Tesfaye Gebreyohannis Hailemariam: Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Science, Addis Ababa University, P.O.Box 9086, Addis Ababa, Ethiopia.
Abaysew Ayele: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia.
Tesfaye Gelanew: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia.
Abay Atnafu: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia.
Michael Brennan: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, BN1 9PX, Brighton, United Kingdom.
Melaku Tilahun: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia.
Dawit Hailu Alemayehu: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia.
Zemedkun Abebe Debella: Addis Ababa Institute of Technology, Addis Ababa Univeristy, P.O. Box 1000, Addis Ababa, Ethiopia.
Yared Merid: Hawassa University College of Medicine and Health Sciences, P.O.Box 1560, Hawassa, Ethiopia.
Workineh Shibeshi: Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Science, Addis Ababa University, P.O.Box 9086, Addis Ababa, Ethiopia.
Abraham Aseffa: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia.
Kidist Bobosha: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia. ORCID
Yonas Hirutu: Armauer Hansen Research Institute, P.O.Box 1005, Addis Ababa, Ethiopia.
Simon J Waddell: Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, BN1 9PX, Brighton, United Kingdom.
Ephrem Engidawork: Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Science, Addis Ababa University, P.O.Box 9086, Addis Ababa, Ethiopia. ORCID
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.
