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We have identified a clonal complex of Mycobacterium bovis present at high frequency in cattle in population samples from several sub-Saharan west-central African countries. This closely related group of bacteria is defined by a specific chromosomal deletion (RDAf1) and can be identified by the absence of spacer 30 in the standard spoligotype typing scheme. We have named this group of strains the African 1 (Af1) clonal complex and have defined the spoligotype signature of this clonal complex as being the same as the M. bovis BCG vaccine strain but with the deletion of spacer 30. Strains of the Af1 clonal complex were found at high frequency in population samples of M. bovis from cattle in Mali, Cameroon, Nigeria, and Chad, and using a combination of variable-number tandem repeat typing and spoligotyping, we show that the population of M. bovis in each of these countries is distinct, suggesting that the recent mixing of strains between countries is not common in this area of Africa. Strains with the Af1-specific deletion (RDAf1) were not identified in M. bovis isolates from Algeria, Burundi, Ethiopia, Madagascar, Mozambique, South Africa, Tanzania, and Uganda. Furthermore, the spoligotype signature of the Af1 clonal complex has not been identified in population samples of bovine tuberculosis from Europe, Iran, and South America. These observations suggest that the Af1 clonal complex is geographically localized, albeit to several African countries, and we suggest that the dominance of the clonal complex in this region is the result of an original introduction into cows naïve to bovine tuberculosis.

Rubaga Division, Kampala, Uganda.To use polymerase chain reaction (PCR) based regions of difference (RD) analysis to study the species diversity of Mycobacterium tuberculosis complex isolates from a community-based sample of tuberculosis (TB) patients from Rubaga and to perform long sequence polymorphism (LSP) analysis to further characterise the M. tuberculosis Uganda genotype, a group of strains previously recognised by their characteristic spoligotype patterns.For the present study, 344 consecutive TB patients attending clinics in Rubaga Division were enrolled. Sample processing and culture were performed at the National Tuberculosis and Reference Laboratory and molecular assays at Makerere Medical School. Species identification was achieved by determining the RDs, while spoligotyping and LSP analysis were performed to characterise the M. tuberculosis Uganda genotype.Of the 344 isolates, 343 (99.7%) were M. tuberculosis sensu stricto, while one was classical M. bovis. The Uganda genotype strains characteristically lacked RD724, a locus that defines one of the major sub-lineages of M. tuberculosis, which suggested that this geographically constrained lineage is specifically adapted to a central African human host population.M. tuberculosis is the most prevalent species of the M. tuberculosis complex in Kampala, and the Uganda genotype is the predominant strain.