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Strains phenotypically indistinguishable fromEscherichia coliand belonging to at least five distinct cryptic lineages, namedEscherichiaclades I to V, that are genetically divergent fromE. coliyet 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 onaesandchuAallele-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 ofEscherichiaare 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.