1
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Matsumoto Y, Lee K, Akasaka R, Honjo H, Koizumi M, Sato T, Kubomura A, Ishijima N, Akeda Y, Ohnishi M, Iyoda S. Increased resistance against tellurite is conferred by a mutation in the promoter region of uncommon tellurite resistance gene tehB in the ter-negative Shiga toxin-producing Escherichia coli O157:H7. Appl Environ Microbiol 2024; 90:e0228323. [PMID: 38757978 DOI: 10.1128/aem.02283-23] [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: 01/09/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Resistance to potassium tellurite (PT) is an important indicator in isolating Shiga toxin-producing Escherichia coli (STEC) O157:H7 and other major STEC serogroups. Common resistance determinant genes are encoded in the ter gene cluster. We found an O157:H7 isolate that does not harbor ter but is resistant to PT. One nonsynonymous mutation was found in another PT resistance gene, tehA, through whole-genome sequence analyses. To elucidate the contribution of this mutation to PT resistance, complementation of tehA and the related gene tehB in isogenic strains and quantitative RT‒PCR were performed. The results indicated that the point mutation not only changed an amino acid of tehA, but also was positioned on a putative internal promoter of tehB and increased PT resistance by elevating tehB mRNA expression. Meanwhile, the amino acid change in tehA had negligible impact on the PT resistance. Comprehensive screening revealed that 2.3% of O157:H7 isolates in Japan did not harbor the ter gene cluster, but the same mutation in tehA was not found. These results suggested that PT resistance in E. coli can be enhanced through one mutational event even in ter-negative strains. IMPORTANCE Selective agents are important for isolating Shiga toxin-producing Escherichia coli (STEC) because the undesirable growth of microflora should be inhibited. Potassium tellurite (PT) is a common selective agent for major STEC serotypes. In this study, we found a novel variant of PT resistance genes, tehAB, in STEC O157:H7. Molecular experiments clearly showed that one point mutation in a predicted internal promoter region of tehB upregulated the expression of the gene and consequently led to increased resistance to PT. Because tehAB genes are ubiquitous across E. coli, these results provide universal insight into PT resistance in this species.
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Affiliation(s)
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryuya Akasaka
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Tokyo College of Biotechnology, Tokyo, Japan
| | - Hayato Honjo
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Tokyo College of Biotechnology, Tokyo, Japan
| | | | - Toshio Sato
- Japan Microbiological Laboratory Co. Ltd., Miyagi, Japan
| | - Akiko Kubomura
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nozomi Ishijima
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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2
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Lee K, Iguchi A, Terano C, Hataya H, Isobe J, Seto K, Ishijima N, Akeda Y, Ohnishi M, Iyoda S. Combined usage of serodiagnosis and O antigen typing to isolate Shiga toxin-producing Escherichia coli O76:H7 from a hemolytic uremic syndrome case and genomic insights from the isolate. Microbiol Spectr 2024; 12:e0235523. [PMID: 38092668 PMCID: PMC10790564 DOI: 10.1128/spectrum.02355-23] [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: 06/05/2023] [Accepted: 10/12/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Hemolytic uremic syndrome (HUS) is a life-threatening disease caused by Shiga toxin-producing Escherichia coli (STEC) infection. The treatment approaches for STEC-mediated typical HUS and atypical HUS differ, underscoring the importance of rapid and accurate diagnosis. However, specific detection methods for STECs other than major serogroups, such as O157, O26, and O111, are limited. This study focuses on the utility of PCR-based O-serotyping, serum agglutination tests utilizing antibodies against the identified Og type, and isolation techniques employing antibody-conjugated immunomagnetic beads for STEC isolation. By employing these methods, we successfully isolated a STEC strain of a minor serotype, O76:H7, from a HUS patient.
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Affiliation(s)
- Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Chikako Terano
- Department of Nephrology and Rheumatology, Tokyo Metropolitan Children’s Medical Center, Tokyo, Japan
- Department of Nephrology, Aichi Children’s Health and Medical Center, Aichi, Japan
| | - Hiroshi Hataya
- Department of Nephrology and Rheumatology, Tokyo Metropolitan Children’s Medical Center, Tokyo, Japan
| | - Junko Isobe
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
| | - Kazuko Seto
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nozomi Ishijima
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - EHEC Working Group in JapanMorimotoYoOgawaKeikoIshiguroMakotoKikuchiMasayukiSampeiMikaAokiYokoSetoJunjiIshikawaKanakoSatoTakashiKikuchiKojiTomariKentaroUenoHiroyukiHazamaKyokoKikuchiTakashiYajimaMasayukiKanazawaSatokoKawaseMasaoKimataKeikoYuruzumeSayaShirozaMikaKitagawaEmikoYoshikawaMisaYokoyamaKojiOnoSatokoFurukawaYumiMatsuyamaMikiFurutaAyakoNodaMakikoKameyamaYoshihikoAotaTatsuakiKatamuneChiharuShimodaYukoAbeYuriTamuraSawakoFurukawaYurikaObaraAtsumi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Department of Nephrology and Rheumatology, Tokyo Metropolitan Children’s Medical Center, Tokyo, Japan
- Department of Nephrology, Aichi Children’s Health and Medical Center, Aichi, Japan
- Department of Bacteriology, Toyama Institute of Health, Imizu, Toyama, Japan
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3
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Le CT, Price EP, Sarovich DS, Nguyen TTA, Powell D, Vu-Khac H, Kurtböke Dİ, Knibb W, Chen SC, Katouli M. Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam. Microb Genom 2022; 8. [PMID: 35786440 PMCID: PMC9455698 DOI: 10.1099/mgen.0.000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
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Affiliation(s)
- Cuong T. Le
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Institute for Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S. Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thu T. A. Nguyen
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Daniel Powell
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Hung Vu-Khac
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - D. İpek Kurtböke
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Wayne Knibb
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
| | - Mohammad Katouli
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- *Correspondence: Mohammad Katouli,
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Eppinger M, Almería S, Allué-Guardia A, Bagi LK, Kalalah AA, Gurtler JB, Fratamico PM. Genome Sequence Analysis and Characterization of Shiga Toxin 2 Production by Escherichia coli O157:H7 Strains Associated With a Laboratory Infection. Front Cell Infect Microbiol 2022; 12:888568. [PMID: 35770066 PMCID: PMC9234449 DOI: 10.3389/fcimb.2022.888568] [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: 03/03/2022] [Accepted: 05/03/2022] [Indexed: 11/21/2022] Open
Abstract
A laboratory-acquired E. coli O157:H7 infection with associated severe sequelae including hemolytic uremic syndrome occurred in an individual working in the laboratory with a mixture of nalidixic acid-resistant (NalR) O157:H7 mutant strains in a soil-biochar blend. The patient was hospitalized and treated with an intravenous combination of metronidazole and levofloxacin. The present study investigated the source of this severe laboratory acquired infection and further examined the influence of the antibiotics used during treatment on the expression and production of Shiga toxin. Genomes of two Stx2a-and eae-positive O157:H7 strains isolated from the patient's stool were sequenced along with two pairs of the wt strains and their derived NalR mutants used in the laboratory experiments. High-resolution SNP typing determined the strains' individual genetic relatedness and unambiguously identified the two laboratory-derived NalR mutant strains as the source of the researcher's life-threatening disease, rather than a conceivable ingestion of unrelated O157:H7 isolates circulating at the same time. It was further confirmed that in sublethal doses, the antibiotics increased toxin expression and production. Our results support a simultaneous co-infection with clinical strains in the laboratory, which were the causative agents of previous O157:H7 outbreaks, and further that the administration of antibiotics may have impacted the outcome of the infection.
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Affiliation(s)
- Mark Eppinger
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sonia Almería
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Anna Allué-Guardia
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States
| | - Lori K Bagi
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Anwar A Kalalah
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Joshua B Gurtler
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Pina M Fratamico
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
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Nishida R, Nakamura K, Taniguchi I, Murase K, Ooka T, Ogura Y, Gotoh Y, Itoh T, Toyoda A, Mainil JG, Piérard D, Seto K, Harada T, Isobe J, Kimata K, Etoh Y, Hamasaki M, Narimatsu H, Yatsuyanagi J, Kameyama M, Matsumoto Y, Nagai Y, Kawase J, Yokoyama E, Ishikawa K, Shiomoto T, Lee K, Kang D, Akashi K, Ohnishi M, Iyoda S, Hayashi T. The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19. Microb Genom 2021; 7. [PMID: 34878971 PMCID: PMC8767318 DOI: 10.1099/mgen.0.000716] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) are foodborne pathogens causing serious diseases, such as haemorrhagic colitis and haemolytic uraemic syndrome. Although O157:H7 STEC strains have been the most prevalent, incidences of STEC infections by several other serotypes have recently increased. O121:H19 STEC is one of these major non-O157 STECs, but systematic whole genome sequence (WGS) analyses have not yet been conducted on this STEC. Here, we performed a global WGS analysis of 638 O121:H19 strains, including 143 sequenced in this study, and a detailed comparison of 11 complete genomes, including four obtained in this study. By serotype-wide WGS analysis, we found that O121:H19 strains were divided into four lineages, including major and second major lineages (named L1 and L3, respectively), and that the locus of enterocyte effacement (LEE) encoding a type III secretion system (T3SS) was acquired by the common ancestor of O121:H19. Analyses of 11 complete genomes belonging to L1 or L3 revealed remarkable interlineage differences in the prophage pool and prophage-encoded T3SS effector repertoire, independent acquisition of virulence plasmids by the two lineages, and high conservation in the prophage repertoire, including that for Stx2a phages in lineage L1. Further sequence determination of complete Stx2a phage genomes of 49 strains confirmed that Stx2a phages in lineage L1 are highly conserved short-tailed phages, while those in lineage L3 are long-tailed lambda-like phages with notable genomic diversity, suggesting that an Stx2a phage was acquired by the common ancestor of L1 and has been stably maintained. Consistent with these genomic features of Stx2a phages, most lineage L1 strains produced much higher levels of Stx2a than lineage L3 strains. Altogether, this study provides a global phylogenetic overview of O121:H19 STEC and shows the interlineage genomic differences and the highly conserved genomic features of the major lineage within this serotype of STEC.
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Affiliation(s)
- Ruriko Nishida
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiji Nakamura
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Itsuki Taniguchi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Tadasuke Ooka
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | | | - Yasuhiro Gotoh
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience of Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | | | - Denis Piérard
- Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Kazuko Seto
- Osaka Institute of Public Health, Osaka, Japan
| | | | | | | | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | | | | | | | - Mitsuhiro Kameyama
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Yuko Matsumoto
- Yokohama City Institute of Public Health, Kanagawa, Japan
| | - Yuhki Nagai
- Mie Prefectural Institute of Public Health and Environmental Sciences, Mie, Japan
| | - Jun Kawase
- Shimane Prefectural Institute of Public Health and Environmental Science, Shimane, Japan
| | - Eiji Yokoyama
- Chiba Prefectural Institute of Public Health, Chiba, Japan
| | | | - Takayuki Shiomoto
- Ishikawa Prefectural Institute of Public Health and Environmental Science, Ishikawa, Japan
| | - Kenichi Lee
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Dongchon Kang
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koichi Akashi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Sunao Iyoda
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuya Hayashi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- *Correspondence: Tetsuya Hayashi,
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6
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Ando N, Sekizuka T, Yokoyama E, Aihara Y, Konishi N, Matsumoto Y, Ishida K, Nagasawa K, Jourdan-Da Silva N, Suzuki M, Kimura H, Le Hello S, Murakami K, Kuroda M, Hirai S, Fukaya S. Whole Genome Analysis Detects the Emergence of a Single Salmonella enterica Serovar Chester Clone in Japan's Kanto Region. Front Microbiol 2021; 12:705679. [PMID: 34385991 PMCID: PMC8354586 DOI: 10.3389/fmicb.2021.705679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/05/2021] [Indexed: 11/18/2022] Open
Abstract
In Japan's Kanto region, the number of Salmonella enterica serovar Chester infections increased temporarily between 2014 and 2016. Concurrently with this temporal increase in the Kanto region, S. Chester isolates belonging to one clonal group were causing repetitive outbreaks in Europe. A recent study reported that the European outbreaks were associated with travelers who had been exposed to contaminated food in Morocco, possibly seafood. Because Japan imports a large amount of seafood from Morocco, we aimed to establish whether the temporal increase in S. Chester infections in the Kanto region was associated with imported Moroccan seafood. Short sequence reads from the whole-genome sequencing of 47 S. Chester isolates from people in the Kanto region (2014-2016), and the additional genome sequences from 58 isolates from the European outbreaks, were analyzed. The reads were compared with the complete genome sequence from a S. Chester reference strain, and 347 single nucleotide polymorphisms (SNPs) were identified. These SNPs were used in this study. Cluster and Bayesian cluster analyses showed that the Japanese and European isolates fell into two different clusters. Therefore, Φ PT and I A S values were calculated to evaluate genetic differences between these clusters. The results revealed that the Japanese and European isolates were genetically distinct populations. Our root-to-tip analysis showed that the Japanese isolates originating from one clone had accumulated mutations, suggesting that an emergence of this organism occurred. A minimum spanning tree analysis demonstrated no correlation between genetic and geographical distances in the Japanese isolates, suggesting that the emergence of the serovar in the Kanto region did not involve person-to-person contact; rather, it occurred through food consumption. The d N /d S ratio indicated that the Japanese strain has evolved under positive selection pressure. Generally, a population of bacterial clones in a reservoir faces negative selection pressure. Therefore, the Japanese strain must have existed outside of any reservoir during its emergence. In conclusion, S. Chester isolates originating from one clone probably emerged in the Kanto region via the consumption of contaminated foods other than imported Moroccan seafood. The emerging strain may have not established a reservoir for survival in the food supply chain resulting in its disappearance after 2017.
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Affiliation(s)
- Naoshi Ando
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Yoshiyuki Aihara
- Division of Bacteriology, Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Noriko Konishi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Yuko Matsumoto
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, Yokohama, Japan
| | | | - Koo Nagasawa
- Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | | | - Motoi Suzuki
- Center for Surveillance, Immunization, and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Faculty of Health Science, School of Medical Technology, Gunma Paz University, Takasaki, Japan
| | - Simon Le Hello
- French National Reference Center for E. coli, Shigella and Salmonella, Institute Pasteur, Paris, France
- Groupe de Recherche sur l’Adaptation Microbienne (GRAM 2.0, EA2656), Normandy University, UNICAEN, UNIROUEN, Caen, France
| | - Koichi Murakami
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashi-Murayama, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Setsuko Fukaya
- Division of Bacteriology, Ibaraki Prefectural Institute of Public Health, Mito, Japan
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7
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Lee K, Iguchi A, Uda K, Matsumura S, Miyairi I, Ishikura K, Ohnishi M, Seto J, Ishikawa K, Konishi N, Obata H, Furukawa I, Nagaoka H, Morinushi H, Hama N, Nomoto R, Nakajima H, Kariya H, Hamasaki M, Iyoda S. Whole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli OX18 from a Fatal Hemolytic Uremic Syndrome Case. Emerg Infect Dis 2021; 27:1509-1512. [PMID: 33900194 PMCID: PMC8084502 DOI: 10.3201/eid2705.204162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report a fatal case of hemolytic uremic syndrome with urinary tract infection in Japan caused by Shiga toxin–producing Escherichia coli. We genotypically identified the isolate as OX18:H2. Whole-genome sequencing revealed 3 potentially pathogenic lineages (OX18:H2, H19, and H34) that have been continuously isolated in Japan.
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8
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Global distribution of epidemic-related Shiga toxin 2 encoding phages among enteroaggregative Escherichia coli. Sci Rep 2020; 10:11738. [PMID: 32678145 PMCID: PMC7366661 DOI: 10.1038/s41598-020-68462-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/08/2020] [Indexed: 12/02/2022] Open
Abstract
Since the Shiga toxin-producing enteroaggregative Escherichia coli (Stx-EAEC) O104:H4 strain caused a massive outbreak across Europe in 2011, the importance of Stx-EAEC has attracted attention from a public health perspective. Two Stx-EAEC O86 isolates were obtained from patients with severe symptoms in Japan in 1999 and 2015. To characterize the phylogeny and pathogenic potential of these Stx-EAEC O86 isolates, whole-genome sequence analyses were performed by short-and long-read sequencing. Among genetically diverse E. coli O86, the Stx-EAEC O86 isolates were clustered with the EAEC O86:H27 ST3570 subgroup. Strikingly, there were only two loci with single nucleotide polymorphisms (SNPs) between the Stx2a phage of a Japanese O86:H27 isolate and that of the European epidemic-related Stx-EAEC O104:H4 isolate. These results provide evidence of global distribution of epidemic-related Stx2a phages among various lineages of E. coli with few mutations.
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Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef. Microbiol Resour Announc 2019; 8:8/40/e00882-19. [PMID: 31582455 PMCID: PMC6776772 DOI: 10.1128/mra.00882-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the complete genome sequence of an enterohemorrhagic Escherichia coli O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011. We present the complete genome sequence of an enterohemorrhagic Escherichia coli O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.
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Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157. Appl Environ Microbiol 2019; 85:AEM.00728-19. [PMID: 31227555 DOI: 10.1128/aem.00728-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/13/2019] [Indexed: 01/06/2023] Open
Abstract
Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary. For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance.IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.
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11
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Kikuchi K, Lee K, Ueno H, Tomari K, Kobori S, Kaetsu A, Matsui M, Suzuki S, Sekizuka T, Kuroda M, Miyazaki M, Ohnishi M. Enterohaemorrhagic Escherichia coli O121:H19 acquired an extended-spectrum β-lactamase gene during the development of an outbreak in two nurseries. Microb Genom 2019; 5. [PMID: 31215859 PMCID: PMC6700663 DOI: 10.1099/mgen.0.000278] [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] [Indexed: 02/06/2023] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) is an important human pathogen worldwide. Although serotype O157 is currently the most dominant and important EHEC strain, serotypes O26, O111, O91, O103 and O121 are also recognized as serious pathogens that affect public health. EHEC outbreaks often occur in nurseries and elderly care facilities. In 2012, a nursery outbreak of EHEC O121 occurred during which the bacterium acquired a plasmid-borne extended-spectrum β-lactamase (ESBL) gene. ESBL-producing E. coli O86 was concurrently isolated from one of the EHEC patients. Therefore, we investigated the isolates by whole-genome sequence (WGS) analysis to elucidate the transmission dynamics of the EHEC strains and the ESBL plasmid. According to WGS-based phylogeny, all 17 EHEC O121 isolates were clonal, while E. coli O86 was genetically distant from the EHEC O121 isolates. The complete sequence of an ESBL plasmid encoding the CTX-M-55 β-lactamase was determined using S1-PFGE bands, and subsequent mapping of the WGS reads confirmed that the plasmid sequences from EHEC O121 and E. coli O86 were identical. Furthermore, conjugation experiments showed that the plasmid was capable of conjugative transfer. These results support the hypothesis that EHEC O121 acquired an ESBL-producing plasmid from E. coli O86 during the outbreak. This report demonstrates the importance of implementing preventive measures during EHEC outbreaks to control both secondary infection and the spread of antimicrobial resistance factors.
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Affiliation(s)
- Koji Kikuchi
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Ueno
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Kentaro Tomari
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Sumie Kobori
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | | | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motonobu Miyazaki
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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12
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Long J, Xu Y, Ou L, Yang H, Xi Y, Chen S, Duan G. Polymorphism of Type I-F CRISPR/Cas system in Escherichia coli of phylogenetic group B2 and its application in genotyping. INFECTION GENETICS AND EVOLUTION 2019; 74:103916. [PMID: 31195154 DOI: 10.1016/j.meegid.2019.103916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/22/2019] [Accepted: 06/07/2019] [Indexed: 12/26/2022]
Abstract
E. coli of phylogenetic group B2 is responsible for many extraintestinal infections, posing a great threat to health. The relatively polymorphic nature of CRISPR in phylogenetically related E. coli strains makes them potential markers for bacterial typing and evolutionary studies. In the current work, we investigated the occurrence and diversity of CRISPR/Cas system and explored its potential for genotyping. Type I-F CRISPR/Cas systems were found in 413 of 1190 strains of E. coli and exhibited the clustering within certain CCs and STs. And CRISPR spacer contents correlated well with MLST types. The divergence analysis of CRISPR showed stronger discriminatory power than MLST, and CRISPR polymorphism was instrumental for differentiating highly closely related strains. The timeline of spacer acquisition and deletion provided important information for inferring the evolution model between distinct serotypes. Identical spacer sequences were shared by strains with the same H-antigen type but not strains with the same O-antigen type. The homology between spacers and antibiotic-resistant plasmids demonstrated the role of Type I-F system in limiting the acquisition of antimicrobial resistance. Collectively, our data presents the dynamic nature of Type I-F CRISPR in E. coli of phylogenetic group B2 and provides new insights into the application of CRISPR-based typing in the species.
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Affiliation(s)
- Jinzhao Long
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yake Xu
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China; School Hospital, Henan University of Science and Technology, Luoyang, Henan, China
| | - Liuyang Ou
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuanlin Xi
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuaiyin Chen
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| | - Guangcai Duan
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China; Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China.
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13
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Relevance of Food Microbiology Issues to Current Trends (2008-2018) in Food Production and Imported Foods. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Mataseje LF, Boyd DA, Fuller J, Haldane D, Hoang L, Lefebvre B, Melano RG, Poutanen S, Van Caeseele P, Mulvey MR. Characterization of OXA-48-like carbapenemase producers in Canada, 2011-14. J Antimicrob Chemother 2019; 73:626-633. [PMID: 29272439 DOI: 10.1093/jac/dkx462] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/07/2017] [Indexed: 01/23/2023] Open
Abstract
Objectives Since the first identification of the OXA-48 carbapenemase in 2001, Enterobacteriaceae harbouring OXA-48-like enzymes have been reported globally. Here, we applied WGS to characterize the molecular epidemiology of these bacterial isolates. Methods Enterobacteriaceae non-susceptible to carbapenems isolated from patients between 2011 and 2014 were voluntarily submitted to the Canadian National Microbiology Laboratory where they were screened for carbapenemase genes. WGS was conducted on OXA-48-like producers using the Illumina MiSeq platform. WGS data were used for single nucleotide variant (SNV) analysis, MLST analysis, detection of resistance genes and partial plasmid characterization. Susceptibilities were determined using Vitek2 and Etest. Patient data provided from sites were reviewed. Results Sixty-seven non-duplicated cases were identified among Escherichia coli (n = 21) and Klebsiella pneumoniae (n = 46). Recent international travel was observed in 40.4% of cases. OXA-181 (52.2%) and OXA-48 (31.3%) were the most common variants, one E. coli OXA-48 producer was found to harbour the acquired colistin resistance gene mcr-1. The dominant STs were ST38 and ST410 in E. coli and ST14 in K. pneumoniae. Three common plasmid types were observed among isolates: IncL/M associated with OXA-48 producers, and ColKP3 and IncX3 associated with OXA-181/232 producers. Conclusions Enterobacteriaceae with OXA-48-like carbapenemases are emerging in Canada. This study highlights the complexity of OXA-48-types identified in Canada owing to travel and the successful clones and plasmids harbouring the OXA-48-like enzyme.
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Affiliation(s)
- Laura F Mataseje
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David A Boyd
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey Fuller
- Provincial Laboratory of Alberta, Alberta Health Services, Edmonton, Alberta, Canada
| | - David Haldane
- Nova Scotia Health Authority, Pathology and Microbiology, Halifax, Nova Scotia, Canada
| | - Linda Hoang
- British Columbia Public Health Microbiology and Reference Laboratory, Provincial Health Services Authority Laboratories, Vancouver, British Columbia, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Roberto G Melano
- Public Health Ontario Laboratories, Laboratory Medicine and Pathobiology, Toronto, Ontario, Canada
| | - Susan Poutanen
- Mount Sinai Hospital, Department of Microbiology, Toronto, Ontario, Canada
| | | | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a “high-risk” clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of the E. coli ST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively. Escherichia coli sequence type 410 (ST410) has been reported worldwide as an extraintestinal pathogen associated with resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In the present study, we investigated national epidemiology of ST410 E. coli isolates from Danish patients. Furthermore, E. coli ST410 was investigated in a global context to provide further insight into the acquisition of the carbapenemase genes blaOXA-181 and blaNDM-5 of this successful lineage. From 127 whole-genome-sequenced isolates, we reconstructed an evolutionary framework of E. coli ST410 which portrays the antimicrobial-resistant clades B2/H24R, B3/H24Rx, and B4/H24RxC. The B2/H24R and B3/H24Rx clades emerged around 1987, concurrently with the C1/H30R and C2/H30Rx clades in E. coli ST131. B3/H24Rx appears to have evolved by the acquisition of the extended-spectrum β-lactamase (ESBL)-encoding gene blaCTX-M-15 and an IncFII plasmid, encoding IncFIA and IncFIB. Around 2003, the carbapenem-resistant clade B4/H24RxC emerged when ST410 acquired an IncX3 plasmid carrying a blaOXA-181 carbapenemase gene. Around 2014, the clade B4/H24RxC acquired a second carbapenemase gene, blaNDM-5, on a conserved IncFII plasmid. From an epidemiological investigation of 49 E. coli ST410 isolates from Danish patients, we identified five possible regional outbreaks, of which one outbreak involved nine patients with blaOXA-181- and blaNDM-5-carrying B4/H24RxC isolates. The accumulated multidrug resistance in E. coli ST410 over the past two decades, together with its proven potential of transmission between patients, poses a high risk in clinical settings, and thus, E. coli ST410 should be considered a lineage with emerging “high-risk” clones, which should be monitored closely in the future. IMPORTANCE Extraintestinal pathogenic Escherichia coli (ExPEC) is the main cause of urinary tract infections and septicemia. Significant attention has been given to the ExPEC sequence type ST131, which has been categorized as a “high-risk” clone. High-risk clones are globally distributed clones associated with various antimicrobial resistance determinants, ease of transmission, persistence in hosts, and effective transmission between hosts. The high-risk clones have enhanced pathogenicity and cause severe and/or recurrent infections. We show that clones of the E. coli ST410 lineage persist and/or cause recurrent infections in humans, including bloodstream infections. We found evidence of ST410 being a highly resistant globally distributed lineage, capable of patient-to-patient transmission causing hospital outbreaks. Our analysis suggests that the ST410 lineage should be classified with the potential to cause new high-risk clones. Thus, with the clonal expansion over the past decades and increased antimicrobial resistance to last-resort treatment options, ST410 needs to be monitored prospectively.
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16
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Kiel M, Sagory-Zalkind P, Miganeh C, Stork C, Leimbach A, Sekse C, Mellmann A, Rechenmann F, Dobrindt U. Identification of Novel Biomarkers for Priority Serotypes of Shiga Toxin-Producing Escherichia coli and the Development of Multiplex PCR for Their Detection. Front Microbiol 2018; 9:1321. [PMID: 29997582 PMCID: PMC6028524 DOI: 10.3389/fmicb.2018.01321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/30/2018] [Indexed: 12/22/2022] Open
Abstract
It would be desirable to have an unambiguous scheme for the typing of Shiga toxin-producing Escherichia coli (STEC) isolates to subpopulations. Such a scheme should take the high genomic plasticity of E. coli into account and utilize the stratification of STEC into subgroups, based on serotype or phylogeny. Therefore, our goal was to identify specific marker combinations for improved classification of STEC subtypes. We developed and evaluated two bioinformatic pipelines for genomic marker identification from larger sets of bacterial genome sequences. Pipeline A performed all-against-all BLASTp analyses of gene products predicted in STEC genome test sets against a set of control genomes. Pipeline B identified STEC marker genes by comparing the STEC core proteome and the "pan proteome" of a non-STEC control group. Both pipelines defined an overlapping, but not identical set of discriminative markers for different STEC subgroups. Differential marker prediction resulted from differences in genome assembly, ORF finding and inclusion cut-offs in both workflows. Based on the output of the pipelines, we defined new specific markers for STEC serogroups and phylogenetic groups frequently associated with outbreaks and cases of foodborne illnesses. These included STEC serogroups O157, O26, O45, O103, O111, O121, and O145, Shiga toxin-positive enteroaggregative E. coli O104:H4, and HUS-associated sequence type (ST)306. We evaluated these STEC marker genes for their presence in whole genome sequence data sets. Based on the identified discriminative markers, we developed a multiplex PCR (mPCR) approach for detection and typing of the targeted STEC. The specificity of the mPCR primer pairs was verified using well-defined clinical STEC isolates as well as isolates from the ECOR, DEC, and HUSEC collections. The application of the STEC mPCR for food analysis was tested with inoculated milk. In summary, we evaluated two different strategies to screen large genome sequence data sets for discriminative markers and implemented novel marker genes found in this genome-wide approach into a DNA-based typing tool for STEC that can be used for the characterization of STEC from clinical and food samples.
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Affiliation(s)
- Matthias Kiel
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Céline Miganeh
- Genostar Bioinformatics, Montbonnot-Saint-Martin, France
| | - Christoph Stork
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | | | | | | | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
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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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