Abstract
The ability of Shiga toxin-producing Escherichia coli (STEC) to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx) subtype. Given the link between Stx2a subtype and disease severity, we sought to identify the stx subtypes present in whole genome sequences (WGS) of 444 isolates of STEC O157. Difficulties in assembling the stx genes in some strains were overcome by using two complementary bioinformatics methods: mapping and de novo assembly. We compared the WGS analysis with the results obtained using a PCR approach and investigated the diversity within and between the subtypes. All strains of STEC O157 in this study had stx1a, stx2a or stx2c or a combination of these three genes. There was over 99% (442/444) concordance between PCR and WGS. When common source strains were excluded, 236/349 strains of STEC O157 had multiple copies of different Stx subtypes and 54 had multiple copies of the same Stx subtype. Of those strains harbouring multiple copies of the same Stx subtype, 33 had variants between the alleles while 21 had identical copies. Strains harbouring Stx2a only were most commonly found to have multiple alleles of the same subtype (42%). Both the PCR and WGS approach to stx subtyping provided a good level of sensitivity and specificity. In addition, the WGS data also showed there were a significant proportion of strains harbouring multiple alleles of the same Stx subtype associated with clinical disease in England.
Highlights
Shiga toxin-producing Escherichia coli (STEC) are a rare but potentially fatal cause of gastroenteritis
Shiga toxin (Stx) subtyping of 444 STEC O157 in the UK—comparison of NGS and PCR Subtyping results from PCR and whole genome sequences (WGS) were identical in 422/444 strains (Table 1); there was agreement for 85 stx2a encoding strains, 153 stx2a/stx2c strains and 187 stx2c strains
Of the two strains where PCR and sequencing were discordant, one strain was positive for stx2c by PCR but no stx2c was identified in the sequencing data by the bioinformatics algorithms described here, and one strain was positive for stx2a by sequencing that was not detected by PCR
Summary
Shiga toxin-producing Escherichia coli (STEC) are a rare but potentially fatal cause of gastroenteritis. They are associated with a wide spectrum of disease ranging from mild to bloody diarrhoea, through to haemorrhagic colitis and haemolytic uraemic syndrome (HUS) (Pennington, 2010). The main reservoir of STEC in England is cattle, it is carried by other animals, mainly ruminants. Transmission to humans occurs through direct or indirect contact with animals or their environments; consumption of contaminated food or water, and through person-to-person contact. How to cite this article Ashton et al (2015), Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing.
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