Rifampicin-resistant Mycobacterium tuberculosis: an emerging threat to human health in Botswana

Rifampicin-resistant tuberculosis (RR-TB) continues to threaten global TB control. The World Health Organisation (WHO) estimated that 400,000 people developed RR-TB in 2023, with Africa being among the regions with the highest burden. Botswana, a high TB/HIV burden country, has reported an increase in RR-TB notifications in recent years; however, the genetic diversity, resistance mechanisms, and treatment outcomes have not been described at a national scale. In this study, we utilised whole-genome sequencing (WGS) in conjunction with routinely collected clinical data to characterise the population structure of circulating Mycobacterium tuberculosis (Mtb) strains, investigate transmission dynamics and assess treatment outcomes. Our findings indicate a high genetic diversity of Mtb strains in Botswana, with lineage 4 being the most prevalent. WGS analyses detected non-canonical rpoB mutations I491F and V170F, which are associated with low-level rifampicin resistance. Variants with these mutations are often missed by the routine molecular assays, which creates a risk of misclassification of cases. Phylogenetic analyses identified genomic clusters which suggest recent transmission within and across different health districts. These findings demonstrate the need for targeted interventions, such as intensified case finding and targeted contact tracing in identified hotspots, to help halt the transmission of RR-TB strains. Treatment success was high; however, mortality was higher among people living with HIV, which suggests the need for careful monitoring of this population. Notably, no variants resistant to new and repurposed drugs were detected in this study. In conclusion, this work demonstrates that RR-TB burden in Botswana is driven by genetically diverse Mtb strains and sustained by ongoing transmission. The detection of variants with mutations outside the rifampicin resistance-determining region highlights the existing diagnostic blind spot. Integrating next-generation sequencing (NGS) into surveillance, together with targeted public health interventions, careful stewardship of new and repurposed drugs, and implementing routine second-line drug susceptibility testing (DST) will protect the current gains, reduce mortality in high-risk populations, and accelerate progress towards the elimination of TB.

Grantor dc:publisher

Stellenbosch : Stellenbosch University

Year dc:date.issued

2026

Author dc:creator

• Mogashoa, Tuelo

Advisors dc:contributor.advisor

• Streicher, Elizabeth Maria
• Dippenaar, Anzaan
• Moyo, Sikhulile
• Gaseitsiwe, Simani

Language dc:language.iso

en

Repository record dc:identifier.uri

https://scholar.sun.ac.za/handle/10019.1/136183

OAI identifier oai:identifier

oai:scholar.sun.ac.za:10019.1/136183