The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups
Version of Record online: 24 DEC 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Environmental Microbiology Reports
Thematic Issue on Environmental Ecology of Pathogens and Resistances
Volume 5, Issue 1, pages 58–65, February 2013
How to Cite
Clermont, O., Christenson, J. K., Denamur, E. and Gordon, D. M. (2013), The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environmental Microbiology Reports, 5: 58–65. doi: 10.1111/1758-2229.12019
- Issue online: 3 FEB 2013
- Version of Record online: 24 DEC 2012
- Accepted manuscript online: 29 NOV 2012 08:52AM EST
- Manuscript Accepted: 21 NOV 2012
- Manuscript Received: 11 OCT 2012
Fig. S1. Maximum likelihood tree depicting our current understanding of the phylo-group structure of Escherichia coli sensu lato. The tree is inferred using general time reversible model of evolution assuming a fixed fraction of invariant sites and that the rate variation among sites is described by a gamma distribution (GTR + G + I) and is based on the partial nucleotide sequence for 13 genes (9819 bp). The genes targeted were aes (Lescat et al., 2009), icd, pabB, polB, putP, trpA and trpB (Le Gall et al., 2007), adk, fumC, gyrB, mdh, purA and recA used in the MLST scheme hosted at the University College Cork (http://mlst.ucc.ie/mlst/dbs/Ecoli). When required, data for the same DNA fragments were extracted from reference genomes (GenBank).
Fig. S2. Flow scheme allowing phylogenetic group determination of an E. coli strain based on the results of PCR amplification of the arpA, chuA and yjaA genes and DNA fragment TSPE4.C2. U is for unknown. See Table 2 for the next steps required by the extended quadruplex method.
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