High-Quality Whole-Genome Sequences for 77 Shiga Toxin-Producing Escherichia coli Strains Generated with PacBio Sequencing

Abstract

Shiga toxin-producing Escherichia coli (STEC) is an enteric foodborne pathogen that can cause mild to severe illness. Here, we report the availability of high-quality whole-genome sequences for 77 STEC strains generated using the PacBio sequencing platform.

Genetic characterization of Shigatoxigenic and enteropathogenic Escherichia coli O80:H2 from diarrhoeic and septicaemic calves and relatedness to human Shigatoxigenic E. coli O80:H2

“…2019) and of the American human 2013C‐4991 EHEC O80:H2 strain (Patel et al . 2018) were included in this comparison (Table ). The genome sequences of the 52 Belgian EPEC and EHEC are available via the Bioproject PRJNA606200 and the GenBank accession numbers are listed in the Table .…”

“…To study the genetic relationships between bovine EHEC, human EHEC and bovine EPEC O80, the newly identified bovine EHEC and EPEC were genome sequenced using Illumina sequencers (Table S1) along with (i) six bovine EPEC from a previous study (Thiry et al 2017) and (ii) 10 human EHEC identified in 2018/2019 at the Belgian National Reference Centre (NRC) STEC. In addition, the previously sequenced genomes of 17 Belgian EHEC and EPEC O80:H2 (nine human EHEC isolated between 2009 and 2016, six bovine EPEC isolated between 2009 and 2015 and two bovine EHEC isolated from a single calf in 1987) (Thiry et al 2017;De Rauw et al 2019) and of the American human 2013C-4991 EHEC O80:H2 strain (Patel et al 2018) were included in this comparison (Table S1). The genome sequences of the 52 Belgian EPEC and EHEC are available via the Bioproject PRJNA606200 and the GenBank accession numbers are listed in the Table S1.…”

“…The phylogenetic analysis was performed using the genome of the American human 2013C-4991 EHEC O80: H2 strain as a reference (Patel et al 2018). A maximum likehood (ML) tree was constructed, as previously described (Nakamura et al 2020).…”

“…Enterohemorrhagic Escherichia coli harbour the eae gene, located on the Locus of Enterocyte Effacement (LEE) pathogenicity island and involved in the production of the AE lesion, and one or more stx genes located on lambdoid phages (Stx phages) (Tozzoli and Scheutz 2014). Besides the seven most frequent and pathogenic serotypes worldwide (Karmali et al 2003;Tozzoli and Scheutz 2014), other serotypes can emerge from time to time, like the O104:H4 serotype in Germany in 2011 (Navarro-Garcia 2015) and the O80:H2 serotype reported in France and in some neighbouring and other countries since 2011 (Soysal et al 2016;Fierz et al 2017;Wijnsma et al 2017;Ingelbeen et al 2018;N€ uesch-Inderbinen et al 2018;Patel et al 2018;De Rauw et al 2019;Lang et al 2019). In France, the EHEC O80:H2 were the second-leading cause of HUS in children in 2014 (Soysal et al 2016) and represents 30% of the HUS cases between 2013 and 2016 (Ingelbeen et al 2018).…”

Is Shiga Toxin-Producing Escherichia coli O45 No Longer a Food Safety Threat? The Danger is Still Out There

“…Two reference E. coli O45:H2 strains (FWSEC0003 and 2011C-4251) were obtained from the NCBI database to facilitate the genomic analyses of virulence and antibiotic resistance genes of STEC O45 strains. E. coli clinical O45:H2 (FWSEC0003) was previously isolated from human feces in Canada [35], and the E. coli O45:H2 strain (2011C-4251) was isolated from samples of human feces obtained in the United States [36]. The virulence gene profiles of six strains (four experimental strains and two reference strains) were obtained using VirulenceFinder 2.0 [37].…”