PREVALENCE AND MOLECULAR CHARACTERIZATION OF DRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS USING GENEXPERT MTB/RIF ULTRA AND MTB/XDR ASSAYS ACROSS AZAD JAMMU AND KASHMIR, PAKISTAN (2025)

Abstract

Background: Tuberculosis (TB) remains a critical public health challenge in Pakistan, yet comprehensive molecular epidemiological data from Azad Jammu and Kashmir (AJK) are lacking. This study aimed to determine the prevalence and molecular drug resistance profiles of Mycobacterium tuberculosis across AJK using the GeneXpert MTB/RIF Ultra and MTB/XDR assays during 2025. Methods: A retrospective, cross-sectional study was conducted across 14 National TB Control Programme (NTP)-designated facilities spanning 10 districts in AJK from January to December 2025. A diagnostic cascade was utilized: MTB/RIF Ultra was performed on 24,988 presumptive pulmonary TB patients, followed by MTB/XDR testing on a subset of 50 cases (18 rifampicin-resistant [RR] and 32 rifampicin-sensitive) to characterize extended resistance. Results: The overall MTB positivity rate was 11.1% (n=2,771), with Trace-level semiquantitative results constituting 17.8% of positives. Rifampicin resistance was identified in 21 cases (0.93% rate). Alarmingly, 61.9% of RR-TB cases were new patients, indicating active primary transmission of resistant strains. Spatial analysis revealed significant heterogeneity: Jhelum Valley recorded the highest district-level positivity rate (16.9%), while Mirpur disproportionately accounted for 47.6% of all RR-TB cases. MTB/XDR analysis exposed high rates of extended resistance; among RR-TB cases, 50.0% exhibited isoniazid (INH) resistance (MDR-TB) and 35.7% showed fluoroquinolone (FQ) resistance (pre-XDR-TB). Crucially, among RIF-sensitive cases, INH mono-resistance and FQ resistance were detected in 19.2% and 27.3% of interpretable results, respectively. Conclusion: AJK faces a substantial and geographically heterogeneous TB burden, marked by significant primary RR-TB transmission and hidden INH and FQ resistance among routinely classified drug-sensitive patients. Expanding reflex MTB/XDR testing, intensifying contact tracing, and strengthening remote specimen transportation networks are urgently needed to optimize targeted TB control strategies in the region.