Computational protocol: Extensive Diversity of Streptococcus pyogenes in a Remote Human Population Reflects Global-Scale Transmission Rather than Localised Diversification

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Protocol publication

[…] This study made use of pure bacterial cultures that had previously been collected in a variety of research projects involving human subjects and from diagnostic service providers, and stored frozen. This study involved no human experimentation or use of previously unpublished human clinical data.The S. pyogenes isolates used were all derived from the NT, and stored at the Menzies School of Health Research in Darwin, Australia. They were collected between 1987 and 2008 and were either clinical isolates obtained from the Royal Darwin Hospital, or collected in the course of research projects carried out in Aboriginal communities emm sequence subtype data are available for 1,732 of these isolates, and these encompass 104 emmST and 142 emm sequence subtypes.Minim typing was performed as previously described . Minim typing is based on MLST. , , , . The S. pyogenes Minim typing system encompasses high resolution melting (HRM) analysis of 10 stretches of DNA internal to the fragments used for MLST. Each fragment encompasses a single nucleotide polymorphism (SNP) that is one part of a set derived from the S. pyogenes MLST database on the basis of maximization of the Simpsons Index of Diversity (D). Other SNPs in the fragments confer additional resolving power. Minim data is interpreted by converting the HRM curves to inferred G+C content. A current key for converting between S. pyogenes Minim data and MLST data is provided as supplementary data (). Minim types are referred to as Melting Types (MelTs).,MLST was performed as described by Enright and co-workers , and the database accessed at http://spyogenes.mlst.net/. Inference of population structures from MLST profiles using goeBURST was performed as previously described by Francisco and co-workers ( and the software was accessed at http://goeburst.phyloviz.net/. […]

Pipeline specifications

Software tools BURST, PHYLOViZ
Databases MLST.net
Applications Phylogenetics, WGS analysis
Organisms Streptococcus pyogenes, Homo sapiens
Diseases Sprains and Strains