Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms

Abstract

In the present study, the genetic relationships as well as the virulome and resistome of newly sequenced O26 and O157 Shiga-toxin producing E. coli (STEC) isolates, collected from dairy farms in Italy, were investigated in comparison to publicly available genomes collected worldwide. The whole genome of Italian isolates was sequenced on Illumina MiSeq Platform. Reads quality control, de novo draft genome assembly, species confirmation and the 7-loci Multi-Locus Sequence Type assignment were performed using INNUca pipeline. Reference-based SNPs calling was performed on O157 and O26 genomes, separately, mapping contigs to high-quality finished genomes. Virulence and antimicrobial resistance determinants were detected in silicousing the tool ABRicate. Phylogenetic reconstructions revealed that genomes clustered mainly based on their 7-loci MLST type. The virulome of tested genomes included 190 determinants. O157 genomes carried chu genes associated to heme mediated iron uptake, whereas O26 genomes harboured genes ybt associated to siderophore mediated iron uptake. Resistome analysis showed the presence of tet(34) on all but one O157 genomes and on only one O26 genomes. Only 4 genomes carried genes associated to multiresistance. In the present study, the genes chu and ybt were identified as potential biomarker for the differentiation of O157 and O26 serotypes.

The Prevalence of Shiga Toxin-Producing Escherichia coli and Enteropathogenic Escherichia coli Isolated from Raw Chicken Meat Samples

“…Also, enterohemolysin, encoded by the hly gene, is an effective factor in the pathogenicity of STEC [ 5 ]. Because only limited and incomplete studies have been conducted on the prevalence and epidemiology of the O157 : H7 serotype in developing countries, its prevalence has been reported as low [ 6 ].…”

Prevalence of Shiga toxin-producing Escherichia coli isolated from chicken meat in west of Iran

“…In addition to shiga toxin, an external membrane protein called Intimin is responsible for the close connection of the bacteria to the intestinal epithelial cells and causes certain damage, called "effacing/attaching," and is coded by the eae gene [3,4]. Also, the enterohemolysin, coded by the hly gene, is an effective factor in the pathogenicity of this serotype [5]. In developing countries, due to incomplete and limited studies on the prevalence and epidemiology of this serotype, the prevalence of O157:H7 is lower [6].…”

Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli

“…Hydroxamate aerobactin is also found in strains BAA-2440 (O111:H8) and BAA-2192 (O145:NM), and the heme utilization operon (chu) in BAA-2192 (O145:NM; Figure 5). We note here that siderophores such as ybt and chu have been proposed biomarkers for serotypes O26, O157, and O145 (Pasquali et al, 2018;Jarocki et al, 2019;Carbonari et al, 2022). Antimicrobial-resistant STEC, though uncommon, have been isolated from humans, animals, and food (Eppinger et al, 2011;Amézquita-López et al, 2016;Mukherjee et al, 2017;Greig et al, 2023;Lee et al, 2023).…”