Whole-Genome Analysis of a Shiga Toxin-Producing Escherichia coli O103:H2 Strain Isolated from Cattle Feces

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) serotype O103 is one of the primary pathogenic contaminants of beef products, contributing to several foodborne outbreaks in recent years. Here, we report the whole-genome sequence of a STEC O103:H2 strain isolated from cattle feces that contains a locus of enterocyte effacement (LEE) pathogenicity island.

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Investigating the Whole-Genome Sequence of a New Locus of Enterocyte Effacement-Positive Shiga Toxin-Producing Escherichia coli O157:H7 Strain Isolated from River Water

Microbiology Resource Announcements ◽

10.1128/mra.00112-20 ◽

2020 ◽

Vol 9 (12) ◽

Cited By ~ 1

Author(s):

Yujie Zhang ◽

Yen-Te Liao ◽

Alexandra Salvador ◽

Xiaohong Sun ◽

Vivian C. H. Wu

Keyword(s):

Escherichia Coli ◽

Genome Sequence ◽

Mississippi River ◽

Shiga Toxin ◽

Environmental Samples ◽

Whole Genome Sequence ◽

Whole Genome ◽

Escherichia Coli O157 ◽

Content Type ◽

Enterocyte Effacement

Diverse Shiga toxin-producing Escherichia coli (STEC) strains have been isolated from several environmental samples. Rivers are associated with the distribution of STEC pathogens in the environment. Thus, we report the complete genome sequence of a locus of enterocyte effacement (LEE)-positive STEC O157:H7 strain isolated from the Mississippi River.

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Complete Genome Sequence of Escherichia coli Phage vB_EcoS Sa179lw, Isolated from Surface Water in a Produce-Growing Area in Northern California

Genome Announcements ◽

10.1128/genomea.00337-18 ◽

2018 ◽

Vol 6 (27) ◽

Cited By ~ 2

Author(s):

Yen-Te Liao ◽

Fang Liu ◽

Xincheng Sun ◽

Robert W. Li ◽

Vivian C. H. Wu

Keyword(s):

Escherichia Coli ◽

Surface Water ◽

Genome Sequence ◽

Shiga Toxin ◽

Virulence Gene ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

E Coli ◽

Escherichia Coli Phage

We report here the whole-genome sequence of a novel Escherichia coli phage, vB_EcoS Sa179lw, isolated from surface water collected in a produce-growing area. With the presence of a putative eae-like gene that was associated with previous non-O157 Shiga toxin-producing E. coli outbreaks, this phage is a candidate for the study of virulence gene transfer.

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Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain B6914-ARS

Genome Announcements ◽

10.1128/genomea.01191-17 ◽

2017 ◽

Vol 5 (44) ◽

Cited By ~ 2

Author(s):

Gaylen A. Uhlich ◽

Erin R. Reichenberger ◽

Bryan J. Cottrell ◽

Pina Fratamico ◽

Elisa Andreozzi

Keyword(s):

Escherichia Coli ◽

Disease Control ◽

Genome Sequence ◽

Shiga Toxin ◽

Applied Research ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Control And Prevention ◽

Shiga Toxin Genes

ABSTRACT Escherichia coli serotype O157:H7 strain B6914-MS1 is an isolate from the Centers for Disease Control and Prevention that is missing both Shiga toxin genes and has been used extensively in applied research studies. Here we report the genome sequence of strain B6914-ARS, a B6914-MS1 clone that has unique biofilm properties.

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Whole-Genome-Based Public Health Surveillance of Less Common Shiga Toxin-Producing Escherichia coli Serovars and Untypeable Strains Identifies Four Novel O Genotypes

Journal of Clinical Microbiology ◽

10.1128/jcm.00768-19 ◽

2019 ◽

Vol 57 (10) ◽

Cited By ~ 5

Author(s):

Christina Lang ◽

Miriam Hiller ◽

Regina Konrad ◽

Angelika Fruth ◽

Antje Flieger

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Shiga Toxin ◽

Virulence Gene ◽

Whole Genome Sequence ◽

Complete Analysis ◽

Watery Diarrhea ◽

Whole Genome ◽

Content Type ◽

Gene Information

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) and the STEC subgroup enterohemorrhagic E. coli cause intestinal infections with symptoms ranging from watery diarrhea to hemolytic-uremic syndrome (HUS). A key tool for the epidemiological differentiation of STEC is serotyping. The serotype in combination with the main virulence determinants gives important insight into the virulence potential of a strain. However, a large fraction of STEC strains found in human disease, including strains causing HUS, belongs to less frequently detected STEC serovars or their O/H antigens are unknown or even untypeable. Recent implementation of whole-genome sequence (WGS) analysis, in principle, allows the deduction of serovar and virulence gene information. Therefore, here we compared classical serovar and PCR-based virulence marker detection with WGS-based methods for 232 STEC strains, focusing on less frequently detected STEC serovars and nontypeable strains. We found that the results of WGS-based extraction showed a very high degree of overlap with those of the more classical methods. Specifically, the rate of concordance was 97% for O antigens (OAGs) and 99% for H antigens (HAGs) of typeable strains and >99% for stx1, stx2, or eaeA for all strains. Ninety-eight percent of nontypeable OAGs and 100% of nontypeable HAGs were defined by WGS analysis. In addition, the novel methods enabled a more complete analysis of strains causing severe clinical symptoms and the description of four novel STEC OAG loci. In conclusion, WGS is a promising tool for gaining serovar and virulence gene information, especially from a public health perspective.

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Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5α

Genome Announcements ◽

10.1128/genomea.00097-18 ◽

2018 ◽

Vol 6 (10) ◽

Cited By ~ 4

Author(s):

Jingchao Chen ◽

Yi Li ◽

Kun Zhang ◽

Hailei Wang

Keyword(s):

Escherichia Coli ◽

Comparative Analysis ◽

Genome Sequence ◽

Resistant Strain ◽

Resistance Mechanism ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

E Coli ◽

T4 Bacteriophage

ABSTRACT The genomes of many strains of Escherichia coli have been sequenced, as this organism is a classic model bacterium. Here, we report the genome sequence of Escherichia coli DH5α, which is resistant to a T4 bacteriophage (CCTCC AB 2015375), while its other homologous E. coli strains, such as E. coli BL21, DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of the genome of the DH5α strain, along with comparative analysis of its genome sequence along with other sequences of E. coli strains, may help to reveal the bacteriophage resistance mechanism of E. coli .

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

Genome Announcements ◽

10.1128/genomea.00391-18 ◽

2018 ◽

Vol 6 (19) ◽

Cited By ~ 4

Author(s):

Pooja N. Patel ◽

Rebecca L. Lindsey ◽

Lisley Garcia-Toledo ◽

Lori A. Rowe ◽

Dhwani Batra ◽

...

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

Foodborne Pathogen ◽

Severe Illness ◽

Whole Genome ◽

Genome Sequences ◽

Pacbio Sequencing ◽

High Quality ◽

Content Type ◽

Sequencing Platform

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.

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Prevalence of Shiga Toxin–Producing Escherichia coli in Beef Cattle

Journal of Food Protection ◽

10.4315/0362-028x-68.10.2224 ◽

2005 ◽

Vol 68 (10) ◽

pp. 2224-2241 ◽

Cited By ~ 119

Author(s):

HUSSEIN S. HUSSEIN ◽

LAURIE M. BOLLINGER

Keyword(s):

Escherichia Coli ◽

Beef Cattle ◽

Hemolytic Uremic Syndrome ◽

Health Risks ◽

Shiga Toxin ◽

Beef Industry ◽

Potential Health ◽

Cattle Feces ◽

Beef Products ◽

Uremic Syndrome

A large number of Shiga toxin–producing Escherichia coli (STEC) strains have caused major outbreaks and sporadic cases of human illnesses, including mild diarrhea, bloody diarrhea, hemorrhagic colitis, and the life-threatening hemolytic uremic syndrome. These illnesses have been traced to both O157 and non-O157 STEC. In a large number of STEC-associated outbreaks, the infections were attributed to consumption of ground beef or other beef products contaminated with cattle feces. Thus, beef cattle are considered reservoirs of STEC and can pose significant health risks to humans. The global nature of the human food supply suggests that safety concerns with beef will continue and the challenges facing the beef industry will increase at the production and processing levels. To be prepared to address these concerns and challenges, it is critical to assess the role of beef cattle in human STEC infections. In this review, published reports on STEC in beef cattle were evaluated to achieve the following specific objectives: (i) assess the prevalence of STEC in beef cattle, and (ii) determine the potential health risks of STEC strains from beef cattle. The latter objective is critically important because many beef STEC isolates are highly virulent. Global testing of beef cattle feces revealed wide ranges of prevalence rates for O157 STEC (i.e., 0.2 to 27.8%) and non-O157 STEC (i.e., 2.1 to 70.1%). Of the 261 STEC serotypes found in beef cattle, 44 cause hemolytic uremic syndrome and 37 cause other illnesses.

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The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19

Microbial Genomics ◽

10.1099/mgen.0.000716 ◽

2021 ◽

Vol 7 (12) ◽

Author(s):

Ruriko Nishida ◽

Keiji Nakamura ◽

Itsuki Taniguchi ◽

Kazunori Murase ◽

Tadasuke Ooka ◽

...

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

Common Ancestor ◽

Detailed Comparison ◽

Genomic Diversity ◽

Whole Genome Sequence ◽

Genomic Features ◽

Content Type ◽

Complete Genomes ◽

The Common

Shiga toxin (Stx)-producing Escherichia coli (STEC) are foodborne pathogens causing serious diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Although O157:H7 STEC strains have been the most prevalent, incidences of STEC infections by several other serotypes have recently increased. O121:H19 STEC is one of these major non-O157 STECs, but systematic whole genome sequence (WGS) analyses have not yet been conducted on this STEC. Here, we performed a global WGS analysis of 638 O121:H19 strains, including 143 sequenced in this study, and a detailed comparison of 11 complete genomes, including four obtained in this study. By serotype-wide WGS analysis, we found that O121:H19 strains were divided into four lineages, including major and second major lineages (named L1 and L3, respectively), and that the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS) was acquired by the common ancestor of O121:H19. Analyses of 11 complete genomes belonging to L1 or L3 revealed remarkable interlineage differences in the prophage pool and prophage-encoded T3SS effector repertoire, independent acquisition of virulence plasmids by the two lineages, and high conservation in the prophage repertoire, including that for Stx2a phages in lineage L1. Further sequence determination of complete Stx2a phage genomes of 49 strains confirmed that Stx2a phages in lineage L1 are highly conserved short-tailed phages, while those in lineage L3 are long-tailed lambda-like phages with notable genomic diversity, suggesting that an Stx2a phage was acquired by the common ancestor of L1 and has been stably maintained. Consistent with these genomic features of Stx2a phages, most lineage L1 strains produced much higher levels of Stx2a than lineage L3 strains. Altogether, this study provides a global phylogenetic overview of O121:H19 STEC and shows the interlineage genomic differences and the highly conserved genomic features of the major lineage within this serotype of STEC.

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

Microorganisms ◽

10.3390/microorganisms8050782 ◽

2020 ◽

Vol 8 (5) ◽

pp. 782 ◽

Cited By ~ 1

Author(s):

Yujie Zhang ◽

Yen-Te Liao ◽

Xiaohong Sun ◽

Vivian C.H. Wu

Keyword(s):

Escherichia Coli ◽

Virulence Factors ◽

Shiga Toxin ◽

Evolutionary Relationship ◽

Severe Illness ◽

Next Generation Sequencing Technology ◽

E Coli ◽

Related Information ◽

Foodborne Outbreaks ◽

Enterocyte Effacement

Many Shiga toxin-producing Escherichia coli (STEC) strains, including the serogroups of O157 and most of the top six non-O157 serotypes, are frequently associated with foodborne outbreaks. Therefore, they have been extensively studied using next-generation sequencing technology. However, related information regarding STEC O45 strains is scarce. In this study, three environmental E. coli O45:H16 strains (RM11911, RM13745, and RM13752) and one clinical E. coli O45:H2 strain (SJ7) were sequenced and used to characterize virulence factors using two reference E. coli O45:H2 strains of clinical origin. Subsequently, whole-genome-based phylogenetic analysis was conducted for the six STEC O45 strains and nine other reference STEC genomes, in order to evaluate their evolutionary relationship. The results show that one locus of enterocyte effacement pathogenicity island was found in all three STEC O45:H2 strains, but not in the STEC O45:H16 strains. Additionally, E. coli O45:H2 strains were evolutionarily close to E. coli O103:H2 strains, sharing high homology in terms of virulence factors, such as Stx prophages, but were distinct from E. coli O45:H16 strains. The findings show that E. coli O45:H2 may be as virulent as E. coli O103:H2, which is frequently associated with severe illness and can provide genomic evidence to facilitate STEC surveillance.

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