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Kalalah AA, Koenig SSK, Feng P, Bosilevac JM, Bono JL, Eppinger M. Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes. Microorganisms 2024; 12:699. [PMID: 38674643 PMCID: PMC11052207 DOI: 10.3390/microorganisms12040699] [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: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Shiga toxin-producing Escherichia coli are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the stx+ strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated stx- strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx1a- and ΦStx2a-prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Peter Feng
- U.S. Food and Drug Administration (FDA), College Park, MD 20740, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
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2
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Weinroth MD, Clawson ML, Harhay GP, Eppinger M, Harhay DM, Smith TPL, Bono JL. Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition. Front Microbiol 2023; 14:1303387. [PMID: 38169669 PMCID: PMC10758439 DOI: 10.3389/fmicb.2023.1303387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.
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Affiliation(s)
- Margaret D. Weinroth
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Michael L. Clawson
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Gregory P. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Dayna M. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Timothy P. L. Smith
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - James L. Bono
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
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3
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Hirai S, Yokoyama E, Shiwa Y, Ishige T, Ando N, Shimizu T, Murakami S. Clarification of relationship between single-nucleotide polymorphism panels of Shiga toxin-producing Escherichia coli O157:H7/H- strains. J Vet Med Sci 2022; 84:1399-1405. [PMID: 35989264 PMCID: PMC9586023 DOI: 10.1292/jvms.22-0242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Eighty strains of enterohemorrhagic Escherichia coli O157:H7/H- were
analyzed by three single-nucleotide polymorphism (SNP) panels using whole-genome
sequencing data. The partial concordance of SNP types among the different SNP panels was
observed on minimum spanning trees reconstructed with SNP data. As for lineage I/II
strains, some of the clade 7 strains belonged to one unique SNP type as determined by
three panels, suggesting that clade 7 should be divided into at least two genotypes,
namely, the unique type and the rest. In addition, clade 8 contained two unique genotypes,
which was consistent with the previous prediction. Similarly, for lineage II, clade 12
should be divided into three genotype strains. In contrast, many strains of several clades
belonging to lineage I were clustered into the same node on each minimum spanning tree
upon testing with the three SNP panels. Previous studies reported that lineage I diverged
more recently than lineages I/II and II. Such low diversity in lineage I in this study may
have arisen because this lineage has not accumulated SNPs because of its relatively recent
divergence. Based on the concordance observed in this study, some of the previously
published O157 genotype distribution data were successfully interpreted to clarify the
clade distribution, which was well supported by previous literature.
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Affiliation(s)
- Shinichiro Hirai
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases
| | - Eiji Yokoyama
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases.,Division of Bacteriology, Chiba Prefectural Institute of Public Health
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture.,Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of Agriculture
| | - Naoshi Ando
- Division of Bacteriology, Chiba Prefectural Institute of Public Health
| | - Takeshi Shimizu
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University
| | - Satoshi Murakami
- Laboratory of Animal Health, Department of Animal Science, Tokyo University of Agriculture
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4
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Sim EM, Kim R, Gall M, Arnott A, Howard P, Valcanis M, Howden BP, Sintchenko V. Added Value of Genomic Surveillance of Virulence Factors in Shiga Toxin-Producing Escherichia coli in New South Wales, Australia. Front Microbiol 2022; 12:713724. [PMID: 35002991 PMCID: PMC8733641 DOI: 10.3389/fmicb.2021.713724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/22/2021] [Indexed: 11/25/2022] Open
Abstract
The disease caused by Shiga toxin-producing Escherichia coli (STEC) remains a significant public health challenge globally, but the incidence of human STEC infections in Australia remains relatively low. This study examined the virulence characteristics and diversity of STEC isolates in the state of New South Wales between December 2017 and May 2020. Utilisation of both whole and core genome multi-locus sequence typing (MLST) allowed for the inference of genomic diversity and detection of isolates that were likely to be epidemiologically linked. The most common STEC serotype and stx subtype detected in this study were O157:H7 and stx1a, respectively. A genomic scan of other virulence factors present in STEC suggested interplay between iron uptake system and virulence factors that mediate either iron release or countermeasures against host defence that could result in a reduction of stx1a expression. This reduced expression of the dominant stx genotype could contribute to the reduced incidence of STEC-related illness in Australia. Genomic surveillance of STEC becomes an important part of public health response and ongoing interrogation of virulence factors in STEC offers additional insights for the public health risk assessment.
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Affiliation(s)
- Eby M Sim
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Ryan Kim
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Mailie Gall
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Alicia Arnott
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Peter Howard
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
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5
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Morita S, Sato S, Maruyama S, Nagasaka M, Murakami K, Inada K, Uchiumi M, Yokoyama E, Asakura H, Sugiyama H, Takai S, Maeda K, Kabeya H. Whole-genome sequence analysis of Shiga toxin-producing Escherichia coli O157 strains isolated from wild deer and boar in Japan. J Vet Med Sci 2021; 83:1860-1868. [PMID: 34629335 PMCID: PMC8762402 DOI: 10.1292/jvms.21-0454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The prevalence of Shiga toxin-producing Escherichia coli O157 (STEC O157) strains in wild deer and boar in Japan was investigated. STEC O157 strains were isolated from 1.9% (9/474) of the wild deer and 0.7% (3/426) of the wild boar examined. Pulsed-field gel electrophoresis (PFGE) analysis classified the wild deer and boar strains into four and three PFGE patterns, respectively. The PFGE pattern of one wild boar strain was similar to that of a cattle strain that had been isolated from a farm in the same area the wild boar was caught, suggesting that a STEC O157 strain may have been transmitted between wild boar and cattle. Clade analysis indicated that, although most of the strains were classified in clade 12, two strains were classified in clade 7. Whole-genome sequence (WGS) analysis indicated that all the strains carried mdfA, a drug resistance gene for macrolide antibiotics, and also pathogenicity-related genes similar to those in the Sakai strain. In conclusion, our study emphasized the importance of food hygiene in processing meat from Japanese wild animals for human consumption.
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Affiliation(s)
- Satoshi Morita
- Laboratory of Veterinary Food Hygiene, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
| | - Shingo Sato
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
| | - Mariko Nagasaka
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
| | - Kou Murakami
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
| | - Kazuya Inada
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
| | - Masako Uchiumi
- Laboratory of Veterinary Food Hygiene, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health
| | - Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences
| | - Hiromu Sugiyama
- Department of Parasitology, National Institute of Infectious Diseases
| | - Shinji Takai
- Laboratory of Animal Hygiene, School of Veterinary Medicine, Kitasato University
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Disease
| | - Hidenori Kabeya
- Laboratory of Veterinary Food Hygiene, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University
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6
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Kawase J, Hirai S, Yokoyama E, Hayashi F, Kurosaki M, Kawakami Y, Fukuma A, Sakai T, Kotani M, Asakura H. Phylogeny, Prevalence, and Shiga Toxin (Stx) Production of Clinical Escherichia coli O157 Clade 2 Strains Isolated in Shimane Prefecture, Japan. Curr Microbiol 2020; 78:265-273. [PMID: 33095293 DOI: 10.1007/s00284-020-02252-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
This study investigated the genetic and pathogenic variation of the subgroups of clade 2 strains of Shiga toxin (Stx)-producing Escherichia coli (STEC) O157. A total of 111 strains of STEC O157 isolated in Shimane prefecture, Japan, were classified in clade 2 (n = 39), clade 3 (n = 16), clade 4/5 (n = 3), clade 7 (n = 14), clade 8 (n = 17), and clade 12 (n = 22) by single-nucleotide polymorphism analysis and lineage-specific polymorphism assay-6. These results showed a distinct difference from our previous study in which clade 3 strains were the most prevalent strains in three other prefectures in Japan, indicating that the clade distribution of O157 strains was different in different geographic areas in Japan. Phylogenetic analysis using insertion sequence (IS) 629 distribution data showed that clade 2 strains formed two clusters, designated 2a and 2b. Stx2 production by cluster 2b strains was significantly higher than by cluster 2a strains (P < 0.01). In addition, population genetic analysis of the clade 2 strains showed significant linkage disequilibrium in the IS629 distribution of the strains in clusters 2a and 2b (P < 0.05). The ΦPT values calculated using the IS629 distribution data indicated that strains in clusters 2a and 2b were genetically different (P < 0.001). Cluster 2b strains are a highly pathogenic phylogenetic group and their geographic spread may be a serious public health concern.
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Affiliation(s)
- Jun Kawase
- Division of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, 582 Nishihamasada, Matsue City, Shimane, 690-0122, Japan.
| | - Shinichiro Hirai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama City, Tokyo, 208-0011, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba, 260-8715, Japan
| | - Fumi Hayashi
- Division of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, 582 Nishihamasada, Matsue City, Shimane, 690-0122, Japan
| | - Morito Kurosaki
- Division of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, 582 Nishihamasada, Matsue City, Shimane, 690-0122, Japan
| | - Yuta Kawakami
- Division of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, 582 Nishihamasada, Matsue City, Shimane, 690-0122, Japan
| | - Aiko Fukuma
- Division of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, 582 Nishihamasada, Matsue City, Shimane, 690-0122, Japan
| | - Tomotake Sakai
- Division of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, 582 Nishihamasada, Matsue City, Shimane, 690-0122, Japan
| | - Mayuko Kotani
- Division of Bacteriology, Shimane Prefectural Institute of Public Health and Environmental Science, 582 Nishihamasada, Matsue City, Shimane, 690-0122, Japan
| | - Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Tonomachi 3-25-26, Kawasaki-ku, Kawasaki City, Kanagawa, 210-9501, Japan
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7
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Nyong EC, Zaia SR, Allué-Guardia A, Rodriguez AL, Irion-Byrd Z, Koenig SSK, Feng P, Bono JL, Eppinger M. Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes. Front Microbiol 2020; 11:619. [PMID: 32351476 PMCID: PMC7175801 DOI: 10.3389/fmicb.2020.00619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
The toxigenic conversion of Escherichia coli strains by Shiga toxin-converting (Stx) bacteriophages were prominent and recurring events in the stepwise evolution of enterohemorrhagic E. coli (EHEC) O157:H7 from an enteropathogenic (EPEC) O55:H7 ancestor. Atypical, attenuated isolates have been described for both non-sorbitol fermenting (NSF) O157:H7 and SF O157:NM serotypes, which are distinguished by the absence of Stx, the characteristic virulence hallmark of Stx-producing E. coli (STEC). Such atypical isolates either never acquired Stx-phages or may have secondarily lost stx during the course of infection, isolation, or routine subculture; the latter are commonly referred to as LST (Lost Shiga Toxin)-isolates. In this study we analyzed the genomes of 15 NSF O157:H7 and SF O157:NM strains from North America, Europe, and Asia that are characterized by the absence of stx, the virulence hallmark of STEC. The individual genomic basis of the Stx (-) phenotype has remained largely undetermined as the majority of STEC genomes in public genome repositories were generated using short read technology and are in draft stage, posing a major obstacle for the high-resolution whole genome sequence typing (WGST). The application of LRT (long-read technology) sequencing provided us with closed genomes, which proved critical to put the atypical non-shigatoxigenic NSF O157:H7 and SF O157:NM strains into the phylogenomic context of the stepwise evolutionary model. Availability of closed chromosomes for representative Stx (-) NSF O157:H7 and SF O157:NM strains allowed to describe the genomic basis and individual evolutionary trajectories underlying the absence of Stx at high accuracy and resolution. The ability of LRT to recover and accurately assemble plasmids revealed a strong correlation between the strains' featured plasmid genotype and chromosomally inferred clade, which suggests the coevolution of the chromosome and accessory plasmids. The identified ancestral traits in the pSFO157 plasmid of NSF O157:H7 strain LSU-61 provided additional evidence for its intermediate status. Taken together, these observations highlight the utility of LRTs for advancing our understanding of EHEC O157:H7/NM pathogenome evolution. Insights into the genomic and phenotypic plasticity of STEC on a lineage- and genome-wide scale are foundational to improve and inform risk assessment, biosurveillance, and prevention strategies.
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Affiliation(s)
- Emmanuel C. Nyong
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sam R. Zaia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Anna Allué-Guardia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Armando L. Rodriguez
- Research Computing Support Group, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Zaina Irion-Byrd
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | | | - James L. Bono
- United States Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture (ARS-USDA), Clay Center, NE, United States
| | - Mark Eppinger
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
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8
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Juliana G, Jimena C, Mariel S, Ana B. Molecular subtyping and clonal relatedness of human and cattle verotoxin-producing Escherichia coli O157:H7 isolates. Microb Pathog 2020; 145:104183. [PMID: 32247643 DOI: 10.1016/j.micpath.2020.104183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/21/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022]
Abstract
Verotoxin-producing Escherichia coli O157:H7 is the dominant serotype isolated from patients with hemolytic-uremic syndrome (HUS) and, Argentina has the highest rate of HUS in the world. However, not all O157:H7 isolates have the same ability to infect and cause disease in humans. It has been postulated that O157:H7 strains integrate subpopulations related to the origin and virulence. In order to study the population structure and genetic diversity of VTEC O157:H7 from Argentina, a combination of molecular subtyping methods such as multiple loci VNTR analysis (MLVA), single nucleotide polymorphisms (SNP) and phylogroups assignment were used. According to MLVA, high genetic diversity was found among strains isolated from cattle, humans and food. On the other hand, 92% of the isolates presented the allele tir 255 T > A T and 95% were assigned to phylogroup E. We did not find a significant association between the isolates origin and the allele T presence (P > 0,05) postulated as significantly overrepresented in human isolates. Our results show that human and cattle VTEC O157:H7 isolates from Argentina are a homogeneous group and, although it presents high genetic diversity in relation to their MLVA and virulence profiles, it is not possible to distinguish divergent populations. The presence in all the strains of a high number of T3SS effectors genes and the no association of genetic subtypes with strain source, is an alert about the potential risk in public health that VTEC O157:H7 cattle strains possess and, at less, a partial explication about the high incidence of HUS in Argentina.
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Affiliation(s)
- González Juliana
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CIC-UNCPBA, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Buenos Aires, Argentina; Laboratorio de Microbiología de Los Alimentos, Departamento de Tecnología y Calidad de Los Alimentos, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Buenos Aires, Argentina
| | - Cadona Jimena
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CIC-UNCPBA, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Buenos Aires, Argentina
| | - Sanso Mariel
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CIC-UNCPBA, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Buenos Aires, Argentina
| | - Bustamante Ana
- Laboratorio de Inmunoquímica y Biotecnología, Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CIC-UNCPBA, Facultad de Ciencias Veterinarias, UNCPBA, Tandil, Buenos Aires, Argentina.
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9
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Cowley LA, Dallman TJ, Jenkins C, Sheppard SK. Phage Predation Shapes the Population Structure of Shiga-Toxigenic Escherichia coli O157:H7 in the UK: An Evolutionary Perspective. Front Genet 2019; 10:763. [PMID: 31543896 PMCID: PMC6730009 DOI: 10.3389/fgene.2019.00763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/18/2019] [Indexed: 01/19/2023] Open
Abstract
Bacterial–host interactions are non-linear and actually threefold, involving significant selection through predatory lytic bacteriophages in the host environment. In studies of human and animal gut microbiome bacteria, it is important to consider phage in all host–pathogen interactions. We use an important zoonotic pathogen, Shiga toxigenic Escherichia coli (STEC) O157:H7, to investigate this. Our study provides evidence that phage resistance profiles are well maintained at the sub-lineage level with variation in profiles within sub-lineages uncommon. This indicates that phage resistance heterogeneity happened early on in the STEC O157:H7 natural history and that occasional “wobbles” do not often outcompete the stable lineage unless combined with a competitive advantage. We discuss an example of this in the acquisition of stx2a that, while an important virulence factor, also conveys increased phage cross-resistance. We also discuss the role of phage resistance in co-occurrence of the three stable lineages worldwide and whether differing phage resistance is maintaining diversity.
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Affiliation(s)
- Lauren A Cowley
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Timothy J Dallman
- National Infection Services, Public Health England, London, United Kingdom
| | - Claire Jenkins
- National Infection Services, Public Health England, London, United Kingdom
| | - Samuel K Sheppard
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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10
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Ingle DJ, Gonçalves da Silva A, Valcanis M, Ballard SA, Seemann T, Jennison AV, Bastian I, Wise R, Kirk MD, Howden BP, Williamson DA. Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia. Microb Genom 2019; 5. [PMID: 31107203 PMCID: PMC6562248 DOI: 10.1099/mgen.0.000268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomics-based studies of STEC have been predominately focused upon STEC collected in the Northern Hemisphere. Here, we demonstrate the population structure of 485 STEC isolates in Australia, and show that several clonal groups (CGs) common to Australia were infrequently detected in a representative selection of contemporary STEC genomes from around the globe. Further, phylogenetic analysis demonstrated that lineage II of the global O157:H7 STEC was most prevalent in Australia, and was characterized by a frameshift mutation in flgF, resulting in the H-non-motile phenotype. Strong concordance between in silico and phenotypic serotyping was observed, along with concordance between in silico and conventional detection of stx genes. These data represent the most comprehensive STEC analysis from the Southern Hemisphere, and provide a framework for future national genomics-based surveillance of STEC in Australia.
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Affiliation(s)
- Danielle J. Ingle
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Melbourne Bioinformatics Group, Victoria, Australia
| | - Amy V. Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Queensland, Australia
| | | | - Rolf Wise
- SA Pathology, South Australia, Australia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Deborah A. Williamson
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- *Correspondence: Deborah A. Williamson,
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Longitudinal Study of Shiga Toxin-Producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk. Appl Environ Microbiol 2019; 85:AEM.02910-18. [PMID: 30709824 PMCID: PMC6585499 DOI: 10.1128/aem.02910-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/28/2019] [Indexed: 01/12/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) and Campylobacter jejuni are notable health hazards associated with the consumption of raw milk. These bacteria may colonize the intestines of asymptomatic cattle and enter bulk tank milk via fecal contamination during milking. We studied the frequency of STEC O157:H7 and C. jejuni contamination in tank milk (n = 785) and the in-line milk filters of milking machines (n = 631) versus the frequency of isolation from cattle feces (n = 257) on three Finnish dairy farms for 1 year. Despite simultaneous isolation of STEC O157:H7 (17%) or C. jejuni (53%) from cattle, these bacteria were rarely isolated from milk filters (2% or <1%, respectively) and milk (0%). As revealed by phylogenomics, one STEC O157:H7 strain at a time was detected on each farm and persisted for ≤12 months despite rigorous hygienic measures. C. jejuni strains of a generalist sequence type (ST-883 and ST-1080) persisted in the herds for ≥11 months, and several other C. jejuni types were detected sporadically. The stx gene carried by STEC was detected more frequently from milk filters (37%) than from milk (7%), suggesting that milk filters are more suitable sampling targets for monitoring than milk. A questionnaire of on-farm practices suggested lower stx contamination of milk when major cleansing in the barn, culling, or pasturing of dairy cows was applied, while a higher average outdoor temperature was associated with higher stx contamination. Because pathogen contamination occurred despite good hygiene and because pathogen detection from milk and milk filters proved challenging, we recommend heat treatment for raw milk before consumption.IMPORTANCE The increased popularity of raw milk consumption has created demand for relaxing legislation, despite the risk of contamination by pathogenic bacteria, notably STEC and C. jejuni However, the epidemiology of these milk-borne pathogens on the herd level is still poorly understood, and data are lacking on the frequency of milk contamination on farms with cattle shedding these bacteria in their feces. This study suggests (i) that STEC contamination in milk can be reduced, but not prevented, by on-farm hygienic measures while fecal shedding is observable, (ii) that milk filters are more suitable sampling targets for monitoring than milk although pathogen detection from both sample matrices may be challenging, and (iii) that STEC and C. jejuni genotypes may persist in cattle herds for several months. The results can be utilized in developing and targeting pathogen monitoring and risk management on the farm level and contributed to the revision of Finnish legislation in 2017.
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12
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Oprea M, Ciontea AS, Militaru M, Dinu S, Cristea D, Usein CR. Molecular Typing of Escherichia coli O157 Isolates from Romanian Human Cases. Jpn J Infect Dis 2018; 71:455-461. [PMID: 30068889 DOI: 10.7883/yoken.jjid.2018.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Verocytotoxin-producing Escherichia coli (VTEC) of serogroup O157 are among the most important causes of severe cases of foodborne disease and outbreaks worldwide. As little is known about the characteristic of these strains in Romania, we aimed to provide reference information on the virulence gene content, phylogenetic background, and genetic diversity of 7 autochthonous O157 strains collected during 2016 and 2017 from epidemiologically non-related cases. These strains were typed by a combination of phenotypic and molecular methods routinely used by the national reference laboratory. Additionally, 4 of them were subjected to whole-genome sequencing (WGS), and public web-based tools were used to extract information on virulence gene profiles, multilocus sequence types (MLST), and single nucleotide polymorphism (SNP)-based phylogenetic relatedness. Molecular typing provided evidence of the circulation of a polyclonal population while distinguishing a cluster of non-sorbitol-fermenting, glucuronidase-negative, phylogenetic group E, MLST 1804 strains, representing lineage II and clade 7, which harbored vtx2c, eae-gamma, and ehxA genes. A good correlation between the routine typing methods and WGS data was observed. However, SNP-based genotyping provided a higher resolution in depicting the relationships between the O157:H7 strains than that provided by Pulse-field gel electrophoresis. This study should be a catalyst for improved laboratory-based surveillance of autochthonous VTEC.
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Affiliation(s)
- Mihaela Oprea
- Cantacuzino National Medico-Military Institute for Research and Development.,The Research Institute of the University of Bucharest
| | | | - Mădălina Militaru
- Cantacuzino National Medico-Military Institute for Research and Development
| | - Sorin Dinu
- Cantacuzino National Medico-Military Institute for Research and Development
| | - Daniela Cristea
- Cantacuzino National Medico-Military Institute for Research and Development
| | - Codruţa-Romaniţa Usein
- Cantacuzino National Medico-Military Institute for Research and Development.,Carol Davila University of Medicine and Pharmacy
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13
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Pianciola L, Rivas M. Genotypic Features of Clinical and Bovine Escherichia coli O157 Strains Isolated in Countries with Different Associated-Disease Incidences. Microorganisms 2018; 6:microorganisms6020036. [PMID: 29702577 PMCID: PMC6027531 DOI: 10.3390/microorganisms6020036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/20/2018] [Accepted: 04/25/2018] [Indexed: 01/19/2023] Open
Abstract
There is great geographical variation in the frequency of Escherichia coli O157 infections that correlates with important differences in the bovine reservoir of each country. Our group carried out a broad molecular characterization of human and bovine E. coli O157 strains circulating in Argentina using different methodologies. Our data allows us to conclude that in Argentina, a high homogeneity is observed in both cattle and human strains, with almost exclusive circulation of strains belonging to the hypervirulent clade 8 described by Manning. The aim of this review was to compare the genetic background of E. coli O157 strains isolated in countries that have conducted similar studies, to try to correlate specific O157 genotypes with the incidence and severity of E. coli O157 associated diseases. The characteristics of the strains that cause disease in humans reflect the predominant genotypes in cattle in each of the countries analyzed. The main features clearly linked to high incidence or severity of E. coli O157 infections are lineage-specific polymorphism assay-6 lineage I/II, clade 8 strains and probably, clade 6 strains, the stx2a/stx2c genotype, the presence of q933 and q21 simultaneously, and putative virulence factor EC_3286. In countries with an absence of these features in O157 strains, the overall incidence of O157 disease is low. Argentina, where these characteristics are detected in most strains, shows the highest incidence of hemolytic uremic syndrome (HUS) worldwide.
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Affiliation(s)
- Luis Pianciola
- Laboratorio Central, Subsecretaría de Salud de Neuquén, Gregorio Martínez 65, Neuquén 8300, Argentina.
| | - Marta Rivas
- Servicio Fisiopatogenia, INEI-ANLIS "Carlos G. Malbrán", Av. Vélez Sarsfield 563, Buenos Aires 1281, Argentina.
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14
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Enterohemorrhagic Escherichia coli O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades. PLoS One 2018; 13:e0191834. [PMID: 29381715 PMCID: PMC5790261 DOI: 10.1371/journal.pone.0191834] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/11/2018] [Indexed: 11/19/2022] Open
Abstract
Enterohemorrhagic Escherichia coli O157 (O157) strains can be classified into clades (one of several phylogenetic groups) by single nucleotide polymorphisms (SNPs): these are clade 1, clade 2, clade 3, descendant and ancestral clades 4/5, clade 6, clade 7, clade 8, clade 9, and clade 12. Some recent studies showed that some O157 strains in clade 8 produced a larger amount of Shiga toxin (Stx) 2 than other strains. In this study, 1121 epidemiologically unlinked strains of O157 isolated in Chiba Prefecture, Japan were classified into clades during 1996–2014. Clade 8 strains were further classified into subclade 8a (67 strains) and subclade 8b (48 strains) using SNP analysis. In the absence of mitomycin C (MMC), subclade 8a strains in this study produced significantly greater amounts of Stx2 than subclade 8b strains. However, in the presence of MMC, the levels of Stx2 production in subclade 8b strains were significantly greater than subclade 8a strains. On the other hand, a recent study reported that the Stx2 production level in O157 strains was determined mainly by the subtypes of Stx2a phage (ϕStx2_α, β, γ, δ, ε, and ζ). Using O157 strains in this study, the Stx2a phages were classified into these subtypes. In this study, all strains of subclades 8a and 8b carried ϕStx2a_γ and ϕStx2a_δ, respectively. Some strains in clade 6 also carried ϕStx2a_δ. In the presence of MMC, subclade 8b strains produced significantly greater amounts of Stx2 than clade 6 strains carrying ϕStx2_δ. In this study, we propose that Stx2 production in subclade 8b strains in the presence of MMC might be enhanced due to genetic factors other than ϕStx2_δ.
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15
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Yokoyama E, Hirai S, Ishige T, Murakami S. Application of whole genome sequence data in analyzing the molecular epidemiology of Shiga toxin-producing Escherichia coli O157:H7/H. Int J Food Microbiol 2017; 264:39-45. [PMID: 29107195 DOI: 10.1016/j.ijfoodmicro.2017.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/28/2017] [Accepted: 10/16/2017] [Indexed: 10/18/2022]
Abstract
Seventeen clusters of Shiga toxin-producing Escherichia coli O157:H7/- (O157) strains, determined by cluster analysis of pulsed-field gel electrophoresis patterns, were analyzed using whole genome sequence (WGS) data to investigate this pathogen's molecular epidemiology. The 17 clusters included 136 strains containing strains from nine outbreaks, with each outbreak caused by a single source contaminated with the organism, as shown by epidemiological contact surveys. WGS data of these strains were used to identify single nucleotide polymorphisms (SNPs) by two methods: short read data were directly mapped to a reference genome (mapping derived SNPs) and common SNPs between the mapping derived SNPs and SNPs in assembled data of short read data (common SNPs). Among both SNPs, those that were detected in genes with a gap were excluded to remove ambiguous SNPs from further analysis. The effectiveness of both SNPs was investigated among all the concatenated SNPs that were detected (whole SNP set); SNPs were divided into three categories based on the genes in which they were located (i.e., backbone SNP set, O-island SNP set, and mobile element SNP set); and SNPs in non-coding regions (intergenic region SNP set). When SNPs from strains isolated from the nine single source derived outbreaks were analyzed using an unweighted pair group method with arithmetic mean tree (UPGMA) and a minimum spanning tree (MST), the maximum pair-wise distances of the backbone SNP set of the mapping derived SNPs were significantly smaller than those of the whole and intergenic region SNP set on both UPGMAs and MSTs. This significant difference was also observed when the backbone SNP set of the common SNPs were examined (Steel-Dwass test, P≤0.01). When the maximum pair-wise distances were compared between the mapping derived and common SNPs, significant differences were observed in those of the whole, mobile element, and intergenic region SNP set (Wilcoxon signed rank test, P≤0.01). When all the strains included in one complex on an MST or one cluster on a UPGMA were designated as the same genotype, the values of the Hunter-Gaston Discriminatory Power Index for the backbone SNP set of the mapping derived and common SNPs were higher than those of other SNP sets. In contrast, the mobile element SNP set could not robustly subdivide lineage I strains of tested O157 strains using both the mapping derived and common SNPs. These results suggested that the backbone SNP set were the most effective for analysis of WGS data for O157 in enabling an appropriation of its molecular epidemiology.
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Affiliation(s)
- Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba 260-8715, Japan.
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chuo, Chiba City, Chiba 260-8715, Japan
| | - Taichiro Ishige
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya, Tokyo 256-0054, Japan
| | - Satoshi Murakami
- Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, 1737, Funako, Atsugi, Kanagawa 243-0034, Japan
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16
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Virulence traits and different nle profiles in cattle and human verotoxin-producing Escherichia coli O157:H7 strains from Argentina. Microb Pathog 2017; 102:102-108. [DOI: 10.1016/j.micpath.2016.11.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/28/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022]
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17
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Dallman TJ, Ashton PM, Byrne L, Perry NT, Petrovska L, Ellis R, Allison L, Hanson M, Holmes A, Gunn GJ, Chase-Topping ME, Woolhouse MEJ, Grant KA, Gally DL, Wain J, Jenkins C. Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK. Microb Genom 2015; 1:e000029. [PMID: 28348814 PMCID: PMC5320567 DOI: 10.1099/mgen.0.000029] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/22/2015] [Indexed: 11/18/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) O157:H7 is a recently emerged zoonotic pathogen with considerable morbidity. Since the emergence of this serotype in the 1980s, research has focussed on unravelling the evolutionary events from the E. coli O55:H7 ancestor to the contemporaneous globally dispersed strains observed today. In this study, the genomes of over 1000 isolates from both human clinical cases and cattle, spanning the history of STEC O157:H7 in the UK, were sequenced. Phylogenetic analysis revealed the ancestry, key acquisition events and global context of the strains. Dated phylogenies estimated the time to evolution of the most recent common ancestor of the current circulating global clone to be 175 years ago. This event was followed by rapid diversification. We show the acquisition of specific virulence determinates has occurred relatively recently and coincides with its recent detection in the human population. We used clinical outcome data from 493 cases of STEC O157:H7 to assess the relative risk of severe disease including haemolytic uraemic syndrome from each of the defined clades in the population and show the dramatic effect Shiga toxin repertoire has on virulence. We describe two strain replacement events that have occurred in the cattle population in the UK over the last 30 years, one resulting in a highly virulent strain that has accounted for the majority of clinical cases in the UK over the last decade. There is a need to understand the selection pressures maintaining Shiga-toxin-encoding bacteriophages in the ruminant reservoir and the study affirms the requirement for close surveillance of this pathogen in both ruminant and human populations.
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Affiliation(s)
| | - Philip M Ashton
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Lisa Byrne
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Neil T Perry
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Liljana Petrovska
- Animal Laboratories and Plant Health Agency, Woodham Lane, Surrey KT15 3NB, UK
| | - Richard Ellis
- Animal Laboratories and Plant Health Agency, Woodham Lane, Surrey KT15 3NB, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Mary Hanson
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Anne Holmes
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - George J Gunn
- Future Farming Systems, R&D Division, SRUC, Drummondhill, Stratherrick Rd., Inverness IV2 4JZ, Scotland, UK
| | - Margo E Chase-Topping
- Centre for Immunity, Infection and Evolution, Kings Buildings, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Mark E J Woolhouse
- Centre for Immunity, Infection and Evolution, Kings Buildings, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kathie A Grant
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin EH25 9RG, UK
| | - John Wain
- University of East Anglia, Norwich NR4 7TJ, UK
| | - Claire Jenkins
- Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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18
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Hirai S, Yokoyama E, Etoh Y, Seto J, Ichihara S, Suzuki Y, Maeda E, Sera N, Horikawa K, Sato S, Yamamoto T. Putative classification of clades of enterohemorrhagic Escherichia coli O157 using an IS-printing system. Lett Appl Microbiol 2015; 61:267-73. [PMID: 26031479 DOI: 10.1111/lam.12448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/11/2015] [Accepted: 05/25/2015] [Indexed: 11/30/2022]
Abstract
UNLABELLED Enterohemorrhagic Escherichia coli O157 (O157) strains can be classified in clades by single nucleotide polymorphisms (SNPs), but this analysis requires significant laboratory effort. As the distribution of insertion sequence (IS) 629 insertions has been reported to be biased among different clades, O157 isolates can be putatively classified in clades by comparison with an IS629 distribution database. A database of the IS629 distribution in O157 strains isolated in Chiba Prefecture and their classification in clades was determined by SNP analysis and IS-printing, an easy and quick analytical tool for IS629 in the O157 genome. The IS629 distribution in O157 strains isolated in Fukuoka and Yamagata Prefectures was determined by IS-printing. These strains were putatively classified in clades by Relative Likelihood calculations that compared the IS-printing data and the IS629 distribution database. Concordance Ratios were calculated, which compared the number of strains putatively classified in a clade by Relative Likelihood to the number of strains classified in that clade by SNP analysis. For the Fukuoka and Yamagata strains, the Concordance Ratios for clades 3, 6 and 8 were 97-100%, for clade 7 about 88%, and for clades 2 and 12 over 90%. In conclusion, O157 clade 2, 3, 6, 7, 8 and 12 strains could be putatively classified by IS-printing. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrated that enterohemorrhagic E. coli O157 (O157) strains could be putatively classified in clades using an IS-printing system. IS-printing was previously developed as a relatively quick and easy tool for analysis of insertion sequence 629 in the O157 genome. Since most local government public health institutes in Japan carry out IS-printing for early detection of O157 outbreaks, these data should be useful for putative classification of O157 strains in each area.
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Affiliation(s)
- S Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.,Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
| | - E Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Y Etoh
- Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - J Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - S Ichihara
- Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Y Suzuki
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - E Maeda
- Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - N Sera
- Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - K Horikawa
- Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - S Sato
- Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - T Yamamoto
- Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
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19
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Yokoyama E, Hachisu Y, Iwamoto T, Nakanishi N, Arikawa K, Wada T, Seto J, Kishida K. Comparative analysis of Mycobacterium tuberculosis Beijing strains isolated in three remote areas of Japan. INFECTION GENETICS AND EVOLUTION 2015; 34:444-9. [PMID: 26096775 DOI: 10.1016/j.meegid.2015.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/04/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
A quantitative and qualitative comparison was carried out of Mycobacterium tuberculosis Beijing strains isolated in three remote areas of Japan. A total of 452 strains from Chiba Prefecture, 75 from Yamagata Prefecture, and 315 from Kobe City were analyzed for 24 loci by variable number of tandem repeats typing (24(Beijing)-VNTR). All strains were classified in six Beijing subgroups (B(SUB)), B1 to B5 and T, based on a minimum spanning tree reconstructed using data of a standard set of 15 VNTR loci. No significant difference was found in the distribution of strains in the B(SUB) in the three areas, with one exception due to a B5 outbreak in Yamagata, indicating no significant quantitative difference in the B(SUB) in the three areas (P<0.01, Chi-square test). In addition, when strains in each B(SUB) isolated in the three areas were mixed and standardized index of association (I(A)(s)) and variance (Φ(PT)) values were calculated, no significant qualitative difference in the B(SUB) in the three areas was found. These results suggested that the B(SUB) diverged prior to the introduction of M. tuberculosis Beijing strains into Japan. Differences in the distribution of strains in each B(SUB) between Japan and continental Asian countries suggested there had been genetic drift in the continental Asian countries in which B4 had been dominant.
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Affiliation(s)
- Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.
| | - Yushi Hachisu
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Tomotada Iwamoto
- Department of Infectious Disease, Kobe Institute of Health, Hyogo, Japan
| | - Noriko Nakanishi
- Department of Infectious Disease, Kobe Institute of Health, Hyogo, Japan
| | - Kentaro Arikawa
- Department of Infectious Disease, Kobe Institute of Health, Hyogo, Japan
| | - Takayuki Wada
- Department of International Health, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Junji Seto
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Kazunori Kishida
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
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Shimizu T, Hirai S, Yokoyama E, Ichimura K, Noda M. An evolutionary analysis of nitric oxide reductase gene norV in enterohemorrhagic Escherichia coli O157. INFECTION GENETICS AND EVOLUTION 2015; 33:176-81. [PMID: 25936496 DOI: 10.1016/j.meegid.2015.04.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 11/24/2022]
Abstract
A novel virulence gene, norV, that encodes nitric oxide (NO) reductase, was examined to investigate the emergence of enterohemorrhagic Escherichia coli (EHEC) O157 subgroup C clusters 2 and 3 from subgroup C cluster 1. Deletion of norV occurred at a point between cluster 1 and cluster 2 just after or at the same time that an stx2 bacteriophage, which retains Shiga toxin 2 gene, was inserted into wrbA, which encodes a novel multimeric flavodoxin-like protein, in EHEC O157. Sensitivity of NO to anaerobic growth was correlated with the deletion of norV in all EHEC O157 individuals tested. The C467A mutation of fimH, which encodes minor component of type 1 fimbriae, occurred within cluster 1, not as a transition from cluster 1 to cluster 2, indicating that there is a cluster 1 minority branch that leads to cluster 2. These data refine the evolutionary history of an emerging EHEC O157.
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Affiliation(s)
- Takeshi Shimizu
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba 260-8670, Japan.
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chiba 260-8715, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2 Nitona, Chiba 260-8715, Japan
| | - Kimitoshi Ichimura
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba 260-8670, Japan
| | - Masatoshi Noda
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba 260-8670, Japan
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Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress. Appl Environ Microbiol 2015; 81:3946-52. [PMID: 25841005 DOI: 10.1128/aem.04188-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/24/2015] [Indexed: 11/20/2022] Open
Abstract
An increase in the number of cases of Shiga toxin-producing Escherichia coli (STEC) O157 phage type 2 (PT2) in England in September 2013 was epidemiologically linked to watercress consumption. Whole-genome sequencing (WGS) identified a phylogenetically related cluster of 22 cases (outbreak 1). The isolates comprising this cluster were not closely related to any other United Kingdom strain in the Public Health England WGS database, suggesting a possible imported source. A second outbreak of STEC O157 PT2 (outbreak 2) was identified epidemiologically following the detection of outbreak 1. Isolates associated with outbreak 2 were phylogenetically distinct from those in outbreak 1. Epidemiologically unrelated isolates on the same branch as the outbreak 2 cluster included those from human cases in England with domestically acquired infection and United Kingdom domestic cattle. Environmental sampling using PCR resulted in the isolation of STEC O157 PT2 from irrigation water at one implicated watercress farm, and WGS showed this isolate belonged to the same phylogenetic cluster as outbreak 2 isolates. Cattle were in close proximity to the watercress bed and were potentially the source of the second outbreak. Transfer of STEC from the field to the watercress bed may have occurred through wildlife entering the watercress farm or via runoff water. During this complex outbreak investigation, epidemiological studies, comprehensive testing of environmental samples, and the use of novel molecular methods proved invaluable in demonstrating that two simultaneous outbreaks of STEC O157 PT2 were both linked to the consumption of watercress but were associated with different sources of contamination.
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Hirai S, Yokoyama E, Etoh Y, Seto J, Ichihara S, Suzuki Y, Maeda E, Sera N, Horikawa K, Yamamoto T. Analysis of the population genetics of clades of enterohaemorrhagic Escherichia coli O157:H7/H- isolated in three areas in Japan. J Appl Microbiol 2014; 117:1191-7. [PMID: 25047966 DOI: 10.1111/jam.12604] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/30/2014] [Accepted: 07/15/2014] [Indexed: 11/30/2022]
Abstract
AIMS The genetic differences of enterohaemorrhagic Escherichia coli O157 (O157) strains isolated from humans in three widely-separated areas in Japan were analysed to provide information on possible geographic aspects of O157 pathogenicity. METHODS AND RESULTS Epidemiologically unlinked O157 strains were isolated in Chiba (300 strains), Fukuoka (260 strains) and Yamagata (81 strains) prefectures. These strains were classified in clades by single nucleotide polymorphism in seven loci and lineage-specific polymorphism assay-6, and differences between the strains in each clade were compared by population genetic analyses using the IS-printing system. Analysis of the clades from the three areas showed linkage disequilibrium of the strains in each clade. Comparison of the genetic differences of strains from the three areas in each clade, from calculated ΦPT values, indicated that the strains in each clade were the same population in all three areas, except possibly the clade 12 strains. CONCLUSIONS Population genetics analyses confirmed that the distribution of O157 strains in the clades isolated in three areas in Japan were similar and stable. SIGNIFICANCE AND IMPACT OF THE STUDY The pathogenicity of O157 strains infecting humans was comparable due to the similar, stable geographic distribution of O157 clades.
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Affiliation(s)
- S Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan; Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
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Yokoyama E, Murakami K, Shiwa Y, Ishige T, Ando N, Kikuchi T, Murakami S. Phylogenetic and population genetic analysis of Salmonella enterica subsp. enterica serovar Infantis strains isolated in Japan using whole genome sequence data. INFECTION GENETICS AND EVOLUTION 2014; 27:62-8. [PMID: 24999237 DOI: 10.1016/j.meegid.2014.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 06/09/2014] [Accepted: 06/14/2014] [Indexed: 01/26/2023]
Abstract
Salmonella enterica subsp. enterica serovar Infantis has been reported to be carried asymptomatically in chickens and isolated from some human patients with diarrhea. The aim of this study was to investigate the phylogeny of S. Infantis strains isolated in Japan from chicken meat, chicken egg shells, environmental samples from a grading and packing center for chicken eggs (GP center), diarrhea patients, and asymptomatic carriers based on whole genome sequence data. The S. Infantis strains were in five clusters in a phylogenetic tree reconstructed by the maximum likelihood method. The five clusters were confirmed by neighbor-net and Bayesian cluster analyses. Two of the five clusters formed a group containing all of the strains isolated from chicken meat and some of the strains isolated from diarrhea patients and asymptomatic carriers. The median-joining network reconstructed in this study showed that strains in one of these two clusters diverged from one node with similar relatively short branches, suggesting clonal dissemination of these strains. The other three clusters formed a group containing all of the strains isolated from chicken egg shells and the GP center, and the remaining strains from diarrhea patients and asymptomatic carriers. Interestingly, strains isolated from patients did not cluster in only one group, indicating that none of the S. Infantis strains in this study had significantly higher human pathogenicity. The population genetic analyses in this study showed the separation of the five clusters into two groups was concordant with the sources where the strains in the clusters were isolated. These results suggested that evolutionary groups with higher hierarchy than the clusters identified in this study may be present, although such groups could not be determined by phylogenetic, neighbor-net, and Bayesian analyses in this study. Determination of higher level S. Infantis evolutionary groups should be investigated using other types of genetic markers.
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Affiliation(s)
- Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.
| | - Koichi Murakami
- Division of Pathology and Bacteriology, Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Taichiro Ishige
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Naoshi Ando
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Takashi Kikuchi
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Satoshi Murakami
- Laboratory of Animal Hygiene, Department of Animal Science, Tokyo University of Agriculture, Kanagawa, Japan
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Etoh Y, Hirai S, Ichihara S, Maeda E, Yokoyama E, Sera N, Horikawa K, Yamamoto T. Evolutionary model of the divergence of enterohemorrhagic Escherichia coli O157 lineage I/II clades reconstructed from high resolution melting and Shiga-like toxin 2 analyses. INFECTION GENETICS AND EVOLUTION 2014; 24:140-5. [DOI: 10.1016/j.meegid.2014.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/24/2014] [Accepted: 03/13/2014] [Indexed: 11/28/2022]
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Mellor GE, Besser TE, Davis MA, Beavis B, Jung W, Smith HV, Jennison AV, Doyle CJ, Chandry PS, Gobius KS, Fegan N. Multilocus genotype analysis of Escherichia coli O157 isolates from Australia and the United States provides evidence of geographic divergence. Appl Environ Microbiol 2013; 79:5050-8. [PMID: 23770913 PMCID: PMC3754714 DOI: 10.1128/aem.01525-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/12/2013] [Indexed: 01/31/2023] Open
Abstract
Escherichia coli O157 is a food-borne pathogen whose major reservoir has been identified as cattle. Recent genetic information has indicated that populations of E. coli O157 from cattle and humans can differ genetically and that this variation may have an impact on their ability to cause severe human disease. In addition, there is emerging evidence that E. coli O157 strains from different geographical regions may also be genetically divergent. To investigate the extent of this variation, we used Shiga toxin bacteriophage insertion sites (SBI), lineage-specific polymorphisms (LSPA-6), multilocus variable-number tandem-repeat analysis (MLVA), and a tir 255T>A polymorphism to examine 606 isolates representing both Australian and U.S. cattle and human populations. Both uni- and multivariate analyses of these data show a strong association between the country of origin and multilocus genotypes (P < 0.0001). In addition, our results identify factors that may play a role in virulence that also differed in isolates from each country, including the carriage of stx1 in the argW locus uniquely observed in Australian isolates and the much higher frequency of stx2-positive (also referred to as stx2a) strains in the U.S. isolates (4% of Australian isolates versus 72% of U.S. isolates). LSPA-6 lineages differed between the two continents, with the majority of Australian isolates belonging to lineage I/II (LI/II) (LI, 2%; LI/II, 85%; LII, 13%) and the majority of U.S. isolates belonging to LI (LI, 60%; LI/II, 16%; LII, 25%). The results of this study provide strong evidence of phylogeographic structuring of E. coli O157 populations, suggesting divergent evolution of enterohemorrhagic E. coli O157 in Australia and the United States.
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Affiliation(s)
- Glen E. Mellor
- CSIRO Animal, Food and Health Sciences, Archerfield BC, QLD, Australia
| | - Thomas E. Besser
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, Washington, USA
| | - Margaret A. Davis
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, Washington, USA
| | - Brittany Beavis
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, Washington, USA
| | - WooKyung Jung
- Washington State University, Department of Veterinary Microbiology and Pathology, Pullman, Washington, USA
| | - Helen V. Smith
- Queensland Health Forensic and Scientific Services, Archerfield BC, QLD, Australia
| | - Amy V. Jennison
- Queensland Health Forensic and Scientific Services, Archerfield BC, QLD, Australia
| | - Christine J. Doyle
- Queensland Health Forensic and Scientific Services, Archerfield BC, QLD, Australia
| | - P. Scott Chandry
- CSIRO Animal, Food and Health Sciences, Werribee, VIC, Australia
| | - Kari S. Gobius
- CSIRO Animal, Food and Health Sciences, Werribee, VIC, Australia
| | - Narelle Fegan
- CSIRO Animal, Food and Health Sciences, Werribee, VIC, Australia
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Meng Q, Xiong Y, Lan R, Ye C, Wang T, Qi T, Wang Y, Wang H, Bai X, Bai X, Ji S, Jin D, Yuan X, Zhao A, Sun H, Jing H, Xu J. SNP genotyping of enterohemorrhagic Escherichia coli O157:H7 isolates from China and genomic identity of the 1999 Xuzhou outbreak. INFECTION GENETICS AND EVOLUTION 2013; 16:275-81. [DOI: 10.1016/j.meegid.2013.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 02/19/2013] [Accepted: 02/22/2013] [Indexed: 11/16/2022]
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Hirai S, Yokoyama E, Yamamoto T. Linkage disequilibrium of the IS629 insertion among different clades of enterohemorrhagic Escherichia coli O157:H7/H-strains. INFECTION GENETICS AND EVOLUTION 2013; 18:94-9. [PMID: 23684793 DOI: 10.1016/j.meegid.2013.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/16/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022]
Abstract
The distribution of insertion sequence (IS) 629 was investigated among enterohemorrhagic Escherichia coli O157:H7/H-(O157) strains in different clades. Minimum spanning tree analysis showed that most strains in each clade clustered in a separate branch, indicating biased distribution of the IS629 insertion in different clades. The standardized index of association of the IS629 distribution data showed linkage disequilibrium in the strains in every clade, indicating that IS629 distribution data could be used for population genetic analysis. For this population genetic analysis, the Φ(PT) value, an analogue of F(ST), was calculated and indicated that clade 7 strains could be split into two clades based on their lineages. The degree of pairwise linkage disequilibrium was quite different among these two groups. The clade 7 split was in agreement with the model of O157 paraphyletic evolution and a new designation of the lineage II clades was proposed. The prevalence of strains with an IS629 insertion in certain loci was significantly different in different clades. Some of these significant differences were in loci in strains in branches of clades that were close in the O157 phylogenetic model, suggesting that IS629 insertion/deletion was not directly related to the divergence of O157 clades.
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Affiliation(s)
- Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan.
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