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Lee W, Ha J, Choi J, Jung Y, Kim E, An ES, Kim SH, Shin H, Ryu S, Kim SH, Kim HY. Genetic and virulence characteristics of hybrid Shiga toxin-producing and atypical enteropathogenic Escherichia coli strains isolated in South Korea. Front Microbiol 2024; 15:1398262. [PMID: 38812694 PMCID: PMC11133561 DOI: 10.3389/fmicb.2024.1398262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction The predominant hybrid pathogenic E. coli, enterohemorrhagic E. coli (EHEC), combines characteristics of Shiga toxin-producing E. coli (STEC) and enteropathogenic E. coli (EPEC), contributing to global outbreaks with severe symptoms including fatal consequences. Since EHEC infection was designated as a notifiable disease in 2000 in South Korea, around 2000 cases have been reported, averaging approximately 90 cases annually. Aim In this work, genome-based characteristic analysis and cell-based assay of hybrid STEC/aEPEC strains isolated from livestock feces, animal source foods, and water in South Korea was performed. Methods To identify the virulence and antimicrobial resistance genes, determining the phylogenetic position of hybrid STEC/aEPEC strains isolated in South Korea, a combination of real-time PCR and whole-genome sequencing (WGS) was used. Additionally, to assess the virulence of the hybrid strains and compare them with genomic characterization, we performed a cell cytotoxicity and invasion assays. Results The hybrid STEC/aEPEC strains harbored stx and eae genes, encoding Shiga toxins and E. coli attachment/effacement related protein of STEC and EPEC, respectively. Furthermore, all hybrid strains harbored plasmid-carried enterohemolysin(ehxCABD), a key virulence factor in prevalent pathogenic E. coli infections, such as diarrheal disease and hemolytic-uremic syndrome (HUS). Genome-wide phylogenetic analysis revealed a close association between all hybrid strains and specific EPEC strains, suggesting the potential acquisition of Stx phages during STEC/aEPEC hybrid formation. Some hybrid strains showed cytotoxic activity against HeLa cells and invasive properties against epithelial cells. Notably, all STEC/aEPEC hybrids with sequence type (ST) 1,034 (n = 11) exhibited higher invasiveness than those with E2348/69. This highlights the importance of investigating potential correlations between STs and virulence characteristics of E. coli hybrid strains. Conclusion Through genome-based characterization, we confirmed that the hybrid STEC/aEPEC strains are likely EPEC strains that have acquired STEC virulence genes via phage. Furthermore, our results emphasize the potential increased danger to humans posed by hybrid STEC/aEPEC strains isolated in South Korea, containing both stx and eaeA, compared to STEC or EPEC alone.
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Jina Ha
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Jaehyun Choi
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Yewon Jung
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Eun Sook An
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Hakdong Shin
- Department of Biotechnology, and Carbohydrate Bioproduct Research Center, Sejong University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea
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Qiu L, Chirman D, Clark JR, Xing Y, Hernandez Santos H, Vaughan EE, Maresso AW. Vaccines against extraintestinal pathogenic Escherichia coli (ExPEC): progress and challenges. Gut Microbes 2024; 16:2359691. [PMID: 38825856 PMCID: PMC11152113 DOI: 10.1080/19490976.2024.2359691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024] Open
Abstract
The emergence of antimicrobial resistance (AMR) is a principal global health crisis projected to cause 10 million deaths annually worldwide by 2050. While the Gram-negative bacteria Escherichia coli is commonly found as a commensal microbe in the human gut, some strains are dangerously pathogenic, contributing to the highest AMR-associated mortality. Strains of E. coli that can translocate from the gastrointestinal tract to distal sites, called extraintestinal E. coli (ExPEC), are particularly problematic and predominantly afflict women, the elderly, and immunocompromised populations. Despite nearly 40 years of clinical trials, there is still no vaccine against ExPEC. One reason for this is the remarkable diversity in the ExPEC pangenome across pathotypes, clades, and strains, with hundreds of genes associated with pathogenesis including toxins, adhesins, and nutrient acquisition systems. Further, ExPEC is intimately associated with human mucosal surfaces and has evolved creative strategies to avoid the immune system. This review summarizes previous and ongoing preclinical and clinical ExPEC vaccine research efforts to help identify key gaps in knowledge and remaining challenges.
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Affiliation(s)
- Ling Qiu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Dylan Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Haroldo Hernandez Santos
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Ellen E. Vaughan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
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Zhou B, Szymanski CM, Baylink A. Bacterial chemotaxis in human diseases. Trends Microbiol 2023; 31:453-467. [PMID: 36411201 PMCID: PMC11238666 DOI: 10.1016/j.tim.2022.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/21/2022]
Abstract
To infect and cause disease, bacterial pathogens must localize to specific regions of the host where they possess the metabolic and defensive acumen for survival. Motile flagellated pathogens exercise control over their localization through chemotaxis to direct motility based on the landscape of exogenous nutrients, toxins, and molecular cues sensed within the host. Here, we review advances in understanding the roles chemotaxis plays in human diseases. Chemotaxis drives pathogen colonization to sites of inflammation and injury and mediates fitness advantages through accessing host-derived nutrients from damaged tissue. Injury tropism may worsen clinical outcomes through instigating chronic inflammation and subsequent cancer development. Inhibiting bacterial chemotactic systems could act synergistically with antibacterial medicines for more effective and specific eradication.
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Affiliation(s)
- Bibi Zhou
- University of Georgia, Department of Microbiology and Complex Carbohydrate Research Center, Athens, GA 30602, USA
| | - Christine M Szymanski
- University of Georgia, Department of Microbiology and Complex Carbohydrate Research Center, Athens, GA 30602, USA
| | - Arden Baylink
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, WA 99164, USA.
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Aditya A, Rahaman SO, Biswas D. Impact of Lactobacillus-originated metabolites on enterohemorrhagic E. coli in rumen fluid. FEMS Microbiol Ecol 2022; 98:6795928. [PMID: 36331030 DOI: 10.1093/femsec/fiac128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/17/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Rumen is one of the richest microbial ecosystems naturally harboring many zoonotic pathogens. Controlling the colonization of cattle originated zoonotic pathogens in rumen, particularly enterohemorrhagic Escherichia coli (EHEC), is critical in reducing foodborne enteric diseases in humans. In this study, we aimed to inhibit the growth of EHEC in a simulated rumen system with collected rumen fluids (RFs) using live probiotics, synbiotics, and their metabolites. EHEC inoculated RF was treated with live wild type Lactobacillus casei (LCwt), LCwt with 0.5% peanut flour (LCwt+PF), an engineered LC capable of overexpressing linoleate isomerase (LCCLA), and their metabolites collected in cell-free culture supernatants (CFCSwt, CFCSwt+PF, and CFCSCLA) at various time points. A growth stimulatory effect toward Lactobacillus spp. was exerted by all CFCS, while the EHEC was suppressed. Among other treatments only LCwt+PF reduced EHEC by 2.68 logs after 72 h. This observation was also supported by metataxonomic analysis. A reduction in Bacteroidetes and Proteobacteria while increase in Firmicutes was observed at 48 h by the presence of CFCSs as compared to the control. Our observation implies probiotic-originated metabolites modulate rumen microbiota positively which can be deployed to control the transmission of cattle-borne pathogens specifically EHEC.
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Affiliation(s)
- Arpita Aditya
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, United States
| | - Shaik O Rahaman
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, United States
| | - Debabrata Biswas
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, United States.,Biological Sciences Program, University of Maryland, College Park, MD 20742, United States.,Centre for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, United States
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5
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Gelalcha BD, Brown SM, Crocker HE, Agga GE, Kerro Dego O. Regulation Mechanisms of Virulence Genes in Enterohemorrhagic Escherichia coli. Foodborne Pathog Dis 2022; 19:598-612. [PMID: 35921067 DOI: 10.1089/fpd.2021.0103] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is one of the most common E. coli pathotypes reported to cause several outbreaks of foodborne illnesses. EHEC is a zoonotic pathogen, and ruminants, especially cattle, are considered important reservoirs for the most common EHEC serotype, E. coli O157:H7. Humans are infected indirectly through the consumption of food (milk, meat, leafy vegetables, and fruits) and water contaminated by animal feces or direct contact with carrier animals or humans. E. coli O157:H7 is one of the most frequently reported causes of foodborne illnesses in developed countries. It employs two essential virulence mechanisms to trigger damage to the host. These are the development of attaching and effacing (AE) phenotypes on the intestinal mucosa of the host and the production of Shiga toxin (Stx) that causes hemorrhagic colitis and hemolytic uremic syndrome. The AE phenotype is controlled by the pathogenicity island, the locus of enterocyte effacement (LEE). The induction of both AE and Stx is under strict and highly complex regulatory mechanisms. Thus, a good understanding of these mechanisms, major proteins expressed, and environmental cues involved in the regulation of the expression of the virulence genes is vital to finding a method to control the colonization of reservoir hosts, especially cattle, and disease development in humans. This review is a concise account of the current state of knowledge of virulence gene regulation in the LEE-positive EHEC.
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Affiliation(s)
- Benti D Gelalcha
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Selina M Brown
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Hannah E Crocker
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Getahun E Agga
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, United States Department of Agriculture, Bowling Green, Kentucky, USA
| | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
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Castro VS, Ortega Polo R, Figueiredo EEDS, Bumunange EW, McAllister T, King R, Conte-Junior CA, Stanford K. Inconsistent PCR detection of Shiga toxin-producing Escherichia coli: Insights from whole genome sequence analyses. PLoS One 2021; 16:e0257168. [PMID: 34478476 PMCID: PMC8415614 DOI: 10.1371/journal.pone.0257168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/25/2021] [Indexed: 01/10/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) have been linked to food-borne disease outbreaks. As PCR is routinely used to screen foods for STEC, it is important that factors leading to inconsistent detection of STEC by PCR are understood. This study used whole genome sequencing (WGS) to investigate causes of inconsistent PCR detection of stx1, stx2, and serogroup-specific genes. Fifty strains isolated from Alberta feedlot cattle from three different studies were selected with inconsistent or consistent detection of stx and serogroup by PCR. All isolates were initially classified as STEC by PCR. Sequencing was performed using Illumina MiSeq® with sample library by Nextera XT. Virtual PCRs were performed using Geneious and bacteriophage content was determined using PHASTER. Sequencing coverage ranged from 47 to 102x, averaging 74x, with sequences deposited in the NCBI database. Eleven strains were confirmed by WGS as STEC having complete stxA and stxB subunits. However, truncated stx fragments occurred in twenty-two other isolates, some having multiple stx fragments in the genome. Isolates with complete stx by WGS had consistent stx1 and stx2 detection by PCR, although one also having a stx2 fragment had inconsistent stx2 PCR. For all STEC and 18/39 non-STEC, serogroups determined by PCR agreed with those determined by WGS. An additional three WGS serotypes were inconclusive and two isolates were Citrobacter spp. Results demonstrate that stx fragments associated with stx-carrying bacteriophages in the E. coli genome may contribute to inconsistent detection of stx1 and stx2 by PCR. Fourteen isolates had integrated stx bacteriophage but lacked complete or fragmentary stx possibly due to partial bacteriophage excision after sub-cultivation or other unclear mechanisms. The majority of STEC isolates (7/11) did not have identifiable bacteriophage DNA in the contig(s) where stx was located, likely increasing the stability of stx in the bacterial genome and its detection by PCR.
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Affiliation(s)
- Vinicius Silva Castro
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Food and Nutrition, Federal University of Mato Grosso, Cuiaba, Brazil
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada
| | - Rodrigo Ortega Polo
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | | | | | - Tim McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Canada
| | - Robin King
- Alberta Agriculture and Forestry, Edmonton, Canada
| | | | - Kim Stanford
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada
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7
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Im H, Hwang SH, Kim BS, Choi SH. Pathogenic potential assessment of the Shiga toxin-producing Escherichia coli by a source attribution-considered machine learning model. Proc Natl Acad Sci U S A 2021; 118:e2018877118. [PMID: 33986113 PMCID: PMC8157976 DOI: 10.1073/pnas.2018877118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Instead of conventional serotyping and virulence gene combination methods, methods have been developed to evaluate the pathogenic potential of newly emerging pathogens. Among them, the machine learning (ML)-based method using whole-genome sequencing (WGS) data are getting attention because of the recent advances in ML algorithms and sequencing technologies. Here, we developed various ML models to predict the pathogenicity of Shiga toxin-producing Escherichia coli (STEC) isolates using their WGS data. The input dataset for the ML models was generated using distinct gene repertoires from positive (pathogenic) and negative (nonpathogenic) control groups in which each STEC isolate was designated based on the source attribution, the relative risk potential of the isolation sources. Among the various ML models examined, a model using the support vector machine (SVM) algorithm, the SVM model, discriminated between the two control groups most accurately. The SVM model successfully predicted the pathogenicity of the isolates from the major sources of STEC outbreaks, the isolates with the history of outbreaks, and the isolates that cannot be assessed by conventional methods. Furthermore, the SVM model effectively differentiated the pathogenic potentials of the isolates at a finer resolution. Permutation importance analyses of the input dataset further revealed the genes important for the estimation, proposing the genes potentially essential for the pathogenicity of STEC. Altogether, these results suggest that the SVM model is a more reliable and broadly applicable method to evaluate the pathogenic potential of STEC isolates compared with conventional methods.
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Affiliation(s)
- Hanhyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Center for Food Safety and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
| | - Seung-Ho Hwang
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Center for Food Safety and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
| | - Byoung Sik Kim
- Department of Food Science and Engineering, Ewha Womans University, 03760 Seoul, Republic of Korea
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea;
- Department of Agricultural Biotechnology and Center for Food Safety and Toxicology, Seoul National University, 08826 Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, 08826 Seoul, Republic of Korea
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García A, Fox JG. A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts. Comp Med 2021; 71:3-45. [PMID: 33419487 PMCID: PMC7898170 DOI: 10.30802/aalas-cm-20-000054] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/17/2020] [Accepted: 09/19/2020] [Indexed: 11/05/2022]
Abstract
E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.
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Key Words
- aa, aggregative adherence
- a/e, attaching and effacing
- aepec, atypical epec
- afa, afimbrial adhesin
- aida-i, adhesin involved in diffuse adherence
- aiec, adherent invasive e. coli
- apec, avian pathogenic e. coli
- atcc, american type culture collection
- bfp, bundle-forming pilus
- cd, crohn disease
- cdt, cytolethal distending toxin gene
- clb, colibactin
- cnf, cytotoxic necrotizing factor
- cs, coli surface (antigens)
- daec, diffusely adhering e. coli
- db, dutch belted
- eae, e. coli attaching and effacing gene
- eaec, enteroaggregative e. coli
- eaf, epec adherence factor (plasmid)
- eahec, entero-aggregative-hemorrhagic e. coli
- east-1, enteroaggregative e. coli heat-stable enterotoxin
- e. coli, escherichia coli
- ed, edema disease
- ehec, enterohemorrhagic e. coli
- eiec, enteroinvasive e. coli
- epec, enteropathogenic e. coli
- esbl, extended-spectrum β-lactamase
- esp, e. coli secreted protein
- etec, enterotoxigenic e. coli
- expec, extraintestinal pathogenic e. coli
- fyua, yersiniabactin receptor gene
- gi, gastrointestinal
- hly, hemolysin
- hus, hemolytic uremic syndrome
- ibd, inflammatory bowel disease
- la, localized adherence
- lee, locus of enterocyte effacement
- lpf, long polar fimbriae
- lt, heat-labile (enterotoxin)
- mlst, multilocus sequence typing
- ndm, new delhi metallo-β-lactamase
- nzw, new zealand white
- pap, pyelonephritis-associated pilus
- pks, polyketide synthase
- sfa, s fimbrial adhesin
- slt, shiga-like toxin
- st, heat-stable (enterotoxin)
- stec, stx-producing e. coli
- stx, shiga toxin
- tepec, typical epec
- upec, uropathogenic e. coli
- uti, urinary tract infection
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Affiliation(s)
- Alexis García
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts;,
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
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9
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Cytotoxic Escherichia coli strains encoding colibactin, cytotoxic necrotizing factor, and cytolethal distending toxin colonize laboratory common marmosets (Callithrix jacchus). Sci Rep 2021; 11:2309. [PMID: 33504843 PMCID: PMC7841143 DOI: 10.1038/s41598-020-80000-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/08/2020] [Indexed: 11/09/2022] Open
Abstract
Cyclomodulins are virulence factors that modulate cellular differentiation, apoptosis, and proliferation. These include colibactin (pks), cytotoxic necrotizing factor (cnf), and cytolethal distending toxin (cdt). Pathogenic pks+, cnf+, and cdt+ E. coli strains are associated with inflammatory bowel disease (IBD) and colorectal cancer in humans and animals. Captive marmosets are frequently afflicted with IBD-like disease, and its association with cyclomodulins is unknown. Cyclomodulin-encoding E. coli rectal isolates were characterized using PCR-based assays in healthy and clinically affected marmosets originating from three different captive sources. 139 E. coli isolates were cultured from 122 of 143 marmosets. The pks gene was detected in 56 isolates (40%), cnf in 47 isolates (34%), and cdt in 1 isolate (0.7%). The prevalences of pks+ and cnf+ E. coli isolates were significantly different between the three marmoset colonies. 98% of cyclomodulin-positive E. coli belonged to phylogenetic group B2. Representative isolates demonstrated cyclomodulin cytotoxicity, and serotyping and whole genome sequencing were consistent with pathogenic E. coli strains. However, the presence of pks+, cnf+, or cdt+ E. coli did not correlate with clinical gastrointestinal disease in marmosets. Cyclomodulin-encoding E. coli colonize laboratory common marmosets in a manner dependent on the source, potentially impacting reproducibility in marmoset models.
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Engelen F, Thiry D, Devleesschauwer B, Heyndrickx M, Mainil J, De Zutter L, Cox E. Pathogenic potential of Escherichia coli O157 and O26 isolated from young Belgian dairy calves by recto-anal mucosal swab culturing. J Appl Microbiol 2021; 131:964-972. [PMID: 33103320 DOI: 10.1111/jam.14909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/09/2020] [Accepted: 10/22/2020] [Indexed: 01/17/2023]
Abstract
AIMS The purpose of this study was to investigate the occurrence of Escherichia coli O157 and O26 on Belgian dairy cattle farms, the presence of virulence genes in the confirmed isolates and the association of E. coli O26 presence with calf diarrhoea. METHODS AND RESULTS In total, 233 recto-anal mucosal swabs (RAMS) were obtained from healthy and diarrheic dairy calves on three farms, each alternately visited three consecutive times. RAMS were analysed for presence of E. coli O157 and O26, and stx1, stx2 and eae virulence genes. Overall, 19% of RAMS tested positive for E. coli O157, while 31% tested positive for E. coli O26. The majority of isolates possessed both stx and eae, denoting a high pathogenic potential to humans. While both serogroups persisted at farm level, persistence within the same animal over time appeared to be relatively rare. Interestingly, E. coli O26 was already abundantly present at a younger age compared to E. coli O157. Calf diarrhoea could not be associated with presence of E. coli O26. CONCLUSIONS Young dairy calves are important on-farm reservoirs of potentially pathogenic E. coli O157 and O26. A role of E. coli O26 in calf diarrhoea could not be confirmed. SIGNIFICANCE AND IMPACT OF THE STUDY O157 and O26 are responsible for the majority of human STEC infections. Gaining more epidemiological information regarding their occurrence and persistence on cattle farms will contribute to a better understanding of STEC ecology and risk of human transmission.
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Affiliation(s)
- F Engelen
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University (UGent), Merelbeke, Belgium
| | - D Thiry
- Bacteriology, Department of Infectious Diseases, Institute for Fundamental and Applied Research in Animals and Health (FARAH) and Faculty of Veterinary Medicine, University of Liège (ULiège), Liège, Belgium
| | - B Devleesschauwer
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium.,Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - M Heyndrickx
- Unit Technology and Food, Institute for Agricultural and Fisheries Research (ILVO), Melle, Belgium
| | - J Mainil
- Bacteriology, Department of Infectious Diseases, Institute for Fundamental and Applied Research in Animals and Health (FARAH) and Faculty of Veterinary Medicine, University of Liège (ULiège), Liège, Belgium
| | - L De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - E Cox
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University (UGent), Merelbeke, Belgium
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Johanns VC, Epping L, Semmler T, Ghazisaeedi F, Lübke-Becker A, Pfeifer Y, Eichhorn I, Merle R, Bethe A, Walther B, Wieler LH. High-Zinc Supplementation of Weaned Piglets Affects Frequencies of Virulence and Bacteriocin Associated Genes Among Intestinal Escherichia coli Populations. Front Vet Sci 2020; 7:614513. [PMID: 33392299 PMCID: PMC7772137 DOI: 10.3389/fvets.2020.614513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/20/2020] [Indexed: 12/22/2022] Open
Abstract
To prevent economic losses due to post-weaning diarrhea (PWD) in industrial pig production, zinc (Zn) feed additives have been widely used, especially since awareness has risen that the regular application of antibiotics promotes buildup of antimicrobial resistance in both commensal and pathogenic bacteria. In a previous study on 179 Escherichia coli collected from piglets sacrificed at the end of a Zn feeding trial, including isolates obtained from animals of a high-zinc fed group (HZG) and a corresponding control group (CG), we found that the isolate collection exhibited three different levels of tolerance toward zinc, i.e., the minimal inhibitory concentration (MIC) detected was 128, followed by 256 and 512 μg/ml ZnCl2. We further provided evidence that enhanced zinc tolerance in porcine intestinal E. coli populations is clearly linked to excessive zinc feeding. Here we provide insights about the genomic make-up and phylogenetic background of these 179 E. coli genomes. Bayesian analysis of the population structure (BAPS) revealed a lack of association between the actual zinc tolerance level and a particular phylogenetic E. coli cluster or even branch for both, isolates belonging to the HZG and CG. In addition, detection rates for genes and operons associated with virulence (VAG) and bacteriocins (BAG) were lower in isolates originating from the HZG (41 vs. 65% and 22 vs. 35%, p < 0.001 and p = 0.002, resp.). Strikingly, E. coli harboring genes defining distinct pathotypes associated with intestinal disease, i.e., enterotoxigenic, enteropathogenic, and Shiga toxin-producing E. coli (ETEC, EPEC, and STEC) constituted 1% of the isolates belonging to the HZG but 14% of those from the CG. Notably, these pathotypes were positively associated with enhanced zinc tolerance (512 μg/ml ZnCl2 MIC, p < 0.001). Taken together, zinc excess seems to influence carriage rates of VAGs and BAGs in porcine intestinal E. coli populations, and high-zinc feeding is negatively correlated with enteral pathotype occurrences, which might explain earlier observations concerning the relative increase of Enterobacterales considering the overall intestinal microbiota of piglets during zinc feeding trials while PWD rates have decreased.
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Affiliation(s)
- Vanessa C. Johanns
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Lennard Epping
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Fereshteh Ghazisaeedi
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Antina Lübke-Becker
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens and Antibiotic Resistance (FG13), Robert Koch Institute, Wernigerode, Germany
| | - Inga Eichhorn
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Roswitha Merle
- Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Astrid Bethe
- Center for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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13
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Santos ACDM, Santos FF, Silva RM, Gomes TAT. Diversity of Hybrid- and Hetero-Pathogenic Escherichia coli and Their Potential Implication in More Severe Diseases. Front Cell Infect Microbiol 2020; 10:339. [PMID: 32766163 PMCID: PMC7381148 DOI: 10.3389/fcimb.2020.00339] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022] Open
Abstract
Although extraintestinal pathogenic Escherichia coli (ExPEC) are designated by their isolation site and grouped based on the type of host and the disease they cause, most diarrheagenic E. coli (DEC) are subdivided into several pathotypes based on the presence of specific virulence traits directly related to disease development. This scenario of a well-categorized E. coli collapsed after the German outbreak of 2011, caused by one strain bearing the virulence factors of two different DEC pathotypes (enteroaggregative E. coli and Shiga toxin-producing E. coli). Since the outbreak, many studies have shown that this phenomenon is more frequent than previously realized. Therefore, the terms hybrid- and hetero-pathogenic E. coli have been coined to describe new combinations of virulence factors among the classic E. coli pathotypes. In this review, we provide an overview of these classifications and highlight the E. coli genomic plasticity that results in some mixed E. coli pathotypes displaying novel pathogenic strategies, which lead to a new symptomatology related to E. coli diseases. In addition, as the capacity for genome interrogation has grown in the last few years, it is clear that genes encoding some virulence factors, such as Shiga toxin, are found among different E. coli pathotypes to which they have not traditionally been associated, perhaps foreshowing their emergence in new and severe outbreaks caused by such hybrid strains. Therefore, further studies regarding hetero-pathogenic and hybrid-pathogenic E. coli isolates are necessary to better understand and control the spread of these pathogens.
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Affiliation(s)
- Ana Carolina de Mello Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosa Maria Silva
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia Aparecida Tardelli Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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14
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Blankenship HM, Mosci RE, Phan Q, Fontana J, Rudrik JT, Manning SD. Genetic Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Recovered From Patients in Michigan and Connecticut. Front Microbiol 2020; 11:529. [PMID: 32300338 PMCID: PMC7145412 DOI: 10.3389/fmicb.2020.00529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens and non-O157 serotypes have been gradually increasing in frequency. The non-O157 STEC population is diverse and is often characterized using serotyping and/or multilocus sequence typing (MLST). Although spacers within clustered regularly interspaced repeat (CRISPR) regions were shown to comprise horizontally acquired DNA elements, this region does not actively acquire spacers in STEC. Hence, it is useful for further characterizing non-O157 STEC and examining relationships between strains. Our study goal was to evaluate the genetic relatedness of 41 clinical non-O157 isolates identified in Michigan between 2001 and 2005 while comparing to 114 isolates from Connecticut during an overlapping time period. Whole genome sequencing (WGS) was performed, and sequences were extracted for serotyping, MLST and CRISPR analysis. Phylogenetic analysis of MLST and CRISPR data was performed using the Neighbor joining and unweighted pair group method with arithmetic mean (UPGMA) algorithms, respectively. In all, 29 serogroups were identified; eight were unique to Michigan and 13 to Connecticut. “Big-six” serogroup frequencies were similar by state (Michigan: 73.2%, Connecticut: 81.6%), though STEC O121 was not found in Michigan. The distribution of sequence types (STs) and CRISPR profiles was also similar across states. Interestingly, big-six serogroups such as O103 and O26, grouped into different STs located on distinct branches of the phylogeny, further confirming that serotyping alone is not adequate for evaluating strain relatedness. Comparatively, the CRISPR analysis identified 361 unique spacers that grouped into 80 different CRISPR profiles. CRISPR spacers 231 and 317 were isolated from 79.2% (n = 118) and 59.1% (n = 88) of strains, respectively, regardless of serogroup and ST. Spacer profiles clustered according to the MLST analysis, though some discrepancies were noted. Indeed, use of both MLST and CRISPR typing enhanced the discriminatory power when compared to the use of each tool separately. These data highlight the genetic diversity of clinical STEC from different locations and show that CRISPR profiling can be used alongside MLST to discriminate related strains. Use of targeted sequencing approaches are particularly helpful for sites without WGS capabilities and can help define which strains require additional characterization using more discriminatory methods.
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Affiliation(s)
- Heather M Blankenship
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Rebekah E Mosci
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Quyen Phan
- Connecticut Department of Public Health, Hartford, CT, United States
| | - John Fontana
- Connecticut Department of Public Health, Hartford, CT, United States
| | - James T Rudrik
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI, United States
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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15
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Kirchner M, Sayers E, Cawthraw S, Duggett N, Gosling R, Jenkins C, Dallman TJ, Mueller-Doblies D, Anjum MF. A sensitive method for the recovery of Escherichia coli serogroup O55 including Shiga toxin-producing variants for potential use in outbreaks. J Appl Microbiol 2019; 127:889-896. [PMID: 31183950 PMCID: PMC6852171 DOI: 10.1111/jam.14345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/16/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
Abstract
AIM Shiga toxin-producing Escherichia coli (STEC) cause bloody diarrhoea, kidney failure and occasionally death. However, identifying the source of infection caused by STEC other than serogroup O157 is hampered by the availability of sensitive methods for detecting these pathogens. In this study, we developed novel tools for detecting E. coli O55 that is potentially associated with human outbreaks. METHODS AND RESULTS Overall specificity of immuno-magnetic separation (IMS) beads coated with anti-O55 serum was good with exception of cross-reactivity with E. coli O22 and O23, which was eliminated using an O55-specific PCR. Limit of detection for E. coli O55 using O55-IMS beads in spiked cattle faeces was on average 50 CFU per ml (range 1-90), and improved to <10 CFU per ml using the O55-specific PCR, following IMS on samples enriched for 2 h with E. coli O55. Application of these tools to test cattle faeces collected on-farm allowed the isolation of O55:H19, which through whole genome sequencing was compared to STEC O55:H7 human outbreak strains. CONCLUSION These tools provide a sensitive method which could be used to screen samples for STEC O55, whether environmental or human clinical. SIGNIFICANCE AND IMPACT OF THE STUDY Several human outbreaks reported in England were caused by STEC O55:H7. Tools developed here could assist in identification of the environmental source for these isolates, which has not yet been established.
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Affiliation(s)
- M Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - E Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK.,University of East Anglia/Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - S Cawthraw
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - N Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - R Gosling
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | | | - D Mueller-Doblies
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - M F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, UK
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16
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Ghaffari Marandi BH, Zolfaghari MR, Kazemi R, Motamedi MJ, Amani J. Immunization against Vibrio cholerae, ETEC, and EHEC with chitosan nanoparticle containing LSC chimeric protein. Microb Pathog 2019; 134:103600. [PMID: 31202906 DOI: 10.1016/j.micpath.2019.103600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Severe intestinal infections caused by V. cholerae, ETEC and EHEC have contributed to the mortality rate in developing countries. Vibrio Cholera, ETEC and EHEC bacterium with the production of CT, LT and Stx2 toxins respectively lead to severe watery and bloody diarrhea. This study aimed to investigate a trimeric vaccine candidate containing recombinant chimeric protein, encapsulate the protein in chitosan nanoparticles and assess its immunogenicity. METHODS The LSC recombinant gene was used. It is composed of LTB (L), STXB (S) and CTXB (C) subunits respectively. The LSC recombinant protein was expressed and purified and confirmed by western blotting. The purified protein was encapsulated in chitosan nanoparticles, and its size was measured. BalB/c mice were immunized in four groups through oral and injection methods by LSC protein. The antibody titer was then evaluated by ELISA, and finally, the challenge test of the toxins from all three bacteria was done on the immunized mouse. RESULTS After expression and purification LSC protein size of nanoparticles containing protein was measured at 104.6 nm. Nanoparticles were able to induce systemic and mucosal immune responses by generating a useful titer of IgG and IgA. The challenge results with LT, CT and Stx toxins showed that the LSC protein might partially neutralize the effect of toxins. CONCLUSION LSC chimeric protein with the simultaneous three essential antigens have a protective effect against the toxins produced by ETEC, EHEC and Vibrio cholera bacteria and it can be used in vaccines to prevent Diarrhea caused by these three bacteria.
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Affiliation(s)
| | - Mohammad Reza Zolfaghari
- Department of Microbiology, Faculty of Basic Science, Qom Branch, Islamic Azad University, Qom, Iran
| | | | | | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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17
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Lee JB, Kim SK, Wi SM, Cho YJ, Hahn TW, Yu JY, Kim S, Hong S, Kim J, Yoon JW. Molecular epidemiology of sequence type 33 of Shiga toxin-producing Escherichia coli O91:H14 isolates from human patients and retail meats in Korea. J Vet Sci 2019; 20:87-90. [PMID: 30481987 PMCID: PMC6351770 DOI: 10.4142/jvs.2019.20.1.87] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/09/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
Sequence type (ST) 33 of Shiga toxin-producing Escherichia coli (STEC) strain O91:H14 has been proposed as a potential domestic clone of STEC in Korea because of its high prevalence among human patients with mild diarrhea or asymptomatic carriers. Herein, the clonal diversity of 17 STEC O91:H14 isolates of ST33 during 2003 to 2014 was analyzed by pulsed-field gel electrophoresis, including 14 isolates from human patients and 3 from retail meats. Their virulence characteristics, acid resistance, and antimicrobial susceptibility were also determined. Our results showed that all isolates were clustered mainly into three different pulsotypes and were likely low pathogenic without antimicrobial resistance.
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Affiliation(s)
- Jun Bong Lee
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
| | - Se-Kye Kim
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
| | - Seon Mi Wi
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
| | - Young-Jae Cho
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
| | - Tae-Wook Hahn
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
| | - Jae-Yon Yu
- Division of Bacterial Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28159, Korea
| | - Sungsun Kim
- Division of Bacterial Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28159, Korea
| | - Sahyun Hong
- Division of Bacterial Disease, Center for Laboratory Control of Infectious Diseases, Center for Disease Control and Prevention, Cheongju 28159, Korea
| | - Jonghyun Kim
- Division of Bacterial Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Centers for Disease Control and Prevention, Cheongju 28159, Korea
| | - Jang Won Yoon
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea
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Microevolution of epidemiological highly relevant non-O157 enterohemorrhagic Escherichia coli of serogroups O26 and O111. Int J Med Microbiol 2018; 308:1085-1095. [DOI: 10.1016/j.ijmm.2018.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/25/2018] [Accepted: 08/08/2018] [Indexed: 01/20/2023] Open
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19
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García-Meniño I, García V, Mora A, Díaz-Jiménez D, Flament-Simon SC, Alonso MP, Blanco JE, Blanco M, Blanco J. Swine Enteric Colibacillosis in Spain: Pathogenic Potential of mcr-1 ST10 and ST131 E. coli Isolates. Front Microbiol 2018; 9:2659. [PMID: 30455680 PMCID: PMC6230658 DOI: 10.3389/fmicb.2018.02659] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/18/2018] [Indexed: 12/25/2022] Open
Abstract
This is a wide epidemiological study of 499 E. coli isolates recovered from 179 outbreaks of enteric colibacillosis from pig production farms in Spain during a period of 10 years. Most samples were of diarrheagenic cases occurred during the post-wean period (PWD) which showed to be significantly associated with ETEC (67%) followed by aEPEC (21.7%). On the contrary, aEPEC was more prevalent (60.3%) among diarrheas of suckling piglets, followed by ETEC (38.8%). STEC/ETEC or STEC were recovered in 11.3 and 0.9% of PWD and neonatal diarrhea, respectively. Detection of the F4 colonization factor was not significantly different between isolates recovered from neonatal pigs and those recovered post wean (40.5 versus 27.7%) while F18 was only present among PWD isolates (51.5% of ETEC, STEC, and STEC/ETEC isolates). We also found a high prevalence of resistance to colistin related to the presence of the mcr-1 gene (25.6% of the diarreagenic isolates). The characterization of 65 representative mcr-1 isolates showed that all were phenotypically resistant to colistin (>2 μg/ml), and most (61 of 65) multidrug-resistant (MDR). Six ETEC and one STEC mcr-1 isolates were also carriers of ESBL genes. In addition, other seven mcr-1 isolates harbored mcr-4 (three ETEC) and mcr-5 (two ETEC and two aEPEC) genes. In the phylogenetic analysis of the 65 mcr-1 diarrheagenic isolates we found that more than 50% (38 out of 65) belonged to A-ST10 Cplx and from those, 29 isolates showed the clonotype CH11-24. In this study, we also recovered 18 ST131 isolates including seven mcr-1 carriers. To the best of our knowledge, this would be the first report of ST131 mcr-1 isolation in pigs. Worryingly, the swine mcr-1 ST131 carriers also showed MDR, including to trimethoprim-sulfamethoxazole, tobramycin, gentamicin and ciprofloxacin. In the PFGE-macrorestriction comparison of clinical swine and human ST131, we found high similarities (≥85%) between two pig and two human ST131 isolates of virotype D5. Acquisition of mcr-1 by this specific clone means an increased risk due to its special feature of congregating virulence and resistance traits, together with its spread capability. Here we show a potential zoonotic swine source of ST131.
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Affiliation(s)
- Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Saskia C Flament-Simon
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - María Pilar Alonso
- Unidad de Microbiología, Hospital Universitario Lucus Augusti (HULA), Lugo, Spain
| | - Jesús E Blanco
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Miguel Blanco
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
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Karmali MA. Factors in the emergence of serious human infections associated with highly pathogenic strains of shiga toxin-producing Escherichia coli. Int J Med Microbiol 2018; 308:1067-1072. [PMID: 30146439 DOI: 10.1016/j.ijmm.2018.08.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/29/2018] [Accepted: 08/17/2018] [Indexed: 10/28/2022] Open
Abstract
The appearance of highly pathogenic strains of Shiga toxin (Stx)-producingEscherichia. coli (STEC) has owed largely to the acquisition of Stx-encoding prophages by strains of E. coli that have pre-existing potential as enteric pathogens, such as atypical enteropathogenic E. coli (aEPEC) and enteroaggregative E. coli (EAEC). However, while high pathogenic potential is necessary, it is not sufficient for such strains to have a serious public health impact (i.e., large outbreaks, many cases of HUS, or both). To do so requires susceptible hosts and additional elements related to transmission, such as, socio-economic, societal, and lifestyle, factors. Two examples are discussed to illustrate this. The factors involved in the emergence of serious disease associated with E. coli O157:H7 in the 1980s probably included a massive increase in population exposure to this pathogen, likely as a result of the introduction of factory farming of cattle in the 1960s, and the development and wide patronage of fast food hamburger restaurants, and, potentially, waning immunity to intimin as a result of the reduction of incidence of enteropathogenic E. coli (EPEC) infection. In the devastating outbreak of Stx2-positiveEAEC O104:H4 in 2011, the wide distribution of the proposed vehicle of transmission, imported fenugreek seeds, was decisive in the exposure of a large population in Central Europe to this pathogen. Contributing factors likely included a preference for eating raw sprouts as a healthy food choice by the affected cases, many of whom were women. Low population levels of immunity to Stx2 probably contributed to the severe clinical outcome. A better understanding of the factors responsible for the emergence of potentially dangerous STEC pathogens as well as of extensive and serious disease associated with them can enhance public health strategies to respond to them.
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Affiliation(s)
- Mohamed A Karmali
- Public Health Consultant, 388 Princess Avenue, Toronto, M2N 3S9, Canada.
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21
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Li D, Shen M, Xu Y, Liu C, Wang W, Wu J, Luo X, Jia X, Ma Y. Virulence gene profiles and molecular genetic characteristics of diarrheagenic Escherichia coli from a hospital in western China. Gut Pathog 2018; 10:35. [PMID: 30127859 PMCID: PMC6097206 DOI: 10.1186/s13099-018-0262-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/09/2018] [Indexed: 02/05/2023] Open
Abstract
Background Diarrheagenic Escherichia coli (DEC) is one of the most important etiological agents of diarrheal diseases. In this study we investigated the prevalence, virulence gene profiles, antimicrobial resistance, and molecular genetic characteristics of DEC at a hospital in western China. Methods A total of 110 Escherichia coli clinical isolates were collected from the First Affiliated Hospital of Chengdu Medical College from 2015 to 2016. Microbiological methods, PCR, antimicrobial susceptibility test, pulsed-field gel electrophoresis and multilocus sequence typing were used in this study. Results Molecular analysis of six DEC pathotype marker genes showed that 13 of the 110 E. coli isolates (11.82%) were DEC including nine (8.18%) diffusely adherent Escherichia coli (DAEC) and four (3.64%) enteroaggregative Escherichia coli (EAEC). The adherence genes fimC and fimH were present in all DAEC and EAEC isolates. All nine DAEC isolates harbored the virulence genes fyuA and irp2 and four (44.44%) also carried the hlyA and sat genes. The virulence genes fyuA, irp2, cnf1, hlyA, and sat were found in 100%, 100%, 75%, 50%, and 50% of EAEC isolates, respectively. In addition, all DEC isolates were multidrug resistant and had high frequencies of antimicrobial resistance. Molecular genetic characterization showed that the 13 DEC isolates were divided into 11 pulsed-field gel electrophoresis patterns and 10 sequence types. Conclusions To the best of our knowledge, this study provides the first report of DEC, including DAEC and EAEC, in western China. Our analyses identified the virulence genes present in E. coli from a hospital indicating their role in the isolated DEC strains’ pathogenesis. At the same time, the analyses revealed, the antimicrobial resistance pattern of the DEC isolates. Thus, DAEC and EAEC among the DEC strains should be considered a significant risk to humans in western China due to their evolved pathogenicity and antimicrobial resistance pattern.
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Affiliation(s)
- Dan Li
- 1Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China.,2School of Medical Laboratory Science, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Min Shen
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Ying Xu
- 4Clinical Laboratory, The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Chao Liu
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Wen Wang
- 5West China School of Public Health, Sichuan University, Chengdu, 610041 Sichuan China
| | - Jinyan Wu
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Xianmei Luo
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Xu Jia
- 3Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500 Sichuan China
| | - Yongxin Ma
- 1Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan China
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Kinnula S, Hemminki K, Kotilainen H, Ruotsalainen E, Tarkka E, Salmenlinna S, Hallanvuo S, Leinonen E, Jukka O, Rimhanen-Finne R. Outbreak of multiple strains of non-O157 Shiga toxin-producing and enteropathogenic Escherichia coli associated with rocket salad, Finland, autumn 2016. Euro Surveill 2018; 23:1700666. [PMID: 30180926 PMCID: PMC6124187 DOI: 10.2807/1560-7917.es.2018.23.35.1700666] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
In August 2016, an outbreak of Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) with 237 cases occurred in the Helsinki metropolitan area, Finland. Gastroenteritis cases were reported at 11 events served by one catering company. Microbiological and epidemiological investigations suggested rocket salad as the cause of the outbreak. STEC ONT H11 and EPEC O111:H8 strains isolated from food samples containing rocket were identical to the patient isolates. In this outbreak, the reported symptoms were milder than considered before for STEC infection, and the guidelines for STEC control measures need to be updated based on the severity of the illness. Based on our experience in this outbreak, national surveillance criteria for STEC have been updated to meet the practice in reporting laboratories covering both PCR-positive and culture-confirmed findings. We suggest that EPEC could be added to the national surveillance since diagnostics for EPEC are routinely done in clinical laboratories.
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Affiliation(s)
- Sohvi Kinnula
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Kaisa Hemminki
- Environmental Health, Social and Health Services Espoo, Espoo, Finland
| | - Hannele Kotilainen
- City of Helsinki, Communicable Diseases, Epidemiology Unit, Social Services and Health Care Sector, Helsinki, Finland
| | - Eeva Ruotsalainen
- Division of Infectious Diseases, Inflammation Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Saara Salmenlinna
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Saija Hallanvuo
- Finnish Food Safety Authority Evira, Research and Laboratory Services Department, Microbiology Research Unit, Helsinki, Finland
| | - Elina Leinonen
- Finnish Food Safety Authority Evira, Food Safety Department, Microbiological Food Safety Unit, Helsinki, Finland
| | - Ollgren Jukka
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Ruska Rimhanen-Finne
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
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Variability in Characterizing Escherichia coli from Cattle Feces: A Cautionary Tale. Microorganisms 2018; 6:microorganisms6030074. [PMID: 30037096 PMCID: PMC6165469 DOI: 10.3390/microorganisms6030074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 11/17/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are diverse bacteria, with seven serogroups (O26, O45, O103, O111, O121, O145, O157; "Top 7") of interest due to their predominance in human disease. Confirmation of STEC relies on a combination of culturing, immunological and molecular assays, but no single gold standard for identification exists. In this study, we compared analysis of STEC between three independent laboratories (LAB) using different methodologies. In LAB A, colonies of Top 7 were picked after serogroup-specific immunomagnetic separation of feces from western-Canadian slaughter cattle. A fraction of each colony was tested by PCR (stx1, stx2, eae, O group), and Top 7 isolates were saved as glycerol stocks (n = 689). In LAB B, a subsample of isolates (n = 171) were evaluated for stx1 and stx2 using different primer sets. For this, approximately half of the PCR were performed using original DNA template provided by LAB A and half using DNA extracted from sub-cultured isolates. All Top 7 isolates were sub-cultured by LAB A and shipped to LAB C for traditional serotyping (TS) to determine O and H groups, with PCR-confirmation of virulence genes using a third set of primers. By TS, 76% of O groups (525/689) matched PCR-determined O groups. Lowest proportions (p < 0.05) of O group matches between PCR and TS (62.6% and 69.8%) occurred for O26 and O45 serogroups, respectively. PCR-detection of stx differed most between LAB A and LAB C. Excluding isolates where O groups by PCR and TS did not match, detection of stx1 was most consistent (p < 0.01) for O111 and O157:H7/NM. In contrast, for O45 and O103, stx1 was detected in >65% of isolates by LAB A and <5% by LAB C. Stx2 was only detected by LAB C in isolates of serogroups O121, O145, and O157:H7/NM. LAB B also detected stx2 in O26 and O157:H12/H29, while LAB A detected stx2 in all serogroups. Excluding O111 and O157:H7/NM, marked changes in stx detection were observed between initial isolation and sub-cultures of the same isolate. While multiple explanations exist for discordant O-typing between PCR and TS and for differences in stx detection across labs, these data suggest that assays for STEC classification may require re-evaluation and/or standardization.
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Eichhorn I, Heidemanns K, Ulrich RG, Schmidt H, Semmler T, Fruth A, Bethe A, Goulding D, Pickard D, Karch H, Wieler LH. Lysogenic conversion of atypical enteropathogenic Escherichia coli (aEPEC) from human, murine, and bovine origin with bacteriophage Φ3538 Δstx 2::cat proves their enterohemorrhagic E. coli (EHEC) progeny. Int J Med Microbiol 2018; 308:890-898. [PMID: 29937391 DOI: 10.1016/j.ijmm.2018.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/04/2018] [Accepted: 06/16/2018] [Indexed: 10/28/2022] Open
Abstract
Bacteriophages play an important role in the evolution of bacterial pathogens. A phage-mediated transfer of stx-genes to atypical enteropathogenic E. coli (aEPEC) which are prevalent in different hosts, would convert them to enterohemorrhagic E. coli (EHEC). We decided to confirm this hypothesis experimentally to provide conclusive evidence that aEPEC isolated from different mammalian hosts are indeed progenitors of typical EHEC which gain the ability to produce Shiga-Toxin by lysogeny with stx-converting bacteriophages, utilizing the model phage Φ3538 Δstx2::cat. We applied a modified in vitro plaque-assay, using a high titer of a bacteriophage carrying a deletion in the stx2 gene (Φ3538 Δstx2::cat) to increase the detection of lysogenic conversion events. Three wild-type aEPEC strains were chosen as acceptor strains: the murine aEPEC-strain IMT14505 (sequence type (ST)28, serotype Ont:H6), isolated from a striped field mouse (Apodemus agrarius) in the surrounding of a cattle shed, and the human aEPEC-strain 910#00 (ST28, Ont:H6). The close genomic relationship of both strains implies a high zoonotic potential. A third strain, the bovine aEPEC IMT19981, was of serotype O26:H11 and ST21 (STC29). All three aEPEC were successfully lysogenized with phage Φ3538 Δstx2::cat. Integration of the bacteriophage DNA into the aEPEC host genomes was confirmed by amplification of chloramphenicol transferase (cat) marker gene and by Southern-Blot hybridization. Analysis of the whole genome sequence of each of the three lysogens showed that the bacteriophage was integrated into the known tRNA integration site argW, which is highly variable among E. coli. In conclusion, the successful lysogenic conversion of aEPEC with a stx-phage in vitro underlines the important role of aEPEC as progenitors of EHEC. Given the high prevalence and the wide host range of aEPEC acceptors, their high risk of zoonotic transmission should be recognized in infection control measures.
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Affiliation(s)
- Inga Eichhorn
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Katrin Heidemanns
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, University of Hohenheim, Hohenheim, Germany
| | | | | | - Astrid Bethe
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - David Goulding
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Helge Karch
- Institute for Hygiene, University Münster, Münster, Germany
| | - Lothar H Wieler
- Institute for Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany; Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany.
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Krause M, Barth H, Schmidt H. Toxins of Locus of Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli. Toxins (Basel) 2018; 10:toxins10060241. [PMID: 29903982 PMCID: PMC6024878 DOI: 10.3390/toxins10060241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/07/2018] [Accepted: 06/12/2018] [Indexed: 12/16/2022] Open
Abstract
Studies on Shiga toxin-producing Escherichia coli (STEC) typically examine and classify the virulence gene profiles based on genomic analyses. Among the screened strains, a subgroup of STEC which lacks the locus of enterocyte effacement (LEE) has frequently been identified. This raises the question about the level of pathogenicity of such strains. This review focuses on the advantages and disadvantages of the standard screening procedures in virulence profiling and summarizes the current knowledge concerning the function and regulation of toxins encoded by LEE-negative STEC. Although LEE-negative STEC usually come across as food isolates, which rarely cause infections in humans, some serotypes have been implicated in human diseases. In particular, the LEE-negative E. coli O104:H7 German outbreak strain from 2011 and the Australian O113:H21 strain isolated from a HUS patient attracted attention. Moreover, the LEE-negative STEC O113:H21 strain TS18/08 that was isolated from minced meat is remarkable in that it not only encodes multiple toxins, but in fact expresses three different toxins simultaneously. Their characterization contributes to understanding the virulence of the LEE-negative STEC.
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Affiliation(s)
- Maike Krause
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Holger Barth
- Institute of Pharmacology and Toxicology, University of Ulm Medical Center, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, Garbenstrasse 28, University of Hohenheim, 70599 Stuttgart, Germany.
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Nayakvadi S, Alemao CA, Kumar HC, Rajkumar R, Rajkumar S, Chakurkar EB, Keelara S. Detection and molecular characterization of sorbitol fermenting non-O157 Escherichia coli from goats. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Keenswijk W, Vanmassenhove J, Raes A, Dhont E, VandeWalle J. Epidemiology and outcome of acute kidney injury in children, a single center study. Acta Clin Belg 2017; 72:405-412. [PMID: 28303771 DOI: 10.1080/17843286.2017.1302625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Information on the epidemiology of Acute Kidney Injury (AKI) in children is scarce. We performed a single center retrospective cohort study to analyze the incidence of AKI, the male/female ratio, the underlying etiology, and age at presentation. We also aimed to assess outcome measured by mortality, duration of PICU stay, and development of Chronic Kidney Disease (CKD). METHODS Records were searched for children presenting with or developing AKI between 1st January 2008 and 1st January 2015. AKI was classified according to the pediatric Rifle criteria while the cause of AKI was defined as the major underlying disease. RESULTS Of the 28,295 children admitted, 167 episodes of AKI were identified, equaling 5.9 cases per 1000 children. Patients classified as Failure at presentation according to pRifle criteria where significantly more likely to need dialysis (27/50, 54%) compared to those presenting with Injury (12/57, 21.1%) or Risk (6/60, 10 %). Diarrhea-associated Hemolytic Uremic Syndrome (D+HUS) was the most frequent cause (20.3 %) peaking during the summer months, followed by cardiac surgery (13.7%), medication-related nephrotoxicity (13.2%), and acute Glomerulonephritis (12%). The median age of children admitted with AKI was 6.1 years (range 0.1-17) and 50.8% of cases were male. Twenty five (15%) children died while 27 (16.1%) developed CKD. CONCLUSIONS Pediatric AKI poses a significant problem and strategies aimed at prevention, early detection, treatment, and adequate follow-up are needed. D+HUS is the most common underlying cause and effective surveillance of Enterohemorrhagic E. coli infections in association with additional measures is highly recommended.
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Affiliation(s)
- Werner Keenswijk
- Department of Pediatrics, Pediatric Nephrology, Ghent University Hospital, Ghent, Belgium
| | - Jill Vanmassenhove
- Department of Internal Medicine, Division of Nephrology, Ghent University Hospital, Ghent, Belgium
| | - Ann Raes
- Department of Pediatrics, Pediatric Nephrology, Ghent University Hospital, Ghent, Belgium
| | - Evelyn Dhont
- Department of Pediatric Intensive Care, Ghent University Hospital, Ghent, Belgium
| | - Johan VandeWalle
- Department of Pediatrics, Pediatric Nephrology, Ghent University Hospital, Ghent, Belgium
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Yu F, Chen X, Zheng S, Han D, Wang Y, Wang R, Wang B, Chen Y. Prevalence and genetic diversity of human diarrheagenic Escherichia coli isolates by multilocus sequence typing. Int J Infect Dis 2017; 67:7-13. [PMID: 29183841 DOI: 10.1016/j.ijid.2017.11.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The population structure of human diarrheagenic Escherichia coli (DEC) isolates derived from worldwide collections remains undefined. METHODS A total of 1196 clinical isolates were obtained from a multilocus sequence typing (MLST) database. Genetic diversity analysis, MLST analysis, and phylogenetic analysis combined with different pathotypes were performed through a variety of calculation software applications. RESULTS All isolates were categorized as one of 579 different sequence types (STs). The eBURST algorithm resolved these 579 STs into 27 clonal complexes (CCs), 37 concatemers, and 210 singletons, revealing a high level of genetic diversity in the population structure of DEC. CC10 was the most prevalent CC, comprising 276 (23.08%, 276/1196) isolates with 85 (14.68%, 85/579) STs widely distributed in 20 countries. The population structure of five common pathotypes was highly diversified, and isolates with the same ST or CC were heterogeneous for different pathotypes. Sequence variations were more abundant in fumC and gyrB than in the other five genes, and these exhibited the highest degree of nucleotide diversity (0.03886 and 0.03075, respectively) and the greatest number of polymorphic nucleotide sites (137 and 139, respectively). The dN/dS ratios of seven analyzed loci varied from 0.0083 (recA) to 0.0434 (purA), and the ratio for the concatenated sequence was 0.2518, revealing the effects of purifying selection on housekeeping genes during the evolutionary process. Significant allele linkage disequilibrium was detected when the standardized index of association (ISA) was calculated both for the entire collection of isolates (0.3174, p<0.001) and for the 579 STs (0.1475, p<0.001). CONCLUSIONS This study facilitated a comprehensive understanding of the genetic diversity of human DEC distributed across the global population. The results provide genetic evidence that will allow us to uncover the microevolutionary relationships among different pathogenic isolates of DEC.
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Affiliation(s)
- Fei Yu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Chen
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shufa Zheng
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dongsheng Han
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China
| | - Yiyin Wang
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ruonan Wang
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baohong Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Chen
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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Ogura Y, Gotoh Y, Itoh T, Sato MP, Seto K, Yoshino S, Isobe J, Etoh Y, Kurogi M, Kimata K, Maeda E, Piérard D, Kusumoto M, Akiba M, Tominaga K, Kirino Y, Kato Y, Shirahige K, Ooka T, Ishijima N, Lee KI, Iyoda S, Mainil JG, Hayashi T. Population structure of Escherichia coli O26 : H11 with recent and repeated stx2 acquisition in multiple lineages. Microb Genom 2017; 3:e000141. [PMID: 29208163 PMCID: PMC5729918 DOI: 10.1099/mgen.0.000141] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
A key virulence factor of enterohaemorrhagic Escherichia coli (EHEC) is the bacteriophage-encoded Shiga toxin (Stx). Stxs are classified into two types, Stx1 and Stx2, and Stx2-producing strains are thought to cause more severe infections than strains producing only Stx1. Although O26 : H11 is the second most prevalent EHEC following O157 : H7, the majority of O26 : H11 strains produce Stx1 alone. However, Stx2-producing O26 strains have increasingly been detected worldwide. Through a large-scale genome analysis, we present a global phylogenetic overview and evolutionary timescale for E. coli O26 : H11. The origin of O26 has been estimated to be 415 years ago. Sequence type 21C1 (ST21C1), one of the two sublineages of ST21, the most predominant O26 : H11 lineage worldwide, emerged 213 years ago from one of the three ST29 sublineages (ST29C2). The other ST21 lineage (ST21C2) emerged 95 years ago from ST21C1. Increases in population size occurred in the late 20th century for all of the O26 lineages, but most remarkably for ST21C2. Analysis of the distribution of stx2-positive strains revealed the recent and repeated acquisition of the stx2 gene in multiple lineages of O26, both in ST21 and ST29. Other major EHEC virulence genes, such as type III secretion system effector genes and plasmid-encoded virulence genes, were well conserved in ST21 compared to ST29. In addition, more antimicrobial-resistance genes have accumulated in the ST21C1 lineage. Although current attention is focused on several highly virulent ST29 clones that have acquired the stx2 gene, there is also a considerable risk that the ST21 lineage could yield highly virulent clones.
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Affiliation(s)
| | | | | | | | - Kazuko Seto
- Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Shyuji Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | | | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Mariko Kurogi
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | | | - Eriko Maeda
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | | | - Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Masato Akiba
- National Institute of Animal Health, Ibaraki, Japan
| | - Kiyoshi Tominaga
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | | | | | | | | | | | - Ken-ichi Lee
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Sunao Iyoda
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
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Castro VS, Carvalho RCT, Conte-Junior CA, Figuiredo EES. Shiga-toxin ProducingEscherichia coli: Pathogenicity, Supershedding, Diagnostic Methods, Occurrence, and Foodborne Outbreaks. Compr Rev Food Sci Food Saf 2017; 16:1269-1280. [DOI: 10.1111/1541-4337.12302] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Vinicius Silva Castro
- Animal Science Program, Faculdade de Agronomia e Zootecnia; Univ. Federal de Mato Grosso; 78060-900 Mato Grosso Brazil
- Natl. Inst. of Health Quality Control; Fundação Oswaldo Cruz; Rio de Janeiro 21040-900 Rio de Janeiro Brazil
| | - Ricardo César Tavares Carvalho
- Nutrition, Food and Metabolism Program, Faculdade de Nutrição; Univ. Federal de Mato Grosso; 78060-900 Mato Grosso Brazil
| | - Carlos Adam Conte-Junior
- Dept. of Food Technology, Faculdade de Veterinária; Univ. Federal Fluminense; 24230-340 Rio de Janeiro Brazil
- Food Science Program, Inst. de Química; Univ. Federal do Rio de Janeiro; 21941-909 Rio de Janeiro Brazil
- Natl. Inst. of Health Quality Control; Fundação Oswaldo Cruz; Rio de Janeiro 21040-900 Rio de Janeiro Brazil
| | - Eduardo Eustáquio Souza Figuiredo
- Animal Science Program, Faculdade de Agronomia e Zootecnia; Univ. Federal de Mato Grosso; 78060-900 Mato Grosso Brazil
- Nutrition, Food and Metabolism Program, Faculdade de Nutrição; Univ. Federal de Mato Grosso; 78060-900 Mato Grosso Brazil
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31
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Kimura B. Will the emergence of core genome MLST end the role of in silico MLST? Food Microbiol 2017; 75:28-36. [PMID: 30056960 DOI: 10.1016/j.fm.2017.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/02/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022]
Abstract
The technological advancement of molecular epidemiological analysis using next-generation sequencing (NGS) for foodborne pathogens has a groundbreaking impact over the past three years. In particular, the emergence of cg (core genome) multilocus sequence typing(MLST) has a significant impact. This is because this technology made it possible for many researchers to carry out molecular epidemiological analysis on foodborne pathogens in a common language, using common definitions. The resolution of core genome MLST (cgMLST) far surpasses that of MLST, which only uses seven (usually, in some cases five) housekeeping genes. Therefore, cgMLST would in no doubt terminate the role of conventional MLST as the molecular epidemiological tool. However, the role of MLST would probably not end all together. Rather, the sequence type (ST) of the conventional MLST is expected to be used as in silico MLST by a wider range of researchers than ever in the next 10 years. This is because, with the arrival of the NGS era, we have come to be able to obtain ST of conventional MLST by simply entering the NGS text file into one's own PC. In other words, acquisition of ST data is no longer limited to researchers aiming to conduct MLST for the first place. The impact of such a change is large. In silico MLST will continue to be used as a tool for understanding the broad characteristics of bacterial strains. This review aimed to summarize the main information on STs that have been accumulated for representative foodborne pathogens, in particular for potential NGS users in this new era who have been not familiar with MLST until now.
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Affiliation(s)
- Bon Kimura
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology (TUMSAT), Konan 4-5-7, Minato-ku, Tokyo 108-8477, Japan.
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Karmali MA. Emerging Public Health Challenges of Shiga Toxin–ProducingEscherichia coliRelated to Changes in the Pathogen, the Population, and the Environment. Clin Infect Dis 2016; 64:371-376. [DOI: 10.1093/cid/ciw708] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
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Martins FH, Guth BEC, Piazza RMF, Elias WP, Leão SC, Marzoa J, Dahbi G, Mora A, Blanco M, Blanco J, Pelayo JS. Lambs are an important source of atypical enteropathogenic Escherichia coli in southern Brazil. Vet Microbiol 2016; 196:72-77. [PMID: 27939159 DOI: 10.1016/j.vetmic.2016.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/07/2016] [Accepted: 10/09/2016] [Indexed: 12/16/2022]
Abstract
Food-producing animals can harbor Escherichia coli strains with potential to cause diseases in humans. In this study, the presence of enteropathogenic E. coli (EPEC) was investigated in fecal samples from 130 healthy sheep (92 lambs and 38 adults) raised for meat in southern Brazil. EPEC was detected in 19.2% of the sheep examined, but only lambs were found to be positive. A total of 25 isolates was characterized and designated atypical EPEC (aEPEC) as tested negative for bfpA gene and BFP production. The presence of virulence markers linked to human disease as ehxA, paa, and lpfAO113 was observed in 60%, 24%, and 88% of the isolates, respectively. Of the 11 serotypes identified, eight were described among human pathogenic strains, while three (O1:H8, O11:H21 and O125:H19) were not previously detected in aEPEC. Associations between intimin subtypes and phylogroups were observed, including eae-θ2/A, eae-β1/B1, eae-α2/B2 and eae-γ1/D. Although PFGE typing of 16 aEPEC isolates resulted in 14 unique pulsetypes suggesting a genetic diversity, specific clones were found to be distributed in some flocks. In conclusion, potentially pathogenic aEPEC strains are present in sheep raised for meat, particularly in lambs, which can better contribute to dissemination of these bacteria than adult animals.
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Affiliation(s)
- Fernando H Martins
- Departamento de Microbiologia, Universidade Estadual de Londrina, Londrina, PR, Brazil
| | - Beatriz E C Guth
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Roxane M F Piazza
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Waldir P Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP, Brazil
| | - Sylvia C Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Juan Marzoa
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Ghizlane Dahbi
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Miguel Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jacinta S Pelayo
- Departamento de Microbiologia, Universidade Estadual de Londrina, Londrina, PR, Brazil.
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Cadona JS, Bustamante AV, González J, Sanso AM. Genetic Relatedness and Novel Sequence Types of Non-O157 Shiga Toxin-Producing Escherichia coli Strains Isolated in Argentina. Front Cell Infect Microbiol 2016; 6:93. [PMID: 27625995 PMCID: PMC5003923 DOI: 10.3389/fcimb.2016.00093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/16/2016] [Indexed: 11/13/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen responsible for severe disease in humans such as hemolytic uremic syndrome (HUS) and cattle, the principal reservoir. Identification of the clones/lineages is important as several characteristics, among them propensity to cause disease varies with STEC phylogenetic origin. At present, we do not know what STEC clones, especially of non-O157:H7, are circulating in Argentina. To fill this knowledge gap we assessed the genetic diversity of STEC strains isolated in Argentina from various sources, mostly cattle and food, using multilocus sequence typing (MLST). Our objectives were to determine the phylogenetic relationships among strains and to compare them with strains from different geographic origins, especially with those from clinical human cases, in order to evaluate their potential health risk. A total of 59 STEC isolates from 41 serotypes were characterized by MLST. Analysis using EcMLST database identified 38 sequence types (ST), 17 (45%) of which were new STs detected in 18 serotypes. Fifteen out of 38 STs identified were grouped into 11 clonal groups (CGs) and, 23 not grouped in any of the defined CGs. Different STs were found in the same serotype. Results highlighted a high degree of phylogenetic heterogeneity among Argentinean strains and they showed that several cattle and food isolates belonged to the same STs that are commonly associated with clinical human cases in several geographical areas. STEC is a significant public health concern. Argentina has the highest incidence of HUS in the world and this study provides the first data about which STEC clones are circulating. Data showed that most of them might pose a serious zoonotic risk and this information is important for developing public health initiatives. However, the actual potential risk will be defined by the virulence profiles, which may differ among isolates belonging to the same ST.
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Affiliation(s)
- Jimena S Cadona
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Ana V Bustamante
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - Juliana González
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
| | - A Mariel Sanso
- Laboratorio de Inmunoquímica y Biotecnología, Facultad de Ciencias Veterinarias, Centro de Investigación Veterinaria de Tandil, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, Universidad Nacional del Centro de la Provincia de Buenos Aires Tandil, Argentina
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The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle. Appl Environ Microbiol 2016; 82:5455-64. [PMID: 27371579 DOI: 10.1128/aem.00909-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/23/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STEC(per)) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STEC(spo)) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STEC(per) isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STEC(spo) isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STEC(per) isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STEC(spo) isolates. Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STEC(per) from STEC(spo) isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level. IMPORTANCE Ruminants, especially cattle, are sources of food-borne infections by Shiga toxin-producing Escherichia coli (STEC) in humans. Some STEC strains persist in cattle for longer periods of time, while others are detected only sporadically. Persisting strains can serve as gene reservoirs that supply E. coli with virulence factors, thereby generating new outbreak strains. Attempts to reduce the human risk for acquiring STEC infections should therefore include strategies to control such persisting STEC strains. By analyzing representative genes of their core and accessory genomes, we show that bovine STEC with a persistent colonization type emerged independently from sporadically colonizing isolates and evolved in parallel evolutionary branches. However, persistent colonizing strains share similar sets of accessory genes. Defining the genetic patterns that distinguish persistent from sporadically colonizing STEC isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.
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Stanford K, Johnson RP, Alexander TW, McAllister TA, Reuter T. Influence of Season and Feedlot Location on Prevalence and Virulence Factors of Seven Serogroups of Escherichia coli in Feces of Western-Canadian Slaughter Cattle. PLoS One 2016; 11:e0159866. [PMID: 27482711 PMCID: PMC4970752 DOI: 10.1371/journal.pone.0159866] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/08/2016] [Indexed: 11/19/2022] Open
Abstract
Pooled feces collected over two years from 1749 transport trailers hauling western-Canadian slaughter cattle were analysed by PCR for detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157. Sequential immunomagnetic separation was then used to collect bacterial isolates (n = 1035) from feces positive for target serogroups. Isolated bacteria were tested by PCR to confirm serogroup and the presence of eae, ehxA, stx1, and stx2 virulence genes. Based on PCR screening, serogroup prevalence in feces ranged from 7.0% (O145) to 94.4% (O103) with at least 3 serogroups present in 79.5% of samples. Origin of cattle affected serogroup PCR prevalence and O157 was most prevalent in feces from south-west Alberta (P < 0.001). All serogroups demonstrated seasonal variations in PCR prevalence, with O26, O45, O103, O121, and O157 least prevalent (P < 0.001) in cooler winter months, while uncommon serogroups O111 and O145 increased in prevalence during winter (P < 0.001). However, isolates collected during winter were predominantly from serogroups O103 and O45. No seasonal variation was noted in proportion of isolates which were Shiga toxin containing E. coli (STEC; P = 0.18) or positive for Shiga toxin and eae (enterohemorrhagic E. coli; EHEC; P = 0.29). Isolates of serogroups O111, O145, and O157 were more frequently EHEC than were others, although 37.6–54.3% of isolates from other serogroups were also EHEC. Shiga-toxin genes present also varied by geographic origin of cattle (P < 0.05) in all serogroups except O157. As cattle within feedlots are sourced from multiple regions, locational differences in serogroup prevalence and virulence genes imply existence of selection pressures for E. coli and their virulence in western-Canadian cattle. Factors which reduce carriage or expression of virulence genes, particularly in non-O157 serogroups, should be investigated.
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Affiliation(s)
- Kim Stanford
- Alberta Agriculture and Forestry, Lethbridge, Alberta, Canada
- * E-mail:
| | | | | | | | - Tim Reuter
- Alberta Agriculture and Forestry, Lethbridge, Alberta, Canada
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Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM, Feng P. Advances in Molecular Serotyping and Subtyping of Escherichia coli. Front Microbiol 2016; 7:644. [PMID: 27199968 PMCID: PMC4853403 DOI: 10.3389/fmicb.2016.00644] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/18/2016] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.
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Affiliation(s)
- Pina M. Fratamico
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University ParkPA, USA
| | - Yanhong Liu
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - David S. Needleman
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Gian Marco Baranzoni
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Peter Feng
- Division of Microbiology, U.S. Food and Drug Administration, College ParkMD, USA
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Askari Badouei M. Escherichia coli O157: H7 in Iran: Time to Look Closer. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2016. [DOI: 10.17795/ijep37471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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