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Characterization of the cryptic Escherichia lineages: rapid identification and prevalence
Author(s) -
Clermont Olivier,
Gordon David M.,
Brisse Sylvain,
Walk Seth T.,
Denamur Erick
Publication year - 2011
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2011.02519.x
Subject(s) - biology , multilocus sequence typing , clade , escherichia coli , species complex , locus (genetics) , genetics , lineage (genetic) , typing , phylogenetics , evolutionary biology , allele , gene , zoology , genotype , phylogenetic tree
Summary Strains phenotypically indistinguishable from Escherichia coli and belonging to at least five distinct cryptic lineages, named Escherichia clades I to V, that are genetically divergent from E. coli yet members of the genus have been recently found using multi‐locus sequence typing (MLST). Very few epidemiological data are available on these strains as their detection by MLST is not suitable for large‐scale studies. In this work, we developed a rapid PCR method based on aes and chuA allele‐specific amplifications that assigns a strain a cryptic lineage membership. By screening more than 3500 strains with this approach, we show that the cryptic lineages of Escherichia are unlikely to be detected in human faecal samples (2–3% frequency) and even less likely to be isolated from extra‐intestinal body sites (< 1% frequency). They are more abundant in animal faeces ranging from 3–8% in non‐human mammals to 8–28% in birds. Overall, the strains from the clade V are the most abundant and from the clade II very rare. These results suggest that members of the cryptic clades are unlikely to be of significance to human and health but may influence the use of ‘E. coli’ as an indicator of water quality.