Integrating genomic, transcriptomic, and phenotypic information to explore drug resistance in Mycobacterium tuberculosis sub-lineage 4.2.2.2.

Abstract

Aims: Mycobacterium tuberculosis (Mtb) remains a major global health challenge, particularly due to increasing drug resistance. Beyond the well-characterized mutations, the mechanisms involved in driving resistance appear to be more complex. This study investigated the differential gene expression of Ethiopian drug-resistant Mtb sub-lineage 4.2.2.2 clinical isolates through an integrated approach combining phenotypic, transcriptomic, and genomic analyses.

Method and results: RNA sequencing was performed by isolating RNA from six Mtb strains (three drug-sensitive and three drug-resistant) during mid-logarithmic phase growth. Drug resistance was assessed through whole-genome analysis and phenotypic testing using the BACTEC Mycobacteria growth indicator tube (MGIT)™ 960 system. RNA profiling revealed significantly reduced expression of six genes: Rv0096, Rv2780, Rv3136, Rv3136A, Rv3137, and Rv3230c in drug-resistant isolates. These genes are not associated with known drug targets nor resistance mechanisms. Additionally, a discrepancy was noted between phenotypic resistance profiles and whole genome-based predictions, with the latter suggesting broader resistance. For instance, the missense mutation in rpoB p.Ser450Leu and katG p.Ser315Thr were identified with no change in phenotypic drug sensitivity to rifampicin and isoniazid, respectively.

Conclusion: Identification of these differentially expressed genes and their networks could be useful in unraveling the complexities of Mtb drug resistance and in understanding the impact that drug resistance conferring mutations have on the physiology of drug-resistant Mtb.