Intestinal Carriage of Two Distinct -Carrying Strains by a Child with Uncomplicated Diarrhea.

Two distinct -carrying () strains, isolated from a child with uncomplicated diarrhea fifteen weeks apart, were characterized by combining short- and long-read sequencing to compare their genetic relatedness. One strain was characterized as Shiga toxin-producing (STEC)/typical enteropathogenic (tEPEC) O63:H6 with a repertoire of virulence genes including , (α2-subtype), , and . The other STEC with serotype O157:H16, reported for the first time as -carrying in this study, possessed, in addition, (ε-subtype) and , amongst other virulence-related genes. BLAST comparison showed that the -harboring prophage sequences of both strains were highly homologous (99.6% identity and 96.1% coverage). These results were corroborated by core Stx2f phage Multilocus Sequence Typing (cpMLST) as the -harboring prophages of both isolates clustered together when compared to those of 167 other human -carrying . Overall, the -harboring prophages of the two distinct strains isolated from the present case were highly similar, suggesting that the -harboring phage might have been transferred from the STEC/tEPEC O63:H6 strain to the atypical EPEC (aEPEC) O157:H16 strain in the gut of the child.