Detection of Mutations Associated With Antimicrobial Resistance in Mycobacterium Tuberculosis in Selected Health Facilities in Kenya

Abstract

Background: Drug resistant tuberculosis is a huge medical issue in several countries of the world and has continuously become a challenge to its prevention and control. Kenya is ranked as the fifteenth in position of the twenty-two countries with the highest prevalence of tuberculosis with about two thousand three hundred patients suffering from multidrug resistant tuberculosis in 2016. Status of the patterns of mutations associated with drug resistance of Mycobacterium tuberculosis in the country is limited although it has been a threat to national tuberculosis control program and a major public health problem in Kenya. Objective: The main objective of this study was to determine mutations in genes coding for drug resistance in M. tuberculosis from sputum samples. Methodology: This was a cross sectional study carried out in five public health hospital laboratories. A total of 288 routinely analyzed TB smear positive sputum samples were collected and analysed by pyrosequencing. Results: Mutations were detected in 9% (27/288) samples tested. Mutations were detected in genes associated with five of the antibiotics RIF, INH, SM, EMB and AMK and there were no mutations in genes associated with OFL. Mutations were detected on all the four first line antibiotics tested. 85% (23/27) of the samples with mutations were on the rpoB gene (associated with resistance to Rifampicin) from four of the counties. One sample (1/27) had a mutation on katG gene (associated with Isoniazid), eight samples (8/27) had mutations on rpsl gene (associated with Streptomycin), two samples (2/27) had mutations on embB gene (associated with Ethambutol), one sample (1/27) had mutation on rrs (associated with Amikacin) and there were no mutations detected on the gyrA gene (associated with Ofloxacin). Mutations on more

than one gene associated with two or more drugs were detected in seven samples (7/27) and multiple multi-locus mutations were detected on rpoB and rpsl. 98% of the codon changes reported were on the genes associated with 1st line antibiotics and only one on the genes associated with the 2nd line antibiotics. Conclusion: Mutations associated resistance to all the four 1st line TB antibiotics were detected on sputum samples that could hamper treatment of patients with the antibiotics. Mutations on the genes associated with resistance to second line antibiotics were low with 1/288 (0.3%) mutation. Recommendations: Pyrosequencing test for drug resistance genes is an invaluable technology that should be included in the testing algorithm for susceptibility testing in TB reference and research laboratories in Kenya