Intestinal Carriage of Two Distinct stx2f-Carrying Escherichia coli Strains by a Child with Uncomplicated Diarrhea

Two distinct <i>stx_2f</i>-carrying <i>Escherichia coli</i> (<i>E. coli</i>) 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 <i>E. coli</i> (STEC)/typical enteropathogenic <i>E. coli</i> (tEPEC) O63:H6 with a repertoire of virulence genes including <i>stx_2f</i>, <i>eae</i> (α2-subtype), <i>cdt</i>, and <i>bfpA</i>. The other STEC with serotype O157:H16, reported for the first time as <i>stx_2f</i>-carrying <i>Escherichia coli</i> in this study, possessed, in addition, <i>eae</i> (ε-subtype) and <i>cdt</i>, amongst other virulence-related genes. BLAST comparison showed that the <i>stx_2f</i>-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 <i>stx_2f</i>-harboring prophages of both isolates clustered together when compared to those of 167 other human <i>stx_2f</i>-carrying <i>Escherichia coli</i>. Overall, the <i>stx_2f</i>-harboring prophages of the two distinct <i>E. coli</i> strains isolated from the present case were highly similar, suggesting that the <i>stx_2f</i>-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.