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Tracking cross-border transmission of Rwanda’s successful dominant rifampicin-resistant Mycobacterium tuberculosis clone using genomic markers

by Isabel Cuella-Martin, Wim Mulders, Jelle Keysers, Francois Hakizayezu, Hosee Niyompano, Docteur Runyambo, Willem Bram De Rijk, Jody Phelan, Yves Mucyo Habimana, Patrick Migambi, Michel Sawadogo, Claude Mambo Muvunyi, Bouke C. de Jong, Jean Claude Semuto Ngabonziza, Leen Rigouts, and Conor J. Meehan

Posted: March 31, 2026
Server: medRxiv
DOI: 10.64898/2026.03.29.26349652

Background

In Rwanda, genomic surveillance identified a dominant multidrug-resistant tuberculosis (MDR-TB) strain, the R3clone, responsible for approximately 70% of rifampicin-resistant TB cases. Its presence beyond Rwanda remains unexplored.

Methods

Unique genetic signatures of the R3clone were defined using whole-genome sequencing of MDR-TB isolates from Rwanda. We developed a targeted qPCR assay detecting a clone-specific single-nucleotide polymorphism. With these tools, we screened isolates from neighbouring countries and public genomic repositories.

Results

We identified 375 R3clone isolates, including 264 from historical Rwandan collections (1991-2021), 49 from recent Rwandan diagnostic routine (2021-2024), 25 from historical Burundi isolates (2002-2013), and 37 among public repositories from several countries. The R3clone-specific qPCR showed 100% specificity in distinguishing the R3clone from other MTBC (sub-)lineages. Transmission analysis revealed cross-border transmission of the R3clone within the Great Lakes Region.

Conclusion

This study comprehensively assesses cross-border transmission of a dominant MDR-TB strain, highlighting the need for coordinated international surveillance.

Article summary line

Genomic surveillance and targeted molecular diagnostics reveal cross-border transmission of Rwanda’s dominant multidrug-resistant tuberculosis clone throughout the African Great Lakes Region.

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