title: Single nucleotide polymorphisms on the road to strain differentiation in Mycobacterium ulcerans.
abstract: The genomic fine-typing of strains of Mycobacterium ulcerans, the causative agent of the emerging human disease Buruli ulcer, is difficult due to the clonal population structure of geographical lineages. Although large sequence polymorphisms (LSPs) resulted in the clustering of patient isolates originating from across the globe, differentiation of strains within continents using conventional typing methods is very limited. In this study, we analyzed M. ulcerans LSP haplotype-specific insertion sequence elements among 83 M. ulcerans strains and identified single nucleotide polymorphisms (SNPs) that differentiate between regional strains. This is the first genetic discrimination based on SNPs of M. ulcerans strains from African countries where Buruli ulcer is endemic, resulting in the highest geographic resolution of genotyping so far. The findings support the concept of genome-wide SNP analyses as tools to study the epidemiology and evolution of M. ulcerans at a local level.
authors.affiliation: Ghanaian-German Centre for Health Research, University of Ghana, School of Public Health, P.O. Box LG 13, Legon, Accra, Ghana. m.kaeser@unibas.ch
authors.forename: Michael
authors.initials: M
authors.lastname: Käser
authors.forename: Julia
authors.initials: J
authors.lastname: Hauser
authors.forename: Gerd
authors.initials: G
authors.lastname: Pluschke
mesh_terms: D000349:Africa / Q000453:epidemiology; D015373:Bacterial Typing Techniques / Q000379:methods*; D001483:Base Sequence; D054312:Buruli Ulcer / Q000453:epidemiology / Q000382:microbiology*; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D019353:Endemic Diseases; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D019911:Mycobacterium ulcerans / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial