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Tam CC, Du WX, Wang Y, Flannery AR, He X. Rapid and Sensitive Detection of Shiga Toxin-Producing Escherichia coli (STEC) from Food Matrices Using the CANARY Biosensor Assay. Toxins (Basel) 2024; 16:325. [PMID: 39057965 PMCID: PMC11281303 DOI: 10.3390/toxins16070325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) causes a wide spectrum of diseases including hemorrhagic colitis and hemolytic uremic syndrome (HUS). Previously, we developed a rapid, sensitive, and potentially portable assay that identified STEC by detecting Shiga toxin (Stx) using a B-cell based biosensor platform. We applied this assay to detect Stx2 present in food samples that have been implicated in previous STEC foodborne outbreaks (milk, lettuce, and beef). The STEC enrichment medium, modified Tryptone Soy Broth (mTSB), inhibited the biosensor assay, but dilution with the assay buffer relieved this effect. Results with Stx2a toxoid-spiked food samples indicated an estimated limit of detection (LOD) of ≈4 ng/mL. When this assay was applied to food samples inoculated with STEC, it was able to detect 0.4 CFU/g or 0.4 CFU/mL of STEC at 16 h post incubation (hpi) in an enrichment medium containing mitomycin C. Importantly, this assay was even able to detect STEC strains that were high expressors of Stx2 at 8 hpi. These results indicate that the STEC CANARY biosensor assay is a rapid and sensitive assay applicable for detection of STEC contamination in food with minimal sample processing that can complement the current Food Safety Inspection Service (US) methodologies for STEC.
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Affiliation(s)
- Christina C. Tam
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, Agricultural Research Services, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA; (C.C.T.); (W.-X.D.)
| | - Wen-Xian Du
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, Agricultural Research Services, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA; (C.C.T.); (W.-X.D.)
| | - Yangyang Wang
- Smiths Detection, 2202 Lakeside Blvd, Edgewood, MD 21040, USA; (Y.W.); (A.R.F.)
| | - Andrew R. Flannery
- Smiths Detection, 2202 Lakeside Blvd, Edgewood, MD 21040, USA; (Y.W.); (A.R.F.)
| | - Xiaohua He
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, Agricultural Research Services, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA; (C.C.T.); (W.-X.D.)
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McMahon T, Clarke S, Deschênes M, Tapp K, Blais B, Gill A. Real-time PCR primers and probes for the detection of Shiga toxin genes, including novel subtypes. Int J Food Microbiol 2024; 419:110744. [PMID: 38763050 DOI: 10.1016/j.ijfoodmicro.2024.110744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are foodborne enteric pathogens. STEC are differentiated from other E. coli by detection of Shiga toxin (Stx) or its gene (stx). The established nomenclature of Stx identifies ten subtypes (Stx1a, Stx1c, Stxd, Stx2a to Stx2g). An additional nine subtypes have been reported and described (Stx1e, Stx2h to Stx2o). Many PCR protocols only detect a subset of Stx subtypes which limits their inclusivity. Here we describe a real-time PCR assay inclusive of the DNA sequences of representatives of all currently described Stx subtypes. A multiplex real-time PCR assay for detection of stx was developed using nine primers and four probes. Since the identification of STEC does not require differentiation of stx subtypes, the probes use the same fluorescent reporter to enable detection of multiple possible targets in a single reaction. The PCR mixture includes an internal positive control to detect inhibition of the reaction. Thus, the protocol can be performed on a two-channel real-time PCR platform. To reduce the biosafety risk inherent in the use of STEC cultures as process controls, the protocol also includes the option of a non-pathogenic E. coli transformant carrying a plasmid encoding the targeted fragment of the stx2a sequence. The inclusivity of the PCR was assessed against colonies of 137 STEC strains and one strain of Shigella dysenteriae, including strains carrying single copies of stx representing fourteen subtypes (stx1 a, c, d; stx2 a-j and o). Five additional subtypes (stx1e, 2k, 2l, 2m and 2n) were represented by E. coli transformed with plasmids encoding toxoid (enzymatically inactive A subunit) sequences. The exclusivity panel consisted of 70 bacteria, including 21 stx-negative E. coli. Suitability for food analysis was assessed with artificially inoculated ground beef, spinach, cheese, and apple cider. The real-time PCR generated positive results for all 19 stx subtypes, represented by colonies of STEC, S. dysenteriae and E. coli transformants carrying stx toxoid plasmids. Tests of exclusivity panel colonies were all negative. The real-time PCR detected the presence of stx in all inoculated food enrichments tested, and the presence of STEC was confirmed by isolation.
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Affiliation(s)
- Tanis McMahon
- Health Canada/Santé Canada, Bureau of Microbial Hazards, Ottawa, Ontario, Canada
| | - Sarah Clarke
- Health Canada/Santé Canada, Bureau of Microbial Hazards, Ottawa, Ontario, Canada
| | - Mylène Deschênes
- Canadian Food Inspection Agency/Agence canadienne d'inspection des aliments, Ottawa Laboratory Carling, Ottawa, Ontario, Canada
| | - Kyle Tapp
- Canadian Food Inspection Agency/Agence canadienne d'inspection des aliments, Ottawa Laboratory Carling, Ottawa, Ontario, Canada
| | - Burton Blais
- Canadian Food Inspection Agency/Agence canadienne d'inspection des aliments, Ottawa Laboratory Carling, Ottawa, Ontario, Canada
| | - Alexander Gill
- Health Canada/Santé Canada, Bureau of Microbial Hazards, Ottawa, Ontario, Canada.
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Wang X, Yu D, Chui L, Zhou T, Feng Y, Cao Y, Zhi S. A Comprehensive Review on Shiga Toxin Subtypes and Their Niche-Related Distribution Characteristics in Shiga-Toxin-Producing E. coli and Other Bacterial Hosts. Microorganisms 2024; 12:687. [PMID: 38674631 PMCID: PMC11052178 DOI: 10.3390/microorganisms12040687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Shiga toxin (Stx), the main virulence factor of Shiga-toxin-producing E. coli (STEC), was first discovered in Shigella dysenteriae strains. While several other bacterial species have since been reported to produce Stx, STEC poses the most significant risk to human health due to its widespread prevalence across various animal hosts that have close contact with human populations. Based on its biochemical and molecular characteristics, Shiga toxin can be grouped into two types, Stx1 and Stx2, among which a variety of variants and subtypes have been identified in various bacteria and host species. Interestingly, the different Stx subtypes appear to vary in their host distribution characteristics and in the severity of diseases that they are associated with. As such, this review provides a comprehensive overview on the bacterial species that have been recorded to possess stx genes to date, with a specific focus on the various Stx subtype variants discovered in STEC, their prevalence in certain host species, and their disease-related characteristics. This review provides a better understanding of the Stx subtypes and highlights the need for rapid and accurate approaches to toxin subtyping for the proper evaluation of the health risks associated with Shiga-toxin-related bacterial food contamination and human infections.
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Affiliation(s)
- Xuan Wang
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
| | - Daniel Yu
- School of Public Health, Univeristy of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Linda Chui
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada
| | - Tiantian Zhou
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
| | - Yu Feng
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
| | - Yuhao Cao
- School of Basic Medical Sciences, Ningbo University, Ningbo 315000, China;
| | - Shuai Zhi
- School of Public Health, Ningbo University, Ningbo 315000, China; (X.W.); (T.Z.); (Y.F.)
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Sui X, Yang X, Luo M, Wang H, Liu Q, Sun H, Jin Y, Wu Y, Bai X, Xiong Y. Characteristics of Shiga Toxin-Producing Escherichia coli Circulating in Asymptomatic Food Handlers. Toxins (Basel) 2023; 15:640. [PMID: 37999503 PMCID: PMC10675304 DOI: 10.3390/toxins15110640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/22/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a foodborne zoonotic pathogen that causes diarrhea, hemorrhagic colitis (HC), and hemolytic uremic syndrome (HUS) worldwide. Since the infection can be asymptomatic, the circulation of STEC in some asymptomatic carriers, especially in healthy-food-related professionals, is not yet well understood. In this study, a total of 3987 anal swab samples from asymptomatic food handlers were collected, and ten swabs recovered STEC strains (0.251%). Of the ten STEC isolates, seven serotypes and eight sequence types (ST) were determined using whole genome sequencing (WGS). Two stx1 subtypes (stx1a and stx1c) and four stx2 subtypes (stx2a, stx2b, stx2d, and stx2e) were detected. Seven different insertion sites were found in fourteen Stx prophages, and the dmsB and yfhL were the newly identified insertion sites. The ten strains showed the variable Stx transcription levels after the mitomycin C induction. The whole-genome phylogeny indicated that the strains from the asymptomatic food handlers were genetically distant from the strains of HUS patients. The STEC isolates circulating in asymptomatic carriers might pose a low potential to cause disease.
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Affiliation(s)
- Xinxia Sui
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xi Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ming Luo
- Yulin Center for Disease Control and Prevention, Yulin 537000, China
| | - Hua Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qian Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hui Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yujuan Jin
- Longgang Center for Disease Control and Prevention, Shenzhen 518172, China
| | - Yannong Wu
- Yulin Center for Disease Control and Prevention, Yulin 537000, China
| | - Xiangning Bai
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Division of Laboratory Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Yanwen Xiong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Lindsey RL, Prasad A, Feldgarden M, Gonzalez-Escalona N, Kapsak C, Klimke W, Melton-Celsa A, Smith P, Souvorov A, Truong J, Scheutz F. Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States. Microorganisms 2023; 11:2561. [PMID: 37894219 PMCID: PMC10608928 DOI: 10.3390/microorganisms11102561] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.
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Affiliation(s)
- Rebecca L. Lindsey
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (C.K.); (P.S.)
| | - Arjun Prasad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA;
| | - Curtis Kapsak
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (C.K.); (P.S.)
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Angela Melton-Celsa
- Department of Microbiology and Immunology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20184, USA;
| | - Peyton Smith
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (C.K.); (P.S.)
| | - Alexandre Souvorov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (A.P.); (M.F.); (W.K.); (A.S.)
| | - Jenny Truong
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA;
| | - Flemming Scheutz
- The International Escherichia and Klebsiella Centre, Statens Serum Institut, 2300 Copenhagen, Denmark;
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6
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Lee KS, Park JY, Jeong YJ, Lee MS. The Fatal Role of Enterohaemorrhagic Escherichia coli Shiga Toxin-associated Extracellular Vesicles in Host Cells. J Microbiol 2023; 61:715-727. [PMID: 37665555 DOI: 10.1007/s12275-023-00066-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 05/26/2023] [Accepted: 07/05/2023] [Indexed: 09/05/2023]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a specific subset of Shiga toxin-producing Escherichia coli (STEC) strains that are characterized by their ability to cause bloody diarrhea (hemorrhagic colitis) and potentially life-threatening, extraintestinal complications such as hemolytic uremic syndrome (HUS), which is associated with acute renal failure., contributing to severe clinical outcomes. The Shiga toxins (Stxs), produced by EHEC, are primary virulence factors. These potent cytotoxins are composed of one enzymatically active A subunit (StxA) and five receptor-binding B subunits (StxB). Although the toxins are primarily associated with cytotoxic effects, they also elicit other pathogenic consequences due to their induction of a number of biological processes, including apoptosis through ER-stress, pro-inflammatory responses, autophagy, and post-translational modification (PTM). Moreover, several studies have reported the association between Stxs and extracellular vesicles (EVs), including microvesicles and exosomes, demonstrating that Stx-containing EVs secreted by intoxicated macrophages are taken up by recipient cells, such as toxin-sensitive renal proximal tubular epithelial cells. This mechanism likely contributes to the spreading of Stxs within the host, and may exacerbate gastrointestinal illnesses and kidney dysfunction. In this review, we summarize recent findings relating to the host responses, in different types of cells in vitro and in animal models, mediated by Stxs-containing exosomes. Due to their unique properties, EVs have been explored as therapeutic agents, drug delivery systems, and diagnostic tools. Thus, potential therapeutic applications of EVs in EHEC Stxs-mediated pathogenesis are also briefly reviewed.
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Affiliation(s)
- Kyung-Soo Lee
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jun-Young Park
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Yu-Jin Jeong
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| | - Moo-Seung Lee
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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Yano B, Taniguchi I, Gotoh Y, Hayashi T, Nakamura K. Dynamic changes in Shiga toxin (Stx) 1 transducing phage throughout the evolution of O26:H11 Stx-producing Escherichia coli. Sci Rep 2023; 13:4935. [PMID: 36973327 PMCID: PMC10042803 DOI: 10.1038/s41598-023-32111-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Shiga toxin (Stx) is the key virulence factor of Stx-producing Escherichia coli (STEC). All known Stxs (Stx1 and Stx2) are encoded by bacteriophages (Stx phages). Although the genetic diversity of Stx phages has frequently been described, systematic analyses of Stx phages in a single STEC lineage are limited. In this study, focusing on the O26:H11 STEC sequence type 21 (ST21) lineage, where the stx1a gene is highly conserved, we analysed the Stx1a phages in 39 strains representative of the entire ST21 lineage and found a high level of variation in Stx1a phage genomes caused by various mechanisms, including replacement by a different Stx1a phage at the same or different locus. The evolutionary timescale of events changing Stx1a phages in ST21 was also determined. Furthermore, by using an Stx1 quantification system developed in this study, we found notable variations in the efficiency of Stx1 production upon prophage induction, which sharply contrasted with the conserved iron regulated Stx1 production. These variations were associated with the Stx1a phage alteration in some cases but not in other cases; thus, Stx1 production in this STEC lineage was determined by differences not only in Stx1 phages but also in host-encoded factors.
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Affiliation(s)
- Bungo Yano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 815-8582, Japan.
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Miyata T, Taniguchi I, Nakamura K, Gotoh Y, Yoshimura D, Itoh T, Hirai S, Yokoyama E, Ohnishi M, Iyoda S, Ogura Y, Hayashi T. Alteration of a Shiga toxin-encoding phage associated with a change in toxin production level and disease severity in Escherichia coli. Microb Genom 2023; 9:mgen000935. [PMID: 36821793 PMCID: PMC9997748 DOI: 10.1099/mgen.0.000935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/21/2022] [Indexed: 02/25/2023] Open
Abstract
Among the nine clades of Shiga toxin (Stx)-producing Escherichia coli O157:H7, clade 8 is thought to be highly pathogenic, as it causes severe disease more often than other clades. Two subclades have been proposed, but there are conflicting reports on intersubclade differences in Stx2 levels, although Stx2 production is a risk factor for severe disease development. The global population structure of clade 8 has also yet to be fully elucidated. Here, we present genome analyses of a global clade 8 strain set (n =510), including 147 Japanese strains sequenced in this study. The complete genome sequences of 18 of the 147 strains were determined to perform detailed clade-wide genome analyses together with 17 publicly available closed genomes. Intraclade variations in Stx2 production level and disease severity were also re-evaluated within the phylogenetic context. Based on phylogenomic analysis, clade 8 was divided into four lineages corresponding to the previously proposed SNP genotypes (SGs): SG8_30, SG8_31A, SG8_31B and SG8_32. SG8_30 and the common ancestor of the other SGs were first separated, with SG8_31A and SG8_31B emerging from the latter and SG8_32 emerging from SG8_31B. Comparison of 35 closed genomes revealed the overall structure of chromosomes and pO157 virulence plasmids and the prophage contents to be well conserved. However, Stx2a phages exhibit notable genomic diversity, even though all are integrated into the argW locus, indicating that subtype changes in Stx2a phage occurred from the γ subtype to its variant (γ_v1) in SG8_31A and from γ to δ in SG8_31B and SG8_32 via replacement of parts or almost entire phage genomes, respectively. We further show that SG8_30 strains (all carrying γ Stx2a phages) produce significantly higher levels of Stx2 and cause severe disease more frequently than SG8_32 strains (all carrying δ Stx2a phages). Clear conclusions on SG8_31A and SG8_31B cannot be made due to the small number of strains available, but as SG8_31A (carrying γ_v1 Stx2a phages) contains strains that produce much more Stx2 than SG8_30 strains, attention should also be paid to this SG.
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Affiliation(s)
- Tatsuya Miyata
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo 208-0011, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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Montalbano Di Filippo M, Boni A, Chiani P, Marra M, Carollo M, Cristofari L, Minelli F, Knijn A, Morabito S. Exploring the nature of interaction between shiga toxin producing Escherichia coli (STEC) and free-living amoeba - Acanthamoeba sp. Front Cell Infect Microbiol 2022; 12:926127. [PMID: 36159652 PMCID: PMC9504058 DOI: 10.3389/fcimb.2022.926127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Free-living amoebae (FLA) are widely distributed protozoa in nature, known to cause severe eye infections and central nervous system disorders. There is growing attention to the potential role that these protozoa could act as reservoirs of pathogenic bacteria and, consequently, to the possibility that, the persistence and spread of the latter may be facilitated, by exploiting internalization into amoebae. Shiga toxin-producing strains of Escherichia coli (STEC) are zoonotic agents capable of causing serious diseases, such as hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Cattle represent the main natural reservoir of STEC, which are frequently found also in other domestic and wild ruminants, often without causing any evident symptoms of disease. The aspects related to the ecology of STEC strains in animal reservoirs and the environment are poorly known, including the persistence of these microorganisms within niches unfavorable to survival, such as soils or waters. In this study we investigated the interaction between STEC strains of serotype O157: H7 with different virulence gene profiles, and a genus of a wild free-living amoeba, Acanthamoeba sp. Our results confirm the ability of STEC strains to survive up to 20 days within a wild Acanthamoeba sp., in a quiescent state persisting in a non-cultivable form, until they reactivate following some stimulus of an unknown nature. Furthermore, our findings show that during their internalization, the E. coli O157 kept the set of the main virulence genes intact, preserving their pathogenetic potential. These observations suggest that the internalization in free-living amoebae may represent a means for STEC to resist in environments with non-permissive growth conditions. Moreover, by staying within the protozoa, STEC could escape their detection in the vehicles of infections and resist to the treatments used for the disinfection of the livestock environment.
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Affiliation(s)
- Margherita Montalbano Di Filippo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Margherita Montalbano Di Filippo,
| | - Arianna Boni
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Chiani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Manuela Marra
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Carollo
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Lucrezia Cristofari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Fabio Minelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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High Prevalence and Persistence of Escherichia coli Strains Producing Shiga Toxin Subtype 2k in Goat Herds. Microbiol Spectr 2022; 10:e0157122. [PMID: 35938860 PMCID: PMC9431244 DOI: 10.1128/spectrum.01571-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) is a zoonotic pathogen with the ability to cause severe diseases like hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the key virulence factor in STEC and can be classified into two types, Stx1 and Stx2, and different subtypes. Stx2k is a newly reported Stx2 subtype in E. coli strains from diarrheal patients, animals, and raw meats exclusively in China so far. To understand the reservoir of Stx2k-producing E. coli (Stx2k-STEC), we investigated Stx2k-STEC strains in goat herds and examined their genetic characteristics using whole-genome sequencing. A total of 448 STEC strains were recovered from 2,896 goat fecal samples, and 37.95% (170/448) were Stx2k-STEC. Stx2k-STEC strains of serotype O93:H28 and sequence type 4038 (ST4038) were the most predominant and were detected over several years. Notably, 55% of Stx2k-STEC strains carried the heat-labile toxin (LT)-encoding gene (elt) defining enterotoxigenic E. coli (ETEC), thereby exhibiting the hybrid STEC/ETEC pathotype. Stx2k-converting prophage genomes clustered into four groups and exhibited high similarity within each group. Strains from patients, raw meat, sheep, and goats were intermixed distributed in the phylogenetic tree, indicating the risk for cross-species spread of Stx2k-STEC and pathogenic potential for humans. Further studies are required to investigate the Stx2k-STEC strains in other reservoirs and to understand the mechanism of persistence in these hosts. IMPORTANCE Strains of the recently reported Stx2k-STEC have been circulating in a variety of sources over time in China. Here, we show a high prevalence of Stx2k-STEC in goat herds. More than half of the strains were of the hybrid STEC/ETEC pathotype. Stx2k-STEC strains of predominant serotypes have been widespread in the goat herds over several years. Stx2k-converting prophages have exhibited a high level of similarity across geographical regions and time and might be maintained and transmitted horizontally. Given that goat-derived Stx2k-STEC strains share similar genetic backbones with patient-derived strains, the high prevalence of Stx2k-STEC in goats suggests that there is a risk of cross-species spread and that these strains may pose pathogenetic potential to humans. Our study thus highlights the need to monitor human Stx2k-STEC infections in this region and, by extension, in other geographic locations.
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11
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Comparative Genomics of Shiga Toxin-Producing Escherichia coli Strains Isolated from Pediatric Patients with and without Hemolytic Uremic Syndrome from 2000 to 2016 in Finland. Microbiol Spectr 2022; 10:e0066022. [PMID: 35730965 PMCID: PMC9430701 DOI: 10.1128/spectrum.00660-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) infection can cause mild to severe illness, such as nonbloody or bloody diarrhea, and the fatal hemolytic uremic syndrome (HUS). The molecular mechanism underlying the variable pathogenicity of STEC infection is not fully defined so far. Here, we performed a comparative genomics study on a large collection of clinical STEC strains collected from STEC-infected pediatric patients with and without HUS in Finland over a 16-year period, aiming to identify the bacterial genetic factors that can predict the risk to cause HUS and poor renal outcome. Of 240 STEC strains included in this study, 52 (21.7%) were from pediatric patients with HUS. Serotype O157:H7 was the main cause of HUS, and Shiga toxin gene subtype stx2a was significantly associated with HUS. Comparative genomics and pangenome-wide association studies identified a number of virulence and accessory genes overrepresented in HUS-associated STEC compared to non-HUS STEC strains, including genes encoding cytolethal distending toxins, type III secretion system effectors, adherence factors, etc. No virulence or accessory gene was significantly associated with risk factors for poor renal outcome among HUS patients assessed in this study, including need for and duration of dialysis, presence and duration of anuria, and leukocyte counts. Whole-genome phylogeny and multiple-correspondence analysis of pangenomes could not separate HUS STEC from non-HUS STEC strains, suggesting that STEC strains with diverse genetic backgrounds may independently acquire genetic elements that determine their varied pathogenicity. Our findings indicate that nonbacterial factors, i.e., characteristics of the host immunity, might affect STEC virulence and clinical outcomes. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) is a serious public health burden worldwide which causes outbreaks of gastrointestinal diseases and the fatal hemolytic uremic syndrome (HUS) characterized by the triad of mechanical hemolytic anemia, thrombocytopenia, and acute renal failure. Understanding the mechanism underlying the disease severity and patient outcome is of high importance. Using comparative genomics on a large collection of clinical STEC strains from STEC-infected patients with and without HUS, our study provides a reference of STEC genetic factors/variants that can be used as predictors of the development of HUS, which will aid risk assessment at the early stage of STEC infection. Additionally, our findings suggest that nonbacterial factors may play a primary role in the renal outcome in STEC-infected patients with HUS; further studies are needed to validate this.
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12
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Genomic Characterization of Escherichia coli O8 Strains Producing Shiga Toxin 2l Subtype. Microorganisms 2022; 10:microorganisms10061245. [PMID: 35744763 PMCID: PMC9227347 DOI: 10.3390/microorganisms10061245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) can cause diseases ranging from mild diarrhea to fatal extra-intestinal hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the key virulence factor in STEC, two Stx types (Stx1 and Stx2) and several subtypes varying in sequences, toxicity, and host specificity have been identified. Stx2l is a newly-designated subtype related to human disease but lacks thorough characterization. Here, we identified Stx2l from five STEC strains (Stx2l-STECs) recovered from raw mutton and beef in China. Whole-genome sequencing (WGS) was used to characterize the Stx2l-STECs in this study together with Stx2l-STECs retrieved from public databases. Our study revealed that all the analyzed Stx2l-STEC strains belonged to the same serogroup O8. Multilocus sequencing typing (MLST) showed two sequence types (ST88 and ST23) among these strains. Stx2l-converting prophages from different sources shared a highly similar structure and sequence. Single-nucleotide polymorphism (SNP)-based analysis revealed genetic relatedness between the human-derived and food-derived strains belonging to ST23. To conclude, our study supported the designation of Stx2l and demonstrated diverse host range and geographical distribution of Stx2l-STECs.Stx2l-STEC strains from different sources showed a high genetic similarity with an identical O8 serogroup. Further studies are needed to investigate the epidemiological trait and pathogenic potential of Stx2l-STEC strains.
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13
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Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use. Appl Environ Microbiol 2022; 88:e0027722. [PMID: 35442082 PMCID: PMC9088250 DOI: 10.1128/aem.00277-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx2 positive, 19 (2.7%) were eae positive, and stx1-positive isolates were absent. At the sample level, stx2-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx1, 23.9%; stx2, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.
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14
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Characterisation of atypical Shiga toxin gene sequences and description of Stx2j, a new subtype. J Clin Microbiol 2022; 60:e0222921. [PMID: 35225693 DOI: 10.1128/jcm.02229-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shiga toxin (Stx) is the definitive virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx variants are currently organised into a taxonomic system of three Stx1 (a,c,d) and seven Stx2 (a,b,c,d,e,f,g) subtypes. In this study, seven STEC isolates from food and clinical samples possessing stx2 sequences that do not fit current Shiga toxin taxonomy were identified. Genome assemblies of the STEC strains was created from Oxford Nanopore and Illumina sequence data. The presence of atypical stx2 sequences were confirmed by Sanger sequencing, as were Stx2 expression and cytotoxicity. A strain of O157:H7 was found to possess stx1a and a truncated stx2a, which were originally misidentified as an atypical stx2. Two strains possessed unreported variants of Stx2a (O8:H28) and Stx2b (O146:H21). In four of the strains we found three Stx-subtypes that are not included in the current taxonomy. Stx2h (O170:H18) was identified in a Canadian sprout isolate; this subtype has only previously been reported in STEC from Tibetan Marmots. Stx2o (O85:H1) was identified in a clinical isolate. Finally, Stx2j (O158:H23 and O33:H14) was found in lettuce and clinical isolates. The results of this study expands the number of known Stx subtypes, the range of STEC serotypes, and isolation sources in which they may be found. The presence of the Stx2j and Stx2o in clinical isolates of STEC indicates that strains carrying these variants are potential human pathogens. Highlights Atypical Shiga toxin (stx) genes in Escherichia coli were sequenced. Two new variants of stx2a and stx2b are described. Two strains carried subtypes Stx2h and Stx2o, which have only one previous report. Two strains carried a previously undescribed subtype, Stx2j.
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15
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Michelacci V, Montalbano Di Filippo M, Gigliucci F, Arancia S, Chiani P, Minelli F, Roosens NHC, De Keersmaecker SCJ, Bogaerts B, Vanneste K, Morabito S. Population Analysis of O26 Shiga Toxin-Producing Escherichia coli Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing. Front Cell Infect Microbiol 2022; 12:842508. [PMID: 35223557 PMCID: PMC8864317 DOI: 10.3389/fcimb.2022.842508] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) belonging to the O26 serogroup represent an important cause of Hemolitic Uremic Syndrome (HUS) in children worldwide. The localization of STEC virulence genes on mobile genetic elements allowed the emergence of clones showing different assets of this accessory genomic fraction. A novel O26 STEC clone belonging to Sequence Type (ST) 29 and harboring stx2a, ehxA and etpD plasmid-borne genes has emerged and spread in Europe since the mid-1990s, while another ST29 clone positive for stx2d and lacking plasmid-borne virulence genes was recently described as emerging in France. In Italy, O26 has been the most frequently detected STEC serogroup from HUS cases since the late 1990s. In this study we describe the genomic characterization and population structure of 144 O26 STEC strains isolated from human sources in Italy in the period 1989-2020. A total of 89 strains belonged to ST21, 52 to ST29, two to ST396 and one to ST4944. ST29 strains started to be isolated from 1999. 24 strains were shown to harbour stx1a, alone (n=20) or in combination with stx2a (n=4). The majority of the strains (n=118) harbored stx2a genes only and the two ST396 strains harbored stx2d. A Hierarchical Clustering on Principal Components (HCPC) analysis, based on the detection of accessory virulence genes, antimicrobial resistance (AMR) genes and plasmid replicons, classified the strains in seven clusters identified with numbers from 1 to 7, containing two, 13, 39, 63, 16, 10 and one strain, respectively. The majority of the genetic features defining the clusters corresponded to plasmid-borne virulence genes, AMR genes and plasmid replicons, highlighting specific assets of plasmid-borne features associated with different clusters. Core genome Multi Locus Sequence Typing grouped ST21 and ST29 strains in three clades each, with each ST29 clade exactly corresponding to one HCPC cluster. Our results showed high conservation of either the core or the accessory genomic fraction in populations of ST29 O26 STEC, differently from what observed in ST21 strains, suggesting that a different selective pressure could drive the evolution of different populations of these pathogens possibly involving different ecological niches.
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Affiliation(s)
- Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - Federica Gigliucci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Silvia Arancia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Chiani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Fabio Minelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Nancy H. C. Roosens
- Sciensano, Biological Health Risks, Transversal Activities in Applied Genomics, Brussels, Belgium
| | | | - Bert Bogaerts
- Sciensano, Biological Health Risks, Transversal Activities in Applied Genomics, Brussels, Belgium
| | - Kevin Vanneste
- Sciensano, Biological Health Risks, Transversal Activities in Applied Genomics, Brussels, Belgium
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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16
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Zhang X, Payne M, Kaur S, Lan R. Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers. Front Cell Infect Microbiol 2022; 11:772574. [PMID: 35083165 PMCID: PMC8785982 DOI: 10.3389/fcimb.2021.772574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) have more than 470 serotypes. The well-known STEC O157:H7 serotype is a leading cause of STEC infections in humans. However, the incidence of non-O157:H7 STEC serotypes associated with foodborne outbreaks and human infections has increased in recent years. Current detection and serotyping assays are focusing on O157 and top six (“Big six”) non-O157 STEC serogroups. In this study, we performed phylogenetic analysis of nearly 41,000 publicly available STEC genomes representing 460 different STEC serotypes and identified 19 major and 229 minor STEC clusters. STEC cluster-specific gene markers were then identified through comparative genomic analysis. We further identified serotype-specific gene markers for the top 10 most frequent non-O157:H7 STEC serotypes. The cluster or serotype specific gene markers had 99.54% accuracy and more than 97.25% specificity when tested using 38,534 STEC and 14,216 non-STEC E. coli genomes, respectively. In addition, we developed a freely available in silico serotyping pipeline named STECFinder that combined these robust gene markers with established E. coli serotype specific O and H antigen genes and stx genes for accurate identification, cluster determination and serotyping of STEC. STECFinder can assign 99.85% and 99.83% of 38,534 STEC isolates to STEC clusters using assembled genomes and Illumina reads respectively and can simultaneously predict stx subtypes and STEC serotypes. Using shotgun metagenomic sequencing reads of STEC spiked food samples from a published study, we demonstrated that STECFinder can detect the spiked STEC serotypes, accurately. The cluster/serotype-specific gene markers could also be adapted for culture independent typing, facilitating rapid STEC typing. STECFinder is available as an installable package (https://github.com/LanLab/STECFinder) and will be useful for in silico STEC cluster identification and serotyping using genome data.
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Affiliation(s)
- Xiaomei Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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AB 5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins. Toxins (Basel) 2022; 14:toxins14010062. [PMID: 35051039 PMCID: PMC8779504 DOI: 10.3390/toxins14010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB5 toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB5 and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.
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18
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Prevalence and Whole-Genome Sequence-Based Analysis of Shiga Toxin-Producing Escherichia coli Isolates from the Recto-Anal Junction of Slaughter-Age Irish Sheep. Appl Environ Microbiol 2021; 87:e0138421. [PMID: 34644161 DOI: 10.1128/aem.01384-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) organisms are a diverse group of pathogenic bacteria capable of causing serious human illness, and serogroups O157 and O26 are frequently implicated in human disease. Ruminant hosts are the primary STEC reservoir, and small ruminants are important contributors to STEC transmission. This study investigated the prevalence, serotypes, and shedding dynamics of STEC, including the supershedding of serogroups O157 and O26, in Irish sheep. Recto-anal mucosal swab samples (n = 840) were collected over 24 months from two ovine slaughtering facilities. Samples were plated on selective agars and were quantitatively and qualitatively assessed via real-time PCR (RT-PCR) for Shiga toxin prevalence and serogroup. A subset of STEC isolates (n = 199) were selected for whole-genome sequencing and analyzed in silico. In total, 704/840 (83.8%) swab samples were Shiga toxin positive following RT-PCR screening, and 363/704 (51.6%) animals were subsequently culture positive for STEC. Five animals were shedding STEC O157, and three of these were identified as supershedders. No STEC O26 was isolated. Post hoc statistical analysis showed that younger animals are more likely to harbor STEC and that STEC carriage is most prevalent during the summer months. Following sequencing, 178/199 genomes were confirmed as STEC. Thirty-five different serotypes were identified, 15 of which were not yet reported for sheep. Serotype O91:H14 was the most frequently reported. Eight Shiga toxin gene variants were reported, two stx1 and six stx2, and three novel Shiga-toxin subunit combinations were observed. Variant stx1c was the most prevalent, while many strains also harbored stx2b. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) bacteria are foodborne, zoonotic pathogens of significant public health concern. All STEC organisms harbor stx, a critical virulence determinant, but it is not expressed in most serotypes. Sheep shed the pathogen via fecal excretion and are increasingly recognized as important contributors to the dissemination of STEC. In this study, we have found that there is high prevalence of STEC circulating within sheep and that prevalence is related to animal age and seasonality. Further, sheep harbor a variety of non-O157 STEC, whose prevalence and contribution to human disease have been underinvestigated for many years. A variety of Stx variants were also observed, some of which are of high clinical importance.
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Bai X, Scheutz F, Dahlgren HM, Hedenström I, Jernberg C. Characterization of Clinical Escherichia coli Strains Producing a Novel Shiga Toxin 2 Subtype in Sweden and Denmark. Microorganisms 2021; 9:microorganisms9112374. [PMID: 34835499 PMCID: PMC8625421 DOI: 10.3390/microorganisms9112374] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 11/16/2022] Open
Abstract
Shiga toxin (Stx) is the key virulence factor in the Shiga Toxin-Producing Escherichia coli (STEC), which can cause diarrhea and hemorrhagic colitis with potential life-threatening complications. There are two major types of Stx: Stx1 and Stx2. Several Stx1/Stx2 subtypes have been identified in E. coli, varying in sequences, toxicity and host specificity. Here, we report a novel Stx2 subtype (designated Stx2m) from three clinical E. coli strains isolated from diarrheal patients and asymptomatic carriers in Sweden and Denmark. The Stx2m toxin was functional and exhibited cytotoxicity in vitro. The two Swedish Stx2m-producing strains belonged to the same serotype O148:H39 and Multilocus Sequencing Typing (MLST) Sequence Type (ST) 5825, while the Danish strain belonged to the O96:H19 serotype and ST99 type. Whole-genome sequencing (WGS) data analysis revealed that the three Stx2m-producing strains harbored additional virulence genes and the macrolide resistance gene mdf (A). Our findings expand the pool of Stx2 subtypes and highlight the clinical significance of emerging STEC variants. Given the clinical relevance of the Stx2m-producing strains, we propose to include Stx2m in epidemiological surveillance of STEC infections and clinical diagnosis.
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Affiliation(s)
- Xiangning Bai
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 52 Stockholm, Sweden;
- Division of Laboratory Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Flemming Scheutz
- The International Escherichia and Klebsiella Centre, Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Henrik Mellström Dahlgren
- County Council Department of Communicable Disease Control and Prevention, Region Västra Götaland, 411 18 Gothenburg, Sweden;
| | | | - Cecilia Jernberg
- Public Health Agency of Sweden, 171 82 Solna, Sweden;
- Correspondence:
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Elsayed MSAE, Eldsouky SM, Roshdy T, Bayoume AMA, Nasr GM, Salama ASA, Akl BA, Hasan AS, Shahat AK, Khashaba RA, Abdelhalim WA, Nasr HE, Mohammed LA, Salah A. Genetic and antimicrobial resistance profiles of non-O157 Shiga toxin-producing Escherichia coli from different sources in Egypt. BMC Microbiol 2021; 21:257. [PMID: 34556033 PMCID: PMC8461963 DOI: 10.1186/s12866-021-02308-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/28/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal samples, cow's milk, cattle beef, human urine, and ear discharge were screened for 12 virulence genes, phenotypic and genotypic antimicrobial resistance, and multiple-locus variable-number tandem-repeat analysis (MLVA). RESULTS The majority of strains harbored Shiga toxin 1 (stx1) and stx1d, stx2 and stx2e, and ehxA genes, while a minority harbored stx2c subtype and eaeA. We identified 10 stx gene combinations; most of strains 31/60 (51.7%) exhibited four copies of stx genes, namely the stx1, stx1d, stx2, and stx2e, and the strains exhibited a high range of multiple antimicrobial resistance indices. The resistance genes blaCTX-M-1 and blaTEM were detected. For the oxytetracycline resistance genes, most of strains contained tetA, tetB, tetE, and tetG while the tetC was present at low frequency. MLVA genotyping resolved 26 unique genotypes; genotype 21 was highly prevalent. The six highly discriminatory loci DI = 0.9138 are suitable for the preliminary genotyping of STEC from animals and humans. CONCLUSIONS The STEC isolated from animals are virulent, resistant to antimicrobials, and genetically diverse, thus demands greater attention for the potential risk to human.
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Affiliation(s)
- Mohamed Sabry Abd Elraheam Elsayed
- Department of Bacteriology, Mycology, and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Menoufia, Egypt.
| | - Samah Mahmoud Eldsouky
- Department of Otolaryngology and Head and Neck Surgery, Faculty of Medicine, Benha University, Benha, Egypt
| | - Tamer Roshdy
- Department of Molecular Biology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Abeer Mohamed Ahmed Bayoume
- Department of Microbial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Ghada M Nasr
- Department of Molecular Diagnostics, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, 32897, Egypt
| | - Ali S A Salama
- Microbiology Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Behiry A Akl
- Microbiology Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Al Shaimaa Hasan
- Department of Medical Pharmacology, Qena Faculty of Medicine, South Valley University, Qena, Egypt
| | - Amany Kasem Shahat
- Department of Medical Microbiology and Immunology, Benha University, Benha, Egypt
| | - Rana Atef Khashaba
- Department of Clinical Pathology and Chemistry, Benha Faculty of Medicine, Benha University, Benha, Egypt
| | | | - Hend E Nasr
- Department of Medical Biochemistry and Molecular Biology, Benha University, Benha, Egypt
| | | | - Ahmed Salah
- Department of Molecular Biology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
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21
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Gigliucci F, van Hoek AHAM, Chiani P, Knijn A, Minelli F, Scavia G, Franz E, Morabito S, Michelacci V. Genomic Characterization of hlyF-positive Shiga Toxin-Producing Escherichia coli, Italy and the Netherlands, 2000-2019. Emerg Infect Dis 2021; 27:853-861. [PMID: 33622476 PMCID: PMC7920663 DOI: 10.3201/eid2703.203110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Shiga toxin–producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E. coli (ExPEC) strains. We identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands during 2000–2019. The isolates belong to 2 major populations: 1 belongs to sequence type 301 and harbors diverse stx2 subtypes, the intimin variant eae-ξ, and pO157-like and pR444_A plasmids; 1 consists of strains belonging to various sequence types, some of which lack the pO157 plasmid, the locus of enterocyte effacement, and the antimicrobial resistance–encoding region. Our results showed that STEC strains harboring ExPEC-associated virulence genes can include multiple serotypes and that the pR444_A plasmid can be acquired and mobilized by STEC strains.
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22
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Lee KS, Jeong YJ, Lee MS. Escherichia coli Shiga Toxins and Gut Microbiota Interactions. Toxins (Basel) 2021; 13:toxins13060416. [PMID: 34208170 PMCID: PMC8230793 DOI: 10.3390/toxins13060416] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/19/2022] Open
Abstract
Escherichia coli (EHEC) and Shigella dysenteriae serotype 1 are enterohemorrhagic bacteria that induce hemorrhagic colitis. This, in turn, may result in potentially lethal complications, such as hemolytic uremic syndrome (HUS), which is characterized by thrombocytopenia, acute renal failure, and neurological abnormalities. Both species of bacteria produce Shiga toxins (Stxs), a phage-encoded exotoxin inhibiting protein synthesis in host cells that are primarily responsible for bacterial virulence. Although most studies have focused on the pathogenic roles of Stxs as harmful substances capable of inducing cell death and as proinflammatory factors that sensitize the host target organs to damage, less is known about the interface between the commensalism of bacterial communities and the pathogenicity of the toxins. The gut contains more species of bacteria than any other organ, providing pathogenic bacteria that colonize the gut with a greater number of opportunities to encounter other bacterial species. Notably, the presence in the intestines of pathogenic EHEC producing Stxs associated with severe illness may have compounding effects on the diversity of the indigenous bacteria and bacterial communities in the gut. The present review focuses on studies describing the roles of Stxs in the complex interactions between pathogenic Shiga toxin-producing E. coli, the resident microbiome, and host tissues. The determination of these interactions may provide insights into the unresolved issues regarding these pathogens.
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Affiliation(s)
- Kyung-Soo Lee
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea;
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 127 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
| | - Yu-Jin Jeong
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea;
- Correspondence: (Y.-J.J.); (M.-S.L.)
| | - Moo-Seung Lee
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea;
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 127 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
- Correspondence: (Y.-J.J.); (M.-S.L.)
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23
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Vieira KCDO, Silva HRAD, Rocha IPM, Barboza E, Eller LKW. Foodborne pathogens in the omics era. Crit Rev Food Sci Nutr 2021; 62:6726-6741. [PMID: 33783282 DOI: 10.1080/10408398.2021.1905603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
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Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
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24
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Rodríguez-Rubio L, Haarmann N, Schwidder M, Muniesa M, Schmidt H. Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity. Pathogens 2021; 10:404. [PMID: 33805526 PMCID: PMC8065619 DOI: 10.3390/pathogens10040404] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded in the genome of lambdoid bacteriophages, which spend the most time of their life cycle integrated as prophages in specific sites of the bacterial chromosome. Upon spontaneous induction or induction by chemical or physical stimuli, the stx genes are co-transcribed together with the late phase genes of the prophages. After being assembled in the cytoplasm, and after host cell lysis, mature bacteriophage particles are released into the environment, together with Stx. As members of the group of lambdoid phages, Stx phages share many genetic features with the archetypical temperate phage Lambda, but are heterogeneous in their DNA sequences due to frequent recombination events. In addition to Stx phages, the genome of pathogenic STEC bacteria may contain numerous prophages, which are either cryptic or functional. These prophages may carry foreign genes, some of them related to virulence, besides those necessary for the phage life cycle. Since the production of one or more Stx is considered the major pathogenicity factor of STEC, we aim to highlight the new insights on the contribution of Stx phages and other STEC phages to pathogenicity.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Nadja Haarmann
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maike Schwidder
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
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25
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Liu Y, Tian S, Thaker H, Dong M. Shiga Toxins: An Update on Host Factors and Biomedical Applications. Toxins (Basel) 2021; 13:222. [PMID: 33803852 PMCID: PMC8003205 DOI: 10.3390/toxins13030222] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
Shiga toxins (Stxs) are classic bacterial toxins and major virulence factors of toxigenic Shigella dysenteriae and enterohemorrhagic Escherichia coli (EHEC). These toxins recognize a glycosphingolipid globotriaosylceramide (Gb3/CD77) as their receptor and inhibit protein synthesis in cells by cleaving 28S ribosomal RNA. They are the major cause of life-threatening complications such as hemolytic uremic syndrome (HUS), associated with severe cases of EHEC infection, which is the leading cause of acute kidney injury in children. The threat of Stxs is exacerbated by the lack of toxin inhibitors and effective treatment for HUS. Here, we briefly summarize the Stx structure, subtypes, in vitro and in vivo models, Gb3 expression and HUS, and then introduce recent studies using CRISPR-Cas9-mediated genome-wide screens to identify the host cell factors required for Stx action. We also summarize the latest progress in utilizing and engineering Stx components for biomedical applications.
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Affiliation(s)
- Yang Liu
- Department of Nephrology, The First Hospital of Jilin University, Changchun 130021, China
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Songhai Tian
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Hatim Thaker
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Min Dong
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA; (S.T.); (H.T.)
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
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26
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Bai X, Zhang J, Hua Y, Jernberg C, Xiong Y, French N, Löfgren S, Hedenström I, Ambikan A, Mernelius S, Matussek A. Genomic Insights Into Clinical Shiga Toxin-Producing Escherichia coli Strains: A 15-Year Period Survey in Jönköping, Sweden. Front Microbiol 2021; 12:627861. [PMID: 33613494 PMCID: PMC7893091 DOI: 10.3389/fmicb.2021.627861] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens that can cause human infections ranging from asymptomatic carriage to bloody diarrhea (BD) and fatal hemolytic uremic syndrome (HUS). However, the molecular mechanism of STEC pathogenesis is not entirely known. Here, we demonstrated a large scale of molecular epidemiology and in-depth genomic study of clinical STEC isolates utilizing clinical and epidemiological data collected in Region Jönköping County, Sweden, over a 15-year period. Out of 184 STEC isolates recovered from distinct patients, 55 were from patients with BD, and 129 were from individuals with non-bloody stools (NBS). Five individuals developed HUS. Adults were more associated with BD. Serotypes O157:H7, O26:H11, O103:H2, O121:H19, and O104:H4 were more often associated with BD. The presence of Shiga toxin-encoding gene subtypes stx 2a, stx 2a + stx 2c, and stx 1a + stx 2c was associated with BD, while stx 1 a was associated with milder disease. Multiplex virulence and accessory genes were correlated with BD; these genes encode toxins, adhesion, autotransporters, invasion, and secretion system. A number of antimicrobial resistance (AMR) genes, such as aminoglycoside, aminocoumarin, macrolide, and fluoroquinolone resistance genes, were prevalent among clinical STEC isolates. Whole-genome phylogeny revealed that O157 and non-O157 STEC isolates evolved from distinct lineages with a few exceptions. Isolates from BD showed more tendency to cluster closely. In conclusion, this study unravels molecular trait of clinical STEC strains and identifies genetic factors associated with severe clinical outcomes, which could contribute to management of STEC infections and disease progression if confirmed by further functional validation.
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Affiliation(s)
- Xiangning Bai
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ji Zhang
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Ying Hua
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, China
| | | | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Nigel French
- New Zealand Food Safety Science and Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Sture Löfgren
- Laboratory Medicine, Jönköping Region County, Department of Clinical and Experimental Medicine, Linköping University, Jönköping, Sweden
| | | | - Anoop Ambikan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Sara Mernelius
- Laboratory Medicine, Jönköping Region County, Department of Clinical and Experimental Medicine, Linköping University, Jönköping, Sweden
| | - Andreas Matussek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
- Laboratory Medicine, Jönköping Region County, Department of Clinical and Experimental Medicine, Linköping University, Jönköping, Sweden
- Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
- Division of Laboratory Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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27
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McMAHON T, Bastian J, Alshawa I, Gill A. PCR Primers for Screening Food for Verotoxin-Producing Escherichia coli, Inclusive of Three vt1 and Seven vt2 Subtypes. J Food Prot 2021; 84:296-302. [PMID: 32977337 DOI: 10.4315/jfp-20-233] [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: 06/12/2020] [Accepted: 09/21/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT Verotoxin-producing Escherichia coli (VTEC; also known as Shiga toxin-producing E. coli) is a significant cause of foodborne illnesses around the world. Due to the serological and genomic diversity of VTEC, methods of detection for VTEC in food samples require detection of verotoxin or its gene vt (also known as stx). The current taxonomy of vt identifies three vt1 (a, c, d) and seven vt2 (a to g) subtypes. PCR detection of vt is convenient and rapid, but protocols may not detect all currently identified variants or subtypes of vt. The Health Canada Compendium of Analytical Methods protocol for the analysis of food for VTEC is MFLP-52. MFLP-52 includes a VT Screening PCR that is used to determine the presumptive presence of VTEC by the detection of vt in food enrichments and to differentiate VTEC from other isolates. The VT Screening PCR was developed prior to the establishment of the current vt taxonomy. An evaluation of VT Screening PCR for detection of the 10 established vt subtypes was performed, and it was discovered that the method could not detect subtypes vt1d and vt2f. Additional primers and a modified protocol were developed, and the modified VT Screening PCR was tested against an inclusivity panel of 50 VTEC strains, including representatives of 10 vt subtypes, and an exclusivity panel of 30 vt-negative E. coli from various sources, to ensure specificity. The reliability of MFLP-52 with the modified VT Screening PCR was assessed by analysis of four priority food matrices (ground beef, lettuce, cheese, and apple cider) inoculated with a VTEC strain at 2 to 5 CFU/25 g. The modified VT Screening PCR was determined to be able to detect all 10 vt subtypes and reliably detect the presence of VTEC in all tested food enrichments. HIGHLIGHTS
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Affiliation(s)
- Tanis McMAHON
- Health Canada, Bureau of Microbial Hazards, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada K1A 0K9
| | - Jillian Bastian
- Health Canada, Bureau of Microbial Hazards, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada K1A 0K9
| | - Inas Alshawa
- Health Canada, Bureau of Microbial Hazards, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada K1A 0K9
| | - Alexander Gill
- Health Canada, Bureau of Microbial Hazards, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, Canada K1A 0K9.,(ORCID: https://orcid.org/0000-0003-2380-2148 [A.G.])
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28
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A Toxic Environment: a Growing Understanding of How Microbial Communities Affect Escherichia coli O157:H7 Shiga Toxin Expression. Appl Environ Microbiol 2020; 86:AEM.00509-20. [PMID: 32358004 DOI: 10.1128/aem.00509-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) strains, including E. coli O157:H7, cause severe illness in humans due to the production of Shiga toxin (Stx) and other virulence factors. Because Stx is coregulated with lambdoid prophage induction, its expression is especially susceptible to environmental cues. Infections with Stx-producing E. coli can be difficult to model due to the wide range of disease outcomes: some infections are relatively mild, while others have serious complications. Probiotic organisms, members of the gut microbiome, and organic acids can depress Stx production, in many cases by inhibiting the growth of EHEC strains. On the other hand, the factors currently known to amplify Stx act via their effect on the stx-converting phage. Here, we characterize two interactive mechanisms that increase Stx production by O157:H7 strains: first, direct interactions with phage-susceptible E. coli, and second, indirect amplification by secreted factors. Infection of susceptible strains by the stx-converting phage can expand the Stx-producing population in a human or animal host, and phage infection has been shown to modulate virulence in vitro and in vivo Acellular factors, particularly colicins and microcins, can kill O157:H7 cells but may also trigger Stx expression in the process. Colicins, microcins, and other bacteriocins have diverse cellular targets, and many such molecules remain uncharacterized. The identification of additional Stx-amplifying microbial interactions will improve our understanding of E. coli O157:H7 infections and help elucidate the intricate regulation of pathogenicity in EHEC strains.
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29
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Hughes AC, Patfield S, Rasooly R, He X. Validation of a Cell-Based Assay for Detection of Active Shiga Toxins Produced by Escherichia coli in Water. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17217901. [PMID: 33126550 PMCID: PMC7663042 DOI: 10.3390/ijerph17217901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) causes a wide spectrum of diseases, including hemorrhagic colitis and hemolytic uremic syndrome (HUS). Almost 5% of STEC infections result from waterborne exposures, yet there is no test listed in the EPA's current Selected Analytical Methods for the detection of active Shiga toxins (Stxs) in water. In this study, a HeLa cell-based assay is validated for the detection of metabolically active Stxs produced by STEC in water, including tap, bottled, and pond water. Active Stxs are detected even when the number of Stx-producing bacteria is less than 0.4 CFU/mL and the assay performance is not affected by background flora or chlorine in the water. This assay is not only as simple and affordable as cell-free assays but also detects active holotoxins without the use of live animals. In addition, the assay is designed for use in multi-well formats, making it ideal for high-throughput screening of water samples and therefore useful for environmental public health surveillance programs to reduce human risk of infection with STEC.
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Affiliation(s)
- Anna C. Hughes
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA; (A.C.H.); (S.P.); (R.R.)
| | - Stephanie Patfield
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA; (A.C.H.); (S.P.); (R.R.)
- Forensic Services Division, Contra Costa County Office of the Sheriff, 651 Pine St., Martinez, CA 94553, USA
| | - Reuven Rasooly
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA; (A.C.H.); (S.P.); (R.R.)
| | - Xiaohua He
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA; (A.C.H.); (S.P.); (R.R.)
- Correspondence: ; Tel.: +1-(510)-559-5823
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30
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Zuppi M, Tozzoli R, Chiani P, Quiros P, Martinez-Velazquez A, Michelacci V, Muniesa M, Morabito S. Investigation on the Evolution of Shiga Toxin-Converting Phages Based on Whole Genome Sequencing. Front Microbiol 2020; 11:1472. [PMID: 32754128 PMCID: PMC7366253 DOI: 10.3389/fmicb.2020.01472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/05/2020] [Indexed: 12/25/2022] Open
Abstract
Bacteriophages are pivotal elements in the dissemination of virulence genes. The main virulence determinants of Shiga Toxin producing E. coli, Shiga Toxins (Stx), are encoded by genes localized in the genome of lambdoid bacteriophages. Stx comprise two antigenically different types, Stx1 and Stx2, further divided into subtypes. Among these, certain Stx2 subtypes appear to be more commonly occurring in the most severe forms of the STEC disease, haemorrhagic colitis and haemolytic uremic syndrome (HUS). This study aimed at obtaining insights on the evolution of Stx2 bacteriophages, due to their relevance in public health, and we report here on the analysis of the genomic structure of Stx2 converting phages in relation with the known reservoir of the E. coli strains harboring them. Stx2-converting phages conveying the genes encoding different stx2 subtypes have been isolated from STEC strains and their whole genomes have been sequenced, analyzed and compared to those of other Stx2 phages available in the public domain. The phages' regions containing the stx2 genes have been analyzed in depth allowing to make inference on the possible mechanisms of selection and maintenance of certain Stx2 phages in the reservoir. The "stx regions" of different stx2 gene subtypes grouped into three different evolutionary lines in the comparative analysis, reflecting the frequency with which these subtypes are found in different animal niches, suggesting that the colonization of specific reservoir by STEC strains could be influenced by the Stx phage that they carry. Noteworthy, we could identify the presence of nanS-p gene exclusively in the "stx regions" of the phages identified in STEC strains commonly found in cattle. As a matter of fact, this gene encodes an esterase capable of metabolizing sialic acids produced by submaxillary glands of bovines and present in great quantities in their gastrointestinal tract.
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Affiliation(s)
- Michele Zuppi
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Rosangela Tozzoli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Chiani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Pablo Quiros
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Adan Martinez-Velazquez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Valeria Michelacci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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Maria Ferreira Cavalcanti A, Tavanelli Hernandes R, Harummyy Takagi E, Ernestina Cabílio Guth B, de Lima Ori É, Regina Schicariol Pinheiro S, Sueli de Andrade T, Louzada Oliveira S, Cecilia Cergole-Novella M, Rodrigues Francisco G, dos Santos LF. Virulence Profiling and Molecular Typing of Shiga Toxin-Producing E. coli (STEC) from Human Sources in Brazil. Microorganisms 2020; 8:microorganisms8020171. [PMID: 31991731 PMCID: PMC7074907 DOI: 10.3390/microorganisms8020171] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
Since no recent data characterizing Shiga toxin-producing E. coli (STEC) from human infections in Brazil are available, the present study aimed to investigate serotypes, stx genotypes, and accessory virulence genes, and also to perform pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) of 43 STEC strains recovered from 2007 to 2017. Twenty-one distinct serotypes were found, with serotype O111:H8 being the most common. However, serotypes less frequently reported in human diseases were also found and included a hybrid STEC/ETEC O100:H25 clone. The majority of the strains carried stx1a as the sole stx genotype and were positive for the eae gene. Regarding the occurrence of 28 additional virulence genes associated with plasmids and pathogenicity islands, a diversity of profiles was found especially among the eae-harboring strains, which had combinations of markers composed of up to 12 distinct genes. Although PFGE analysis demonstrated genetic diversity between serotypes such as O157:H7, O111:H8, O26:H11, O118:H16, and O123:H2, high genetic relatedness was found for strains of serotypes O24:H4 and O145:H34. MLST allowed the identification of 17 distinct sequence types (STs) with ST 16 and 21 being the most common ones. Thirty-five percent of the strains studied were not typeable by the currently used MLST approach, suggesting new STs. Although STEC O111:H8 remains the leading serotype in Brazil, a diversity of other serotypes, some carrying virulence genes and belonging to STs incriminated as causing severe disease, were found in this study. Further studies are needed to determine whether they have any epidemiological relevance.
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Affiliation(s)
- Adriene Maria Ferreira Cavalcanti
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
| | - Rodrigo Tavanelli Hernandes
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brasil; (R.T.H.); (S.L.O.)
| | - Elizabeth Harummyy Takagi
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
| | - Beatriz Ernestina Cabílio Guth
- Departamento de Microbiologia, Imunologia, Parasitologia, Escola Paulista de Medicina Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brasil;
| | - Érica de Lima Ori
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
| | - Sandra Regina Schicariol Pinheiro
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
| | - Tânia Sueli de Andrade
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
| | - Samara Louzada Oliveira
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brasil; (R.T.H.); (S.L.O.)
| | - Maria Cecilia Cergole-Novella
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
| | - Gabriela Rodrigues Francisco
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
| | - Luís Fernando dos Santos
- Centro de Bacteriologia (National Reference Laboratory for STEC infections and HUS), Instituto Adolfo Lutz, São Paulo 01246-000, SP, Brasil; (A.M.F.C.); (E.H.T.); (S.R.S.P.); (T.S.d.A.); (M.C.C.-N.); (G.R.F.)
- Correspondence: ; Tel.: +55-11-3068-2896
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Monteiro Pires S, Morabito S, Niskanen T, Scheutz F, da Silva Felício MT, Messens W, Bolton D. Pathogenicity assessment of Shiga toxin‐producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC. EFSA J 2020. [DOI: 10.2903/j.efsa.2020.5967] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Structural and Functional Characterization of Stx2k, a New Subtype of Shiga Toxin 2. Microorganisms 2019; 8:microorganisms8010004. [PMID: 31861375 PMCID: PMC7022315 DOI: 10.3390/microorganisms8010004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 01/07/2023] Open
Abstract
Shiga toxin (Stx) is the major virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx evolves rapidly and, as such, new subtypes continue to emerge that challenge the efficacy of existing disease management and surveillance strategies. A new subtype, Stx2k, was recently identified in E. coli isolated from a wide range of sources including diarrheal patients, animals, and raw meats, and was poorly detected by existing immunoassays. In this study, the structure of Stx2kE167Q was determined at 2.29 Å resolution and the conservation of structure with Stx2a was revealed. A novel polyclonal antibody capable of neutralizing Stx2k and an immunoassay, with a 10-fold increase in sensitivity compared to assays using extant antibodies, were developed. Stx2k is less toxic than Stx2a in Vero cell assays but is similar to Stx2a in receptor-binding preference, thermostability, and acid tolerance. Although Stx2k does not appear to be as potent as Stx2a to Vero cells, the wide distribution and blended virulence profiles of the Stx2k-producing strains suggest that horizontal gene transfer through Stx2k-converting phages could result in the emergence of new and highly virulent pathogens. This study provides useful information and tools for early detection and control of Stx2k-producing E. coli, which could reduce public risk of infection by less-known STECs.
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Yang X, Bai X, Zhang J, Sun H, Fu S, Fan R, He X, Scheutz F, Matussek A, Xiong Y. Escherichia coli strains producing a novel Shiga toxin 2 subtype circulate in China. Int J Med Microbiol 2019; 310:151377. [PMID: 31757694 DOI: 10.1016/j.ijmm.2019.151377] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 11/16/2022] Open
Abstract
Shiga toxin (Stx) is the key virulence factor in Shiga toxin producing Escherichia coli (STEC), which can cause diarrhea and hemorrhagic colitis with life-threatening complications. Stx comprises two toxin types, Stx1 and Stx2. Several Stx1/Stx2 subtypes have been identified in E. coli, which are variable in sequences, toxicity and host specificity. Here, we report the identification of a novel Stx2 subtype, designated Stx2k, in E. coli strains widely detected from diarrheal patients, animals, and raw meats in China over time. Stx2k exhibits varied cytotoxicity in vitro among individual strains. The Stx2k converting prophages displayed considerable heterogeneity in terms of insertion site, genetic content and structure. Whole genome analysis revealed that the stx2k-containing strains were genetically heterogeneous with diverse serotypes, sequence types, and virulence gene profiles. The nine stx2k-containing strains formed two major phylogenetic clusters closely with strains belonging to STEC, enterotoxigenic E. coli (ETEC), and STEC/ETEC hybrid. One stx2k-containing strain harbored one plasmid-encoded heat-stable enterotoxin sta gene and two identical copies of chromosome-encoded stb gene, exhibiting STEC/ETEC hybrid pathotype. Our finding enlarges the pool of Stx2 subtypes and highlights the extraordinary genomic plasticity of STEC strains. Given the wide distribution of the Stx2k-producing strains in diverse sources and their pathogenic potential, Stx2k should be taken into account in epidemiological surveillance of STEC infections and clinical diagnosis.
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Affiliation(s)
- Xi Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Ji Zhang
- EpiLab, New Zealand Food Safety Science & Research Centre, School of Veterinary Science, Massey University, New Zealand
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Shanshan Fu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Ruyue Fan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Xiaohua He
- Western Regional Research Center, U.S. Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Flemming Scheutz
- The International Centre for Reference and Research on Escherichia and Klebsiella, Unit of Foodborne Bacteria and Typing, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Andreas Matussek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang Province, China.
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Response to Questions Posed by the Food and Drug Administration Regarding Virulence Factors and Attributes that Define Foodborne Shiga Toxin-Producing Escherichia coli (STEC) as Severe Human Pathogens †. J Food Prot 2019; 82:724-767. [PMID: 30969806 DOI: 10.4315/0362-028x.jfp-18-479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
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- NACMCF Executive Secretariat, * U.S. Department of Agriculture, Food Safety and Inspection Service, Office of Public Health Science, PP3, 9-178, 1400 Independence Avenue S.W., Washington, D.C. 20250-3700, USA
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Patel IR, Gangiredla J, Lacher DW, Mammel MK, Bagi L, Baranzoni GM, Fratamico PM, Roberts EL, DebROY C, Lindsey RL, V Stoneburg D, Martin H, Smith P, Strockbine NA, Elkins CA, Scheutz F, Feng PCH. Interlaboratory Evaluation of the U.S. Food and Drug Administration Escherichia coli Identification Microarray for Profiling Shiga Toxin-Producing Escherichia coli. J Food Prot 2018; 81:1275-1282. [PMID: 29985068 PMCID: PMC6193752 DOI: 10.4315/0362-028x.jfp-18-052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The U.S. Food and Drug Administration Escherichia coli Identification (FDA-ECID) microarray provides rapid molecular characterization of E. coli. The effectiveness of the FDA-ECID for characterizing Shiga toxin-producing E. coli (STEC) was evaluated by three federal laboratories and one reference laboratory with a panel of 54 reference E. coli strains from the External Quality Assurance program. Strains were tested by FDA-ECID for molecular serotyping (O and H antigens), Shiga toxin subtyping, and the presence of the ehxA and eae genes for enterohemolysin and intimin, respectively. The FDA-ECID O typing was 96% reproducible among the four laboratories and 94% accurate compared with the reference External Quality Assurance data. Discrepancies were due to the absence of O41 target loci on the array and to two pairs of O types with identical target sequences. H typing was 96% reproducible and 100% accurate, with discrepancies due to two strains from one laboratory that were identified as mixed by FDA-ECID. Shiga toxin (Stx) type 1 subtyping was 100% reproducible and accurate, and Stx2 subtyping was 100% reproducible but only 64% accurate. FDA-ECID identified most Stx2 subtypes but had difficulty distinguishing among stx2a, stx2c, and stx2d genes because of close similarities of these sequences. FDA-ECID was 100% effective for detecting ehxA and eae and accurately subtyped the eae alleles. This interlaboratory study revealed that FDA-ECID for STEC characterization was highly reproducible for molecular serotyping, stx and eae subtyping, and ehxA detection. However, the array was less useful for distinguishing among the highly homologous O antigen genes and the stx2a, stx2c, and stx2d subtypes.
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Affiliation(s)
- Isha R Patel
- 1 U.S. Food and Drug Administration, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA
| | - Jayanthi Gangiredla
- 1 U.S. Food and Drug Administration, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA
| | - David W Lacher
- 1 U.S. Food and Drug Administration, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA
| | - Mark K Mammel
- 1 U.S. Food and Drug Administration, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA
| | - Lori Bagi
- 2 U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
| | - Gian Marco Baranzoni
- 2 U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
| | - Pina M Fratamico
- 2 U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
| | - Elizabeth L Roberts
- 3 Escherichia coli Reference Center, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Chitrita DebROY
- 3 Escherichia coli Reference Center, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Rebecca L Lindsey
- 4 Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, USA
| | - Devon V Stoneburg
- 4 Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, USA
| | - Haley Martin
- 4 Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, USA
| | - Peyton Smith
- 4 Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, USA
| | - Nancy A Strockbine
- 4 Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, USA
| | - Christopher A Elkins
- 4 Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, USA
| | - Flemming Scheutz
- 5 WHO Collaborating Centre for Reference and Research on Escherichia and Klebsiella, Artillerivej 5, DK-2300, Copenhagen, Denmark; and
| | - Peter C H Feng
- 6 U.S. Food and Drug Administration, Division of Microbiology, 5001 Campus Drive, College Park, Maryland 20740, USA
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lei L, Rehman MU, Huang S, Zhang L, Wang L, Mehmood K, Zhang H, Tong X, Wang M, Li J. Antimicrobial resistance and prevalence of diarrheagenic Escherichia coli (DEC), in diarrheic yaks of Tibetan Plateau, China. Acta Trop 2018; 182:111-114. [PMID: 29470944 DOI: 10.1016/j.actatropica.2018.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/12/2018] [Accepted: 02/17/2018] [Indexed: 11/25/2022]
Abstract
This study was conducted to test the distribution of diarrheagenic Escherichia coli (DEC) associated genes in fecal isolates from diarrheic yaks of a high remote region of China. Briefly, we obtained 203 fecal samples from diarrheic adult yaks and E. coli strains were isolated and identified via standard methods The antibiotic sensitivity of isolates was determined via disk diffusion method and polymerase chain reaction (PCR) was used to detect the DEC virulence associated genes. Results of the current study showed a high rate of resistance to tetracycline (93.6%) and low rate of resistance to ofloxacin (16.7%) antibiotics. Meanwhile, five different diarrheagenic associated virulence traits were detected including; EAEC (11.80%), EHEC (25.62%), EIEC (17.18%), EPEC (36.92%) and ETEC (11.36%). Moreover, E. coli isolates were positive for all tested DEC associated virulence genes ranging from 1.48% to 33%. Additionally, four isolates were positive for more than one virulence genes. In conclusion, our investigation showed a relatively low number of E. coli virulence genes isolated from diarrheic Tibetan yaks, which could be attributed to the high altitude induced harsh environmental conditions that may not help in the growth and survival of pathogenic organisms. In addition, this study highlights the high level of antibiotic resistance in yaks, therefore; preventive measures should be taken to monitor the antibiotic usage in Tibet region of China.
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DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces. PLoS One 2018; 13:e0196490. [PMID: 29708991 PMCID: PMC5927410 DOI: 10.1371/journal.pone.0196490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli O104:H4, a hybrid pathotype reported in a large 2011 foodborne outbreak in Germany, has not been detected in cattle feces. However, cattle harbor and shed in the feces other O104 serotypes, particularly O104:H7, which has been associated with sporadic cases of diarrhea in humans. The objective of our study was to assess the virulence potential of Shiga toxin-producing E. coli (STEC) O104:H7 isolated from feces of feedlot cattle using DNA microarray. Six strains of STEC O104:H7 isolated from cattle feces were analyzed using FDA-E. coli Identification (ECID) DNA microarray to determine their virulence profiles and compare them to the human strains (clinical) of O104:H7, STEC O104:H4 (German outbreak strain), and O104:H21 (milk-associated Montana outbreak strain). Scatter plots were generated from the array data to visualize the gene-level differences between bovine and human O104 strains, and Pearson correlation coefficients (r) were determined. Splits tree was generated to analyze relatedness between the strains. All O104:H7 strains, both bovine and human, similar to O104:H4 and O104:H21 outbreak strains were negative for intimin (eae). The bovine strains were positive for Shiga toxin 1 subtype c (stx1c), enterohemolysin (ehxA), tellurite resistance gene (terD), IrgA homolog protein (iha), type 1 fimbriae (fimH), and negative for genes that code for effector proteins of type III secretory system. The six cattle O104 strains were closely related (r = 0.86-0.98) to each other, except for a few differences in phage related and non-annotated genes. One of the human clinical O104:H7 strains (2011C-3665) was more closely related to the bovine O104:H7 strains (r = 0.81-0.85) than the other four human clinical O104:H7 strains (r = 0.75-0.79). Montana outbreak strain (O104:H21) was more closely related to four of the human clinical O104:H7 strains than the bovine O104:H7 strains. None of the bovine E. coli O104 strains carried genes characteristic of E. coli O104:H4 German outbreak strain and unlike other human strains were also negative for Shiga toxin 2. Because cattle E. coli O104:H7 strains possess stx1c and genes that code for enterohemolysin and a variety of adhesins, the serotype has the potential to be a diarrheagenic foodborne pathogen in humans.
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