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Microbiology 152 (2006), 1297-1305; DOI  10.1099/mic.0.28620-0
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Microbiology 152 (2006), 1297-1305; DOI  10.1099/mic.0.28620-0
© 2006 Society for General Microbiology

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

Jessica E. Cooper and Edward J. Feil

Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK

Correspondence
Edward J. Feil
e.feil{at}bath.ac.uk

The ability to make informed decisions on the suitability of alternative marker loci is central for population and epidemiological investigations. This issue was addressed using Staphylococcus aureus as 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 of S. aureus this threshold is >1 % mean pairwise diversity.

Abbreviations: CAI, codon adaptation index; CE, cell envelope and cellular processes; FCT, fit to the consensus tree; IP, informational pathway; HK, housekeeping; MLST, multilocus sequence typing; MRSA, meticillin-resistant S. aureus; MSSA, meticillin-sensitive S. aureus; OR, orphan; UF, unknown function

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are DQ413277–DQ414234.

Two supplementary tables and two supplementary figures are available with the online version of this paper.




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