Whole-genome sequencing suggests recent transmission of rifampicin-resistant tuberculosis in Botswana

Background Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), continues to be a global health challenge. Transmission of drug-resistant TB (DR-TB) poses a significant threat to effective TB prevention and care strategies. This study's aim was to investigate transmission patterns of DR-TB strains, identify factors associated with the spread and reconstruct their transmission dynamics over the study period in Botswana. Methods We analysed whole-genome sequencing data for 195 rifampicin-resistant Mtb isolates, which were isolated between 2016 and 2023. Potential recent transmission clusters were identified using thresholds of 0 and 5 single-nucleotide polymorphisms (SNPs). The temporal signal for the predominant sublineages was assessed in TemPest, and BEAST was used to infer the evolution of Mtb strains over time. All statistical analyses were performed using STATA version 18. Results Of the 195 RR-TB isolates, 116 (60%) belonged to lineage 4. By inferring close genomic relatedness between isolates (0 SNPs and ≤ 5 SNPs difference), there was evidence of transmission. Phylogenetic analyses and SNP differences showed evidence of potential transmission events within and across different health districts. At a 0-SNP cut-off to define genomic clusters, being female (OR: 1.68, 95% CI: 1.04-2.7, p = 0.04) and being infected with a lineage 4 strain (OR: 2.80, 95% CI: 1.19-6.80, p = 0.02) were associated with clustering. Treatment history (OR: 1.41, 95% CI: 0.74-2.69, p = 0.30), smear result (OR: 1.11, 95% CI: 0.64-1.95, p = 0.71) and HIV status (OR: 0.58, 95% CI: 0.71-1.87, p = 0.58) were not associated with clustering. Conclusions Our study offers insights into the transmission of rifampicin-resistant Mtb in Botswana. The findings indicate that targeted interventions in health districts showing evidence of transmission could help stop the spread of drug-resistant Mtb strains.' Clinical trial number Not applicable.