene of the drug rifampicin is warranted.