Occurrence of Multiple stx1 Genes and Rare Genomic Variation in stx1 Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing <i>Escherichia coli</i> are important foodborne pathogens. There are several subtypes of the Shiga toxin Stx known, with Stx2 (a-o) being more diverse than Stx1 (a, c, d). Multiple occurrences of <i>stx2</i> genes as well as combinations of <i>stx1</i> and <i>stx2</i> have been reported. However, there is a lack of knowledge on the occurrence of multiple <i>stx1</i> genes in STEC strains. Here, we report two strains from food and animal feces which show genomic variations in the <i>stx1</i> operon. The first strain harbors <i>stx1a</i> and <i>stx1c</i> genes, and the second strain shows an inactive <i>stx1</i> operon due to an insertion in the <i>stxA1a</i> subunit gene. The screening of publicly available complete genome sequences of STEC revealed further strains harboring multiple <i>stx1</i> genes, indicating that those strains also occur in human infections. This should be kept in mind when applying routine diagnostic methods like PCR, that do not detect multiple occurrences of <i>stx1</i> genes of the same subtype. Moreover, the impact on the severity of human infections due to multiple <i>stx1</i> genes has not been investigated well.