Tracking cross-border transmission of Rwandas successful dominant rifampicin-resistant Mycobacterium tuberculosis clone using genomic markers
Cuella-Martin, I.; Mulders, W.; Keysers, J.; Hakizayezu, F.; Niyompano, H.; Runyambo, D.; de Rijk, W.-B.; Phelan, J.; Mucyo Habimana, Y.; Migambi, P.; Sawadogo, M.; Mambo Muvunyi, C.; C. de Jong, B.; Ngabonziza, J. C. S.; Rigouts, L.; Meehan, C.
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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.
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