Genomic characterization of drug-resistant Mycobacterium tuberculosis complex in western Kenya reveals predominance of isoniazid resistance and discordance with routine susceptibility testing

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Introduction Whole-genome sequencing (WGS) data on resistance patterns in western Kenya remain limited. We evaluated resistant patterns of Mycobacterium tuberculosis complex (MTBC) isolates from western Kenya based on routine line probe assay (LPA) and/or phenotypic drug-susceptibility testing (DST) using targeted WGS. Methods In this cross-sectional study, 1,053 archived MTBC isolates from 12 counties in western Kenya were analyzed. An enriched subset of 316 isolates was selected for WGS, of which 290 produced high-quality genomes. Genomic data were analyzed to determine lineage distribution and identify drug resistance mutations using WHO mutation catalogue. Results Out of the 1,053 isolates, 127 (12%) showed resistance to at least one anti-TB drug. Isoniazid resistant-rifampicin susceptible (Hr-TB) isolates were the most common (52; 40%), followed by rifampicin-resistant (33;26%) and multidrug-resistant (23;18%). The predominance of Hr-TB is consistent with reports from Kenya and other high-burden settings. Enriched WGS subset identified resistance-associated mutations in 43/290 (14%) isolates, with similar resistance patterns. Rifampicin resistance was mainly associated with rpoB (S450L), while isoniazid resistance was dominated by katG S315 T and inhA promoter mutations. Resistant isolates were mainly concentrated in Kisii, Migori, Homa Bay, and Siaya, predominantly within Lineages 4 and 3. Discordance was observed between routine testing and WGS ( p = 0.026); approximately 86% of discordant isolates carrying mutations of uncertain significance. Conclusion Western Kenya shows geographic DR-TB heterogeneity with predominant Hr-TB, which rifampicin-based diagnostics risk under-detection. Despite observed discordance, Integrating WGS with routine testing will strengthen surveillance, improve isoniazid resistance detection, and support appropriate treatment management in high-burden settings.

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