Genome sequencing and comparative genomics provides insights on the evolutionary dynamics and pathogenic potential of different H-serotypes of Shiga toxin-producing Escherichia coli O104

Serogroup classifications based upon the O-somatic antigen of Shiga toxin-producing Escherichia coli (STEC) provide significant epidemiological information on clinical isolates. Each O-antigen determinant is encoded by a unique cluster of genes present between the gnd and galF chromosomal genes. Alternatively, serogroup-specific polymorphisms might be encoded in loci that are encoded outside of the O-antigen gene cluster. Segments of the core bacterial loci mdh, gnd, gcl, ppk, metA, ftsZ, relA and metG for 30 O26 STEC strains have previously been sequenced, and comparative analyses to O157 distinguished these two serogroups. To screen these loci for serogroup-specific traits within a broader range of clinically significant serogroups, DNA sequences were obtained for 19 strains of 10 additional STEC serogroups. Unique alleles were observed at the gnd locus for each examined STEC serogroup, and this correlation persisted when comparative analyses were extended to 144 gnd sequences from 26 O-serogroups (comprising 42 O : H-serotypes). These included O157, O121, O103, O26, O5 : non-motile (NM), O145 : NM, O113 : H21, O111 : NM and O117 : H7 STEC; and furthermore, non-toxin encoding O157, O26, O55, O6 and O117 strains encoded distinct gnd alleles compared to STEC strains of the same serogroup. DNA sequencing of a 643 bp region of gnd was, therefore, sufficient to minimally determine the O-antigen of STEC through molecular means, and the location of gnd next to the O-antigen gene cluster offered additional support for the co-inheritance of these determinants. The gnd DNA sequence-based serogrouping method could improve the typing capabilities for STEC in clinical laboratories, and was used successfully to characterize O121 : H19, O26 : H11 and O177 : NM clinical isolates prior to serological confirmation during outbreak investigations.

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Whole genome sequencing to characterize shiga toxin-producing Escherichia coli O26 in a public health setting

Journal of Infection and Public Health ◽

10.1016/j.jiph.2019.06.008 ◽

2019 ◽

Vol 12 (6) ◽

pp. 884-889 ◽

Cited By ~ 4

Author(s):

Baha Abdalhamid ◽

Emily L. Mccutchen ◽

Alyssa C. Bouska ◽

Zhang Weiwei ◽

Brianna Loeck ◽

...

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Whole Genome ◽

Public Health Setting

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Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina: TABLE 1

Genome Announcements ◽

10.1128/genomea.01341-16 ◽

2016 ◽

Vol 4 (6) ◽

Cited By ~ 1

Author(s):

Claudia Carolina Carbonari ◽

Nahuel Fittipaldi ◽

Sarah Teatero ◽

Taryn B. T. Athey ◽

Luis Pianciola ◽

...

Keyword(s):

Escherichia Coli ◽

Molecular Epidemiology ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Whole Genome ◽

Escherichia Coli O157 ◽

Genome Sequences ◽

High Quality ◽

Human Infections

Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.

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Pathogenic potential of Shiga toxin-producing Escherichia coli strains of caprine origin: virulence genes, Shiga toxin subtypes, phylogenetic background and clonal relatedness

BMC Veterinary Research ◽

10.1186/s12917-018-1407-2 ◽

2018 ◽

Vol 14 (1) ◽

Cited By ~ 7

Author(s):

Maziar Jajarmi ◽

Mahdi Askari Badouei ◽

Abbas Ali Imani Fooladi ◽

Reza Ghanbarpour ◽

Ali Ahmadi

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

Virulence Genes ◽

Pathogenic Potential ◽

Clonal Relatedness

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Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana

Genes ◽

10.3390/genes11121504 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1504

Author(s):

Frederick Adzitey ◽

Jonathan Asante ◽

Hezekiel M. Kumalo ◽

Rene B. Khan ◽

Anou M. Somboro ◽

...

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Response Factors ◽

Pathogenic Potential ◽

E Coli ◽

Relationship Of ◽

Sequence Types

Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.

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Genome Signatures of Escherichia coli O157:H7 Isolates from the Bovine Host Reservoir

Applied and Environmental Microbiology ◽

10.1128/aem.02554-10 ◽

2011 ◽

Vol 77 (9) ◽

pp. 2916-2925 ◽

Cited By ~ 27

Author(s):

Mark Eppinger ◽

Mark K. Mammel ◽

Joseph E. LeClerc ◽

Jacques Ravel ◽

Thomas A. Cebula

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

Phylogenomic Analysis ◽

Genotypic Differences ◽

Pathogenic Potential ◽

Content Type ◽

E Coli ◽

A Genome ◽

Major Interest ◽

Host Reservoir

ABSTRACTCattle comprise a main reservoir of Shiga toxin-producingEscherichia coliO157:H7 (STEC). The significant differences in host prevalence, transmissibility, and virulence phenotypes among strains from bovine and human sources are of major interest to the public health community and livestock industry. Genomic analysis revealed divergence into three lineages: lineage I and lineage I/II strains are commonly associated with human disease, while lineage II strains are overrepresented in the asymptomatic bovine host reservoir. Growing evidence suggests that genotypic differences between these lineages, such as polymorphisms in Shiga toxin subtypes and synergistically acting virulence factors, are correlated with phenotypic differences in virulence, host ecology, and epidemiology. To assess the genomic plasticity on a genome-wide scale, we have sequenced the whole genome of strain EC869, a bovine-associatedE. coliO157:H7 isolate. Comparative phylogenomic analysis of this key isolate enabled us to place accurately bovine lineage II strains within the genetically homogenousE. coliO157:H7 clade. Identification of polymorphic loci that are anchored both in the chromosomal backbone and horizontally acquired regions allowed us to associate bovine genotypes with altered virulence phenotypes and host prevalence. This study catalogued numerous novel lineage II-specific genome signatures, some of which appear to be associated intimately with the altered pathogenic potential and niche adaptation within the bovine rumen. The presented extended list of polymorphic markers is valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies of this emerging human pathogen.

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