Genome Sequences of 228 Shiga Toxin-Producing Escherichia coli Isolates and 12 Isolates Representing Other Diarrheagenic E. coli Pathotypes

Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition of a Shiga toxin-encoding gene. Targeted amplicon sequencing using next-generation sequencing technology of 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) and three SNPs differentiating Shiga toxin-positive (stx-positive) strains from Shiga toxin-negative (stx-negative) strains were used to infer the phylogenetic relationships of 178 E. coli O26:H11 strains (6 stx-positive strains and 172 stx-negative AEEC strains) from cattle feces to 7 publically available genomes of human clinical strains. The AEEC cattle strains displayed synonymous SNP genotypes with stx2-positive sequence type 29 (ST29) human O26:H11 strains, while stx1 ST21 human and cattle strains clustered separately, demonstrating the close phylogenetic relatedness of these Shiga toxin-negative AEEC cattle strains and human clinical strains. With the exception of seven stx-negative strains, five of which contained espK, three stx-related SNPs differentiated the STEC strains from non-STEC strains, supporting the hypothesis that these AEEC cattle strains could serve as a potential reservoir for new or existing pathogenic human strains. Our results support the idea that targeted amplicon sequencing for SNP genotyping expedites strain identification and genetic characterization of E. coli O26:H11, which is important for food safety and public health.

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“…JHGK00000000 ), 2009C-4826 (GenBank accession no. JHGI00000000 ), ( 44 ), and CFSAN001629 (GenBank accession no. AMXO00000000 ) ( 45 ).…”

Section: Methodsmentioning

confidence: 99%

Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique

Ison

Delannoy

Bugarel

et al. 2016

Appl Environ Microbiol

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“…It was reported that these isolates had identical PFGE band, but their differences were revealed by sequencing. Likewise, Trees et al [17] sequenced 240 isolates related to outbreaks from different sources by PFGE fingerprinting. As a result, whole genome sequencing of 228 isolates showed that they were Shiga toxin-producing E. coli, whereas other 12 isolates were non-Shiga toxin-producing diarrheagenic E. coli.…”

Section: Convergence Of E Coli Isolatesmentioning

confidence: 99%

Isolation and Characterization of <i>Escherichia coli</i> from Animals, Humans, and Environment

Lupindu¹

2017

≪i>Escherichia Coli

25
1
15
0

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Working on a diverse species of bacteria that have hundreds of pathotypes representing hundreds of strains and many closely related family members is a challenge. Appropriate research design is required not only to achieve valid desired outcome but also to minimize the use of resources, including time to outcome and intervention. This chapter outlines basics of Escherichia coli isolation and characterization strategies that can assist in research designing that matches the set objectives. Types of samples to be collected, collection and storage strategies, and processing of samples are described. Different approaches to isolation, confirmation and concentration of various E. coli strains are summarized in this chapter. Characterization and typing of E. coli isolates by biochemical, serological, and molecular methods have been explained so that an appropriate choice is made to suite a specific E. coli strain/pathotype. Some clues on sample and isolate preservation for future use are outlined, and general precautions regarding E. coli handling are also presented to the researcher to avoid improper planning and execution of E. coli-related research. Given different options, the best E. coli research design, however, should try as much as possible to shorten the length of time to outcomes.

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“…Of these, 249 were assembled genomes from the PulseNet STEC genome reference library, deposited by the Centers for Disease Control and Prevention (CDC), Atlanta, GA (accession no. PRJNA218110), and 130 were genome sequences included in a previous study on comparative genome analysis of E. coli (19,20). Four Shigella genomes were available and included from this study.…”

Section: Methodsmentioning
confidence: 99%

Rapid and EasyIn SilicoSerotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data
Joensen
¹
,
Tetzschner
²
,
Iguchi
³

et al. 2015
J Clin Microbiol
707
3
582
1
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c Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. Conventional serotyping of Escherichia coli is a delicate, laborious, time-consuming, and expensive procedure. With whole-genome sequencing (WGS) becoming cheaper, it has vast potential in routine typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-based in silico serotyping of E. coli applicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org). All E. coli isolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE tool. SerotypeFinder was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen genes wzx, wzy, wzm, and wzt and the flagellin genes fliC, flkA, fllA, flmA, and flnA were detected in 569 and 508 genome sequences, respectively. SerotypeFinder for WGS-based O and H typing predicted 560 of 569 O types and 504 of 508 H types, consistent with conventional serotyping. In combination with other available WGS typing tools, E. coli serotyping can be performed solely from WGS data, providing faster and cheaper typing than current routine procedures and making WGS typing a superior alternative to conventional typing strategies. Escherichia coli is usually a harmless commensal, but some strains have evolved the capability to cause disease in humans and/or animals by specific particular pathogenic mechanisms. In some cases, infection can be fatal (1).Serotyping is a method for classification of E. coli that has existed since the 1940s and has since been developed into standardized procedures (2-4). Performance of serotyping requires a high level of expertise and access to cross-absorbed antisera. It is a time-consuming and laborious procedure. O:K:H serotyping is based on a combination of the three immunogenic structures: the lipopolysaccharide (LPS) (O antigen), the capsular antigen (K), and the flagellar (H) antigen.Since few laboratories are able to perform K typing, O:H serotyping has become the gold standard for characterization of pathogenic E. coli. O:H serotyping is crucial in the detection of outbreaks, for epidemiological surveillance, for taxonomic differentiation of E. coli, for detecting pathogenic serotypes within the species, and for clonal and evolutionary studies. In contrast to several more recently developed molecular typing methods, such as pulsed-field gel electrophoresis (PFGE), ribotyping and to some extent multilocus sequence typing (MLST), serotyping provides information that is directly associated with the antigenic response an...

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Genome Sequences of 228 Shiga Toxin-Producing Escherichia coli Isolates and 12 Isolates Representing Other Diarrheagenic E. coli Pathotypes

Cited by 14 publications

References 2 publications

Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique

Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique

Isolation and Characterization of <i>Escherichia coli</i> from Animals, Humans, and Environment

Rapid and EasyIn SilicoSerotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

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