ena-STUDY-WARWICK-25-06-2018-11:22:32:578-1083
The rise of virulent genotypes and an emerging threat of multidrug resistant tuberculosis in Bamako, Mali
BackgroundIn recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Here we present insights into the evolutionary mechanisms driving the emergence of MDR-TB and virulent genotypes in Bamako.MethodsWhole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. A time dated phylogenetic tree was reconstructed using BEAST. Lineage and resistance conferring mutations were inferred using PhyResSe.ResultsPatients included 21 females and 55 males aged from 3 to 78 years and including 61(80.3%) new cases and 15(19.7%) retreatment cases. Among the 76 patients,   12 (16%) were infected by MDR-TB. The dominant lineage was the Euro-American lineage, Lineage 4. Within Lineage 4, the Cameroon genotype was the most prevalent genotype (n = 20, 26%), followed by the Ghana genotype (n=16, 21%). A sub-clade of the Ghana genotype that arose 30 years ago was the principal cause of MDR-TB in Bamako. The Ghana genotype isolates were more likely MDR than other genotypes after controlling for treatment history. A sub-clade of the Cameroon genotype, which emerged ~22 years ago is likely to be involved in community transmission. We identified a clade of four related Beijing isolates that included one MDR-TB isolate.ConclusionCameroon and Ghana genotypes are endemic in Mali . Their association with community transmission and MDR-TB in Bamako respectively is a major concern. The rise of the Beijing genotype in Bamako is worrying, given its high transmissibility and virulence.
BackgroundIn recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Here we present insights into the evolutionary mechanisms driving the emergence of MDR-TB and virulent genotypes in Bamako.MethodsWhole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. A time dated phylogenetic tree was reconstructed using BEAST. Lineage and resistance conferring mutations were inferred using PhyResSe.ResultsPatients included 21 females and 55 males aged from 3 to 78 years and including 61(80.3%) new cases and 15(19.7%) retreatment cases. Among the 76 patients,   12 (16%) were infected by MDR-TB. The dominant lineage was the Euro-American lineage, Lineage 4. Within Lineage 4, the Cameroon genotype was the most prevalent genotype (n = 20, 26%), followed by the Ghana genotype (n=16, 21%). A sub-clade of the Ghana genotype that arose 30 years ago was the principal cause of MDR-TB in Bamako. The Ghana genotype isolates were more likely MDR than other genotypes after controlling for treatment history. A sub-clade of the Cameroon genotype, which emerged ~22 years ago is likely to be involved in community transmission. We identified a clade of four related Beijing isolates that included one MDR-TB isolate.ConclusionCameroon and Ghana genotypes are endemic in Mali . Their association with community transmission and MDR-TB in Bamako respectively is a major concern. The rise of the Beijing genotype in Bamako is worrying, given its high transmissibility and virulence.