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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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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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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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