scholarly journals 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

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.

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

2020 ◽  
Vol 9 (45) ◽  
Author(s):  
Yujie Zhang ◽  
Yen-Te Liao ◽  
Vivian C. H. Wu
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Cattle Feces ◽  
Beef Products ◽  
Foodborne Outbreaks ◽  
Enterocyte Effacement

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.

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

2018 ◽  
Vol 6 (27) ◽  
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.

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

2017 ◽  
Vol 5 (44) ◽  
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.

scholarly journals 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

2020 ◽  
Vol 9 (12) ◽  
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.

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

2019 ◽  
Vol 57 (10) ◽  
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.

scholarly journals Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity

2017 ◽  
Vol 5 (50) ◽  
Author(s):  
Jayanthi Gangiredla ◽  
Mark K. Mammel ◽  
Tammy J. Barnaba ◽  
Carmen Tartera ◽  
Solomon T. Gebru ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Human Health ◽  
Potential Risk ◽  
Phylogenetic Relationships ◽  
Genomic Diversity ◽  
Genome Sequences ◽  
Content Type ◽  
E Coli

ABSTRACT Pathogenic and nonpathogenic Escherichia coli strains present a vast genomic diversity. We report the genome sequences of 2,244 E. coli isolates from multiple animal and environmental sources. Their phylogenetic relationships and potential risk to human health were examined.

scholarly journals Cytotoxic and Apoptotic Effects of Recombinant Subtilase Cytotoxin Variants of Shiga Toxin-Producing Escherichia coli

2015 ◽  
Vol 83 (6) ◽  
pp. 2338-2349 ◽  
Author(s):  
J. Funk ◽  
N. Biber ◽  
M. Schneider ◽  
E. Hauser ◽  
S. Enzenmüller ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Vero Cells ◽  
Toxic Activity ◽  
Content Type ◽  
B Subunits ◽  
Induced Apoptosis ◽  
The Individual ◽  
Apoptotic Effects ◽  
Subtilase Cytotoxin

In this study, the cytotoxicity of the recently described subtilase variant SubAB2-2of Shiga toxin-producingEscherichia coliwas determined and compared to the plasmid-encoded SubAB1and the chromosome-encoded SubAB2-1variant. The genes for the respective enzymatic active (A) subunits and binding (B) subunits of the subtilase toxins were amplified and cloned. The recombinant toxin subunits were expressed and purified. Their cytotoxicity on Vero cells was measured for the single A and B subunits, as well as for mixtures of both, to analyze whether hybrids with toxic activity can be identified. The results demonstrated that all three SubAB variants are toxic for Vero cells. However, the values for the 50% cytotoxic dose (CD50) differ for the individual variants. Highest cytotoxicity was shown for SubAB1. Moreover, hybrids of subunits from different subtilase toxins can be obtained which cause substantial cytotoxicity to Vero cells after mixing the A and B subunits prior to application to the cells, which is characteristic for binary toxins. Furthermore, higher concentrations of the enzymatic subunit SubA1exhibited cytotoxic effects in the absence of the respective B1subunit. A more detailed investigation in the human HeLa cell line revealed that SubA1alone induced apoptosis, while the B1subunit alone did not induce cell death.

scholarly journals Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs

2021 ◽  
Author(s):  
Timothy J. Dallman ◽  
David R. Greig ◽  
Saheer E. Gharbia ◽  
Claire Jenkins
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Sequence Similarity ◽  
Evidence Base ◽  
Point Sources ◽  
Single Linkage ◽  
Phylogenetic Structure ◽  
Content Type ◽  
Geographically Dispersed ◽  
Cluster Threshold

Sequence similarity of pathogen genomes can infer the relatedness between isolates as the fewer genetic differences identified between pairs of isolates, the less time since divergence from a common ancestor. Clustering based on hierarchical single linkage clustering of pairwise SNP distances has been employed to detect and investigate outbreaks. Here, we evaluated the evidence-base for the interpretation of phylogenetic clusters of Shiga toxin-producing Escherichia coli (STEC) O157:H7. Whole genome sequences of 1193 isolates of STEC O157:H7 submitted to Public Health England between July 2015 and December 2016 were mapped to the Sakai reference strain. Hierarchical single linkage clustering was performed on the pairwise SNP difference between all isolates at descending distance thresholds. Cases with known epidemiological links fell within 5-SNP single linkage clusters. Five-SNP single linkage community clusters where an epidemiological link was not identified were more likely to be temporally and/or geographically related than sporadic cases. Ten-SNP single linkage clusters occurred infrequently and were challenging to investigate as cases were few, and temporally and/or geographically dispersed. A single linkage cluster threshold of 5-SNPs has utility for the detection of outbreaks linked to both persistent and point sources. Deeper phylogenetic analysis revealed that the distinction between domestic UK and imported isolates could be inferred at the sub-lineage level. Cases associated with domestically acquired infection that fall within clusters that are predominantly travel associated are likely to be caused by contaminated imported food.

scholarly journals Antibiotic-Mediated Modulations of Outer Membrane Vesicles in Enterohemorrhagic Escherichia coli O104:H4 and O157:H7

2017 ◽  
Vol 61 (9) ◽  
Author(s):  
Andreas Bauwens ◽  
Lisa Kunsmann ◽  
Helge Karch ◽  
Alexander Mellmann ◽  
Martina Bielaszewska
Keyword(s):  
Escherichia Coli ◽  
Outer Membrane ◽  
Shiga Toxin ◽  
Membrane Vesicles ◽  
Polymyxin B ◽  
Outer Membrane Vesicles ◽  
Enterohemorrhagic Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Major Virulence Factor

ABSTRACT Ciprofloxacin, meropenem, fosfomycin, and polymyxin B strongly increase production of outer membrane vesicles (OMVs) in Escherichia coli O104:H4 and O157:H7. Ciprofloxacin also upregulates OMV-associated Shiga toxin 2a, the major virulence factor of these pathogens, whereas the other antibiotics increase OMV production without the toxin. These two effects might worsen the clinical outcome of infections caused by Shiga toxin-producing E. coli. Our data support the existing recommendations to avoid antibiotics for treatment of these infections.

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

2018 ◽  
Vol 6 (10) ◽  
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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