Global population structure of Shiga toxin-producing Escherichia coli O103:H2 and the variation in their major virulence factor-encoding genetic elements

Shiga toxin (Stx)-producing <i>Escherichia coli</i> (STEC) is a major cause of serious gastrointestinal illness, including diarrhoea, haemorrhagic colitis and life-threatening haemolytic-uraemic syndrome. Although O157:H7 STEC strains are the most prevalent, the incidence of STEC infections caused by several other serotypes has recently increased. O103:H2 STEC is one of these major non-O157 STEC strains, but systematic whole-genome sequence (WGS) analyses have not yet been conducted. To gain a global phylogenetic overview of O103:H2 STEC based on WGSs, we analysed 2,701 WGSs of O103:H2 strains, including 193 sequenced in this study. Sequence type (ST)-based classification divided the O103:H2 strains into three distinct <i>E. coli</i> lineages. As the virulence marker genes of typical STECs (<i>stx</i>, <i>eae</i> and <i>ehxA</i>) were found only in the major O103:H2 lineage (<i>n</i>=2,658) comprising ST17 and its single- and double-locus variants, we performed a global phylogenetic analysis of the major lineage. This analysis revealed that this lineage was divided into five clades (C1-C5) and that C1 was the ancestral clade, C2 and C3 emerged from C1 and C4 and C5 emerged from C3. While <i>stx2</i> genes were sporadically distributed in limited STEC O103:H2 strains, <i>stx1a</i>, <i>eae</i> and <i>ehxA</i> were highly conserved throughout the entire STEC O103:H2 lineage. However, through a detailed comparison of seven closed genomes of STEC strains, covering the five clades and including four obtained in this study, we found marked variation in the genetic elements encoding the virulence genes (Stx1a phage, the locus of enterocyte effacement (LEE) and the virulence plasmid), such as rearrangement in the LEE accessory region, a shift in the integration sites of the Stx1a phage due to the replacement of the integrase gene-containing genomic segments, the replacement of the virulence plasmid and the gain and loss of virulence-related genes in the virulence plasmid. Overall, this study highlights the current global population structure of O103:H2 strains and provides evolutionary insights into the variation in virulence determinants within STEC O103:H2, which is relatively understudied among the major STEC lineages.