Profile of drug resistance conferring gene mutations in Mycobacterium tuberculosis among new and previously treated pulmonary tuberculosis cases from Kisumu county, Kenya

Abstract

Tuberculosis (TB) remains a significant public health concern in Kisumu County, Kenya, with a high burden of drug-resistant cases. Existing studies focus on epidemiological aspects, but lack comprehensive investigation into the genetic basis of drug resistance. This research gap hinders the development of targeted interventions and strategies for effective TB control in Kisumu County. This study aimed to investigate the profile of drug resistance-conferring gene mutations in Mycobacterium tuberculosis among new and previously treated pulmonary tuberculosis cases in Kisumu County, Kenya. Specifically, the study aimed to establish drug resistance conferring gene mutations in M. tuberculosis from HIV cases; determine gene mutations in M. tuberculosis that confer resistance to first and second line TB treatment; evaluate the diagnostic performance of molecular line probe assay in M. tuberculosis drug resistance testing among new and previously treated pulmonary TB cases in Kisumu County, Kenya. In this hospital and laboratory based cross- sectional study, sputum samples were collected from 256 TB clinical suspects attending various health facilities in Kisumu County between November 2020 and October 2021. Bacteriological and molecular techniques, including line probe assays, were employed to identify gene mutations and drug resistance patterns. Line probe assay assessed mutations in the genes rpoB, katG, inhA, embABC, pncA, rrs; gyrA, gyrB, and eis. Using statistical package for the social sciences v23, data was descriptively analysed into frequencies and proportions. Binary logistic regression was used to model for predictors of drug resistance while cross tabulation was used to describe mutant patterns. Contingency table was used to assess sensitivity, specificity, PPV and NPV. Out of a sample of 256 from TB suspected cases, 145(56.6%) were confirmed cases of which 113(77.9%) retreatment. Greater variability of mutations was exhibited from HIV positive cases compared to HIV negative cases and age was a predictor to isoniazid resistance, rifampicin resistance(RR) and Multidrug resistance (MDR). Low INH resistant strains had alterations in the promoter region of inhA gene at codon -15 indicating amino acid change of S315T1. High INH resistant strains showed mutations at katG gene, codon 315. The study presented that 2 MDR, 4 RR and 4 high INH resistance had the same nucleotide and amino acid changes and higher number of unknown mutations were exhibited in retreatment cases compared to new cases. Using phenotypic drug susceptibility testing as surrogate marker, genotypic test showed a statistical significant relationship with phenotypic method for detection of INH resistance (p=0.001), RIF resistance (p=0.001) and MDR (p=0.001). Understanding the genetic basis of drug resistance is crucial in guiding appropriate targeted treatment strategies and mitigating the spread of drug resistant strains. The results from the study will also guide policies and TB programs in regional specific anti-TB regimen based on mutation patterns, strengthen TB surveillance, and increase array of TB drug resistance diagnostic options for implementation by County and National governments in Kisumu County, Kenya.