Abstract
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 ( ‘E. coli’ as an indicator of water quality.