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Tracking cross-border transmission of the Rwanda MDR-TB R3clone

I Cuella(1) B Bisimwa(1,2,3) J Keysers(1) L Rigouts(1) B C de Jong(1) J C Semuto Ngabonziza(4,5) C J Meehan(1,6)

1:Institute of Tropical Medicine, Antwerp, Belgium; 2:Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo; 3:Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo; 4:Rwanda Biomedical Centre, Kigali, Rwanda; 5:University of Rwanda, Kigali, Rwanda; 6:Nottingham Trent University, Nottingham, UK

The use of molecular epidemiology to track circulating strains of Mycobacterium tuberculosis is becoming more commonplace in highly endemic settings.  However, most such studies are done on a country-by-country basis, which can limit the ability to find cross-border transmissions. Using a WGS dataset of 308 M. tuberculosis samples collected from 1992-2018 we found that most MDR-TB in Rwanda was due to a single circulating clone (termed the R3clone). We wished to see if this clone was also present in neighbouring countries to better understand the extent of its spread.

Further WGS in Rwanda revealed this clone is still prevalent in the population. To allow for surveillance of this clone, we determined the spoligotype and drug resistance patterns that characterise these isolates and developed a SNP assay specific for the R3clone. This was undertaken by finding SNPs present in all clone isolates and absent in all others in the Rwanda dataset. This SNP (C25631G) was then validated against the 80,000 isolates within the NCBI SRA database.

We used the spoligotype, DR patterns and SNP assay to search for the presence of this clone in stored isolates from the neighbouring country of Burundi. We found that 25/143 (17%) of RR-TB isolates from Burundi spanning 2011-2013 are R3clone, suggesting sustained cross-border transmission. WGS-based phylogenetics indicated most Burundi isolates derived from a single introduction but there was evidence of additional crossings. This indicates that transmission studies should be undertaken beyond country-specific studies, especially in areas with high levels of both TB and migration.

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