Genetic diversity in Mycobacterium ulcerans isolates from Ghana revealed by a newly identified locus containing a variable number of tandem repeats

Abstract

The molecular typing methods used so far for Mycobacterium ulcerans isolates have not been able to identify genetic differences among isolates from Africa. This apparent lack of genetic diversity among M. ulcerans isolates is indicative of a clonal population structure. We analyzed the genetic diversity of 72 African isolates, including 57 strains from Ghana, by variable number of tandem repeat (VNTR) typing based on a newly identified polymorphic locus designated ST1 and the previously described locus MIRU 1. Three different genotypes were found in Ghana, demonstrating for the first time the genetic diversity of M. ulcerans in an African country. While the ST1/MIRU 1 allele combination BD/BAA seems to dominate in Africa, it was only rarely found in isolates from Ghana, where the combination BD/B was dominant and observed in all districts studied. A third variant genotype (C/BAA) was found only in the Amansie-West district. The results indicate that new genetic variants of M. ulcerans emerged and spread within Ghana and support the potential of VNTR-based typing for genotyping of M. ulcerans.

FIG. 1.

Sequence variation of ST1 and MIRU 1 tandem repeat units. The dash indicates a base deletion; dots indicate identical sequence positions; and the asterisk indicates that allele A of MIRU 1 corresponds to variant A2 (23).

FIG. 2.

Map of southern Ghana, showing the residential districts of patients from whom the Ghanaian isolates analyzed in this study were obtained. The ST1/MIRU 1 allele combinations are genotype 1 (BD/B), genotype 2 (C/BAA), and genotype 3 (BD/BAA).

FIG. 3.

Agarose gel electrophoretic analysis of PCR products from amplifications with MIRU 1 primers (upper panel) and ST1 primers (lower panel). The results for selected isolates are shown. Lanes 1, 2, and 6, strains from the Amansie-West district; lanes 3, 4, and 5, strains from the Ga district.