In recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB).
Whole 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. Among the 76
patients, 61(80.3%) new cases and 15(19.7%) retreatment cases, 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 Cameroon genotype, which emerged ~22 years ago was likely to be involved
in community transmission. A sub-clade of the Ghana genotype that arose approximately 30 years ago
was an important cause of MDR-TB in Bamako. The Ghana genotype isolates appeared more likely to be
MDR than other genotypes after controlling for treatment history. We identifed a clade of four related
Beijing isolates that included one MDR-TB isolate. It is a major concern to fnd the Cameroon and Ghana
genotypes involved in community transmission and MDR-TB respectively. The presence of the Beijing
genotype in Bamako remains worrying, given its high transmissibility and virulence
