Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa

Koen Vandelannoote, Kurt Jordaens, Pieter Bomans, Herwig Leirs, Lies Durnez, Dissou Affolabi, Ghislain Sopoh, Julia Aguiar, Delphin Mavinga Phanzu, Kapay Kibadi, Sara Eyangoh, Louis Bayonne Manou, Richard Odame Phillips, Ohene Adjei, Anthony Ablordey, Leen Rigouts, Françoise Portaels, Miriam Eddyani, Bouke de Jong

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Abstract

Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the phylogeographic relationships within the genetically conserved cluster of African M. ulcerans. Our analyses identified 23 different African insertion sequence element single nucleotide polymorphism (ISE-SNP) types that dominate in different areas where Buruli ulcer is endemic. These ISE-SNP types appear to be the initial stages of clonal diversification from a common, possibly ancestral ISE-SNP type. ISE-SNP types were found unevenly distributed over the greater West African hydrological drainage basins. Our findings suggest that geographical barriers bordering the basins to some extent prevented bacterial gene flow between basins and that this resulted in independent focal transmission clusters associated with the hydrological drainage areas. Different phylogenetic methods yielded two well-supported sister clades within the African ISE-SNP types. The ISE-SNP types from the "pan-African clade" were found to be widespread throughout Africa, while the ISE-SNP types of the "Gabonese/Cameroonian clade" were much rarer and found in a more restricted area, which suggested that the latter clade evolved more recently. Additionally, the Gabonese/Cameroonian clade was found to form a strongly supported monophyletic group with Papua New Guinean ISE-SNP type 8, which is unrelated to other Southeast Asian ISE-SNP types.

Original languageEnglish
JournalApplied and Environmental Microbiology
Volume80
Issue number3
Pages (from-to)1197-1209
Number of pages13
ISSN0099-2240
DOIs
Publication statusPublished - 2014

Keywords

  • Africa
  • Buruli Ulcer
  • Cluster Analysis
  • DNA Transposable Elements
  • DNA, Bacterial
  • Endemic Diseases
  • Gene Flow
  • Genotype
  • Humans
  • Mycobacterium ulcerans
  • Phylogeography
  • Polymorphism, Single Nucleotide

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