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 ( 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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