Whole Genome Sequencing for Detecting Drug-Resistant Mutations in Mycobacterium tuberculosis in Zimbabwe

Background: Drug-resistant tuberculosis (DR-TB) is a major public health issue in Zimbabwe. Whole-genome-sequencing (WGS) is recommended for studying drug-resistant mutations, lineages, prevalence, and transmission patterns. However, there are limited data on drug-resistant conferring mutations and WGS use in Zimbabwe. Aim: This study aimed to investigate the drug-resistant mutations, prevalence, and genetic diversity of DR-TB in Zimbabwe using WGS. Methods: We conducted a retrospective study using WGS to analyze DNA extracted from 68 DR-TB isolates identified via phenotypic drug susceptibility testing (pDST) from studies conducted in Zimbabwe from 2011 to 2023. WGS was performed using an Illumina MiSeq machine (Illumina Inc., San Diego, California, USA). Results: WGS identified 16 (23.5%) RR, 35 (51.5%) MDR, 5 (7.4%) Pre-XDR, 3 (4.4%) XDR, and 9 (13.2%) sensitive (non-resistant variants) isolates. The most frequent mutations were rpoB_Ser450Leu, Ser315Thr, embB_Met306Vol, rpsL_Lys43Arg, rrs_514A>C, and gid_102delG. The mmpR5 p. Arg134 mutation conferred cross-resistance to bedaquiline and clofazimine. Concordant rates between WGS-based and pDST predictions of drug-resistance were high for isoniazid (91.3%), Rifampicin (86.3%), Ethambutol (86.4%), fluoroquinolones (100%), Linelozid (100%), and second-line injectables: Amikacin (94.4%), Kanamycin (91.7%), and Capreomycin (100%). The study isolates belonged to lineages 1 to 4, with lineages 4 (n =38, 55.9%) and 2 (n =19, 27.9%) being the most predominant. Conclusion: WGS provides valuable insights into the prevalence, drug-resistant mutations, and genetic diversity of DR-TB in Zimbabwe, thereby aiding the development of effective prevention, treatment, and control strategies.