Whole-genome analysis of drug resistance and transmission patterns in Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan
5 affiliations
- 1Department of Medical Lab Technology, University of Haripur
- 2Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM)
- 3Laboratory Hayatabad Medical Complex, Provincial Tuberculosis Reference
- 4Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology
- 5Department of Microbiology, University of Haripur
Abstract
The emergence of drug-resistant Mycobacterium tuberculosis strains presents a significant challenge to tuberculosis (TB) control programmes worldwide, particularly in high-burden countries, such as Pakistan. This study characterises the genomic diversity and drug resistance mutation profiles of M. tuberculosis isolates from Khyber Pakhtunkhwa using whole-genome sequencing (WGS). A total of 35 clinical M. tuberculosis isolates underwent WGS. Sequence data were quality-filtered and mapped to the H37Rv reference genome, characterising variants, including single-nucleotide polymorphisms (SNPs). Lineage classification, drug resistance profiling, and identification of resistance mutations were performed using TB-Profiler software. SNP-based clustering was used to infer recent transmission events. All four major M. tuberculosis lineages (L1–L4) were detected; however, more than half of the isolates belonged to lineage L3 (CAS, n = 19; 54.3%). Almost all isolates were drug-resistant (34/35), including pre-extensively drug-resistant (pre-XDR, n = 15; 42.9%) and multidrug-resistant (MDR, n = 14; 40.0%) strains. The most frequent resistance-associated mutations included katG S315T (27/35) and inhA c.-777C > T (4/35) for isoniazid resistance, rpoB S450L (24/35) for rifampicin resistance, embB M306I/V (18/35) for ethambutol resistance, and gyrA D94G (8/35) and A90V (5/35) for fluoroquinolone resistance. Compensatory mutations were observed in rpoC and ahpC. Mutations associated with bedaquiline and clofazimine resistance (mmpR5 c.140dupA, c.138_139dupTG) were detected in single isolates. Interestingly, one isolate exhibited a deletion encompassing mmpR5, mmpL5, and mmpS5, potentially increasing bedaquiline susceptibility. Phylogenetic analysis using 6,635 genome-wide SNPs identified two transmission clusters with < 9 SNPs differences, suggesting ongoing local transmission. These results highlight the presence of drug-resistant M. tuberculosis strains in Khyber Pakhtunkhwa, encompassing both globally recognised and novel resistance-associated mutations. Our findings underscore the critical need to integrate WGS into TB surveillance and control programmes in Pakistan to guide targeted interventions and curb the spread of resistant strains.
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BibTeX
@article{khan2026wholegenome,
title = {{Whole-genome analysis of drug resistance and transmission patterns in Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan}},
author = {Muhammad Fayaz Khan and Jody Phelan and Anwar Sheed Anwar and Sadiq Noor Khan and Amjad Ali and Faryal Mehwish Awan and Ayesha Obaid and Dawood Ahmad and Afshan Saleem and Susana Campino and Taane G. Clark and Abdul Jabbar},
journal = {Scientific Reports},
year = {2026},
month = jul,
doi = {10.1038/s41598-026-62482-7},
url = {https://doi.org/10.1038/s41598-026-62482-7},
note = {CC BY},
}
RIS
TY - JOUR
TI - Whole-genome analysis of drug resistance and transmission patterns in Mycobacterium tuberculosis from Khyber Pakhtunkhwa, Pakistan
AU - Muhammad Fayaz Khan
AU - Jody Phelan
AU - Anwar Sheed Anwar
AU - Sadiq Noor Khan
AU - Amjad Ali
AU - Faryal Mehwish Awan
AU - Ayesha Obaid
AU - Dawood Ahmad
AU - Afshan Saleem
AU - Susana Campino
AU - Taane G. Clark
AU - Abdul Jabbar
PY - 2026
DA - 2026/07/01
JO - Scientific Reports
DO - 10.1038/s41598-026-62482-7
UR - https://doi.org/10.1038/s41598-026-62482-7
AB - The emergence of drug-resistant Mycobacterium tuberculosis strains presents a significant challenge to tuberculosis (TB) control programmes worldwide, particularly in high-burden countries, such as Pakistan. This study characterises the genomic diversity and drug resistance mutation profiles of M. tuberculosis isolates from Khyber Pakhtunkhwa using whole-genome sequencing (WGS). A total of 35 clinical M. tuberculosis isolates underwent WGS. Sequence data were quality-filtered and mapped to the H37Rv reference genome, characterising variants, including single-nucleotide polymorphisms (SNPs). Lineage classification, drug resistance profiling, and identification of resistance mutations were performed using TB-Profiler software. SNP-based clustering was used to infer recent transmission events. All four major M. tuberculosis lineages (L1–L4) were detected; however, more than half of the isolates belonged to lineage L3 (CAS, n = 19; 54.3%). Almost all isolates were drug-resistant (34/35), including pre-extensively drug-resistant (pre-XDR, n = 15; 42.9%) and multidrug-resistant (MDR, n = 14; 40.0%) strains. The most frequent resistance-associated mutations included katG S315T (27/35) and inhA c.-777C > T (4/35) for isoniazid resistance, rpoB S450L (24/35) for rifampicin resistance, embB M306I/V (18/35) for ethambutol resistance, and gyrA D94G (8/35) and A90V (5/35) for fluoroquinolone resistance. Compensatory mutations were observed in rpoC and ahpC. Mutations associated with bedaquiline and clofazimine resistance (mmpR5 c.140dupA, c.138_139dupTG) were detected in single isolates. Interestingly, one isolate exhibited a deletion encompassing mmpR5, mmpL5, and mmpS5, potentially increasing bedaquiline susceptibility. Phylogenetic analysis using 6,635 genome-wide SNPs identified two transmission clusters with < 9 SNPs differences, suggesting ongoing local transmission. These results highlight the presence of drug-resistant M. tuberculosis strains in Khyber Pakhtunkhwa, encompassing both globally recognised and novel resistance-associated mutations. Our findings underscore the critical need to integrate WGS into TB surveillance and control programmes in Pakistan to guide targeted interventions and curb the spread of resistant strains.
SN - 2045-2322
ER -