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

Abdalhamid, Baha; McCutchen, Emily; Bouska, Alyssa; Zhang, Weiwei; Loeck, Brianna K.D.; Hinrichs, Steven H.; Iwen, Peter C.

doi:10.1016/j.jiph.2019.06.008

Cited by 13 publications

(9 citation statements)

References 30 publications

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“…Internationally, several studies have revealed a broad diversity of genomic patterns among STEC strains [32,47,[71][72][73]. As far as we know, the present study is the first to analyze genomic patterns of STEC strains circulating in South America.…”

Section: Discussionmentioning

confidence: 82%

Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America

Galarce

Sánchez

Escobar

et al. 2021

Animals

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Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens responsible for causing food-borne diseases in humans. While South America has the highest incidence of human STEC infections, information about the genomic characteristics of the circulating strains is scarce. The aim of this study was to analyze genomic data of STEC strains isolated in South America from cattle, beef, and humans; predicting the antibiotic resistome, serotypes, sequence types (STs), clonal complexes (CCs) and phylogenomic backgrounds. A total of 130 whole genome sequences of STEC strains were analyzed, where 39.2% were isolated from cattle, 36.9% from beef, and 23.8% from humans. The ST11 was the most predicted (20.8%) and included O-:H7 (10.8%) and O157:H7 (10%) serotypes. The successful expansion of non-O157 clones such as ST16/CC29-O111:H8 and ST21/CC29-O26:H11 is highlighted, suggesting multilateral trade and travel. Virulome analyses showed that the predominant stx subtype was stx2a (54.6%); most strains carried ehaA (96.2%), iha (91.5%) and lpfA (77.7%) genes. We present genomic data that can be used to support the surveillance of STEC strains circulating at the livestock-food-human interface in South America, in order to control the spread of critical clones “from farm to table”.

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Section: Discussionmentioning

confidence: 82%

Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America

Galarce

Sánchez

Escobar

et al. 2021

Animals

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“…Plasmids, bacteriophages, transposons, pathogenicity islands, insertion sequences (mobile genetic elements-MGEs) plays important roles in the genomic plasticity of E. coli [15]. Whole genome sequencing is considered the gold standard technique which can accurately serotype strains and evaluate relatedness among isolates based on differences in gene content or allelic variation [16][17][18][19]. This technique revealed that E. coli presents a conserved core of genes (common to pathogenic and commensal strains as well) that acquired, by horizontal gene transfer, small cluster of genes and genomic islands associated with virulence [20].…”

Section: Introductionmentioning

confidence: 99%

Enteropathogenic Escherichia coli—A Summary of the Literature

Mare

Ciurea

Man

et al. 2021

Gastroenterology Insights

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Diarrheal disease is still a major public health concern, as it is still considered an important cause of death in children under five years of age. A few decades ago, the detection of enteropathogenic E. coli was made by detecting the O, H, and K antigens, mostly by agglutination. The recent protocols recommend the molecular methods for diagnosing EPEC, as they can distinguish between typical and atypical EPEC by identifying the presence/absence of specific virulence factors. EPEC are defined as diarrheagenic strains of E. coli that can produce attaching and effacing lesions on the intestinal epithelium while being incapable of producing Shiga toxins and heat-labile or heat-stable enterotoxins. The ability of these strains to produce attaching and effacing lesions enable them to cause localized lesions by attaching tightly to the surface of the intestinal epithelial cells, disrupting the surfaces of the cells, thus leading to the effacement of the microvilli. EPEC are classified on typical and atypical isolates, based on the presence or absence of E. coli adherence factor plasmids. All the EPEC strains are eae positive; typical EPEC strains are eae+, bfpA+, while atypical strains are eae+, bfpA−. No vaccines are currently available to prevent EPEC infections.

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“…Pulsed-field gel electrophoresis (PFGE) is still considered as the gold standard. However, development and access to the next-generation sequencing techniques have caused the analysis of differences in DNA, including whole-genome sequencing (WGS), to gain popularity [34][35][36] and it can be assumed that in the near future, these techniques will replace PFGE. Both these approaches (PFGE and sequencing), although guaranteed to obtain accurate and unequivocal results (especially in the case of sequencing), are expensive and time-consuming and their performance requires access to the specific equipment and the analysis of large sequences of DNA (whole genomes) remains an important bioinformatics challenge.…”

Section: Discussionmentioning

confidence: 99%

New Approaches for Escherichia coli Genotyping

et al. 2020

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Easy-to-perform, fast, and inexpensive methods of differentiation of Escherichia coli strains beyond the species level are highly required. Herein two new, original tools for genotyping of E. coli isolates are proposed. The first of the developed method, a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) test uses a highly variable fliC gene, encoding the H antigen as a molecular target. The designing of universal pair of primers and selection of the optimal restriction enzyme RsaI was preceded by in silico comparative analysis of the sequences of the genes coding for 53 different serotypes of H-antigen (E. coli flagellin). The target fragments of E. coli genomes for MLST method were selected on the basis of bioinformatics analysis of complete sequences of 16 genomes of E. coli. Initially, seven molecular targets were proposed (seven pairs of primers) and five of them were found useful for effective genotyping of E. coli strains. Both developed methods revealed high differentiation power, and a high genetic diversity of the strains tested was observed. Within the group of 71 strains tested, 29 and 47 clusters were revealed with fliC RFLP-PCR and MLST methods, respectively. Differentiation of the strains with the reference BOX-PCR method revealed 31 different genotypes. The in silico analysis revealed that the discriminatory power of the new MLST method is comparable to the Pasteur and Achtman schemes and is higher than the discriminatory power of the method developed by Clermont. From the epidemiology point of view, the outcomes of our investigation revealed that in most cases, the patients were infected with unique strains, probably from environmental sources. However, some strains isolated from different patients of the wards of pediatrics, internal medicine, and neurology were classified to the same genotype when the results of all three methods were taken into account. It could suggest that they were transferred between the patients.

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

Cited by 13 publications

References 30 publications

Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America

Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America

Enteropathogenic Escherichia coli—A Summary of the Literature

New Approaches for Escherichia coli Genotyping

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