Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing

PeerJ
Philip M AshtonT J Dallman

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 th...Continue Reading

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Citations

Nov 3, 2015·International Journal of Food Microbiology·Elisabeth HauserHerbert Schmidt
Oct 2, 2020·Molecular Biology Reports·Jobin John JacobBalaji Veeraraghavan
Nov 21, 2018·Emerging Infectious Diseases·Lisa ByrneClaire Jenkins
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Apr 27, 2017·Frontiers in Cellular and Infection Microbiology·Pragathi B ShridharJianfa Bai
Jan 31, 2019·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Claire JenkinsKathie A Grant
May 21, 2019·Microbial Genomics·Danielle J IngleDeborah A Williamson
Mar 25, 2021·Microbial Genomics·Timothy J DallmanClaire Jenkins
Apr 26, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Ranya MulchandaniJeremy Hawker

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Datasets Mentioned

BETA
PRJNA248064
AB071845.1
AJ249351.2
AB472687.1

Methods Mentioned

BETA
PCR

Software Mentioned

BLASTn
Trimmomatic
MEM
Velvet
MEGA
ClustalW
Samtools
BioPython
BWA
VirulenceFinder

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