The phylogeny of Staphylococcus aureus – which genes make the best intra-species markers?

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Abstract
The ability to make informed decisions on the suitability of alternative marker loci is central for population and epidemiological investigations. This issue was addressed usingStaphylococcus aureusas a model population by generating nucleotide sequence data from 33 gene fragments in a representative sample of 30 strains. Supplementing the data with pre-existing multilocus sequence typing data, an intra-species tree based on ∼17·8 kb of sequence was reconstructed and the goodness of fit of each individual gene tree was computed. No strong association was noted between gene function per se and phylogenetic reliability, but it is suggested that candidate loci should possess at least the average degree of nucleotide diversity for all genes in the genome. In the case ofS. aureusthis threshold is >1 % mean pairwise diversity.