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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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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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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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Pianciola L, D'Astek BA, Mazzeo M, Chinen I, Masana M, Rivas M. Genetic features of human and bovine Escherichia coli O157:H7 strains isolated in Argentina. Int J Med Microbiol 2016; 306:123-30. [PMID: 26935026 DOI: 10.1016/j.ijmm.2016.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/30/2015] [Accepted: 02/15/2016] [Indexed: 11/30/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens associated with human diseases. In Argentina, O157:H7 is the dominant serotype in hemolytic uremic syndrome (HUS) cases. Previously, we have described the almost exclusive circulation of human E. coli O157 strains belonging to the hypervirulent clade 8 in Neuquén Province. The aim of the present study was to investigate, by a broad molecular characterization, if this particular distribution of E. coli O157 clades in Neuquén is similar to the situation in other regions of the country and if it may be originated in a similar profile in cattle, its main reservoir. Two-hundred and eighty O157 strains (54 bovine and 226 human) isolated between 2006 and 2008 in different regions of Argentina were studied. All strains harbored rfbO157, fliCH7, eae, and ehxA genes. The predominant genotype was stx2a/stx2c in human (76.1%) and bovine (55.5%) strains. All human isolates tested by Lineage-Specific Polymorphism Assay (LSPA-6), were lineage I/II; among bovine strains, 94.1% belonged to lineage I/II and 5.9% to lineage I. No LSPA-6 lineage II isolates were detected. Single nucleotide polymorphism (SNP) analysis has revealed the existence of nine clade phylogenetic groups. In our clinical strains collection, 87.6% belonged to the hypervirulent clade 8, and 12.4% were classified as clade 4/5. In bovine isolates, 59.3% strains were clade 8, 33.3% clade 4/5 and 7.4% clade 3. More than 80% of human strains showed the presence of 6 of the 7 virulence determinants described in the TW14359 O157 strain associated with the raw spinach outbreak in the U.S. in 2006. More than 80% of bovine strains showed the presence of 3 of these factors. The q933 allele, which has been related to high toxin production, was present in 98.2% of clinical strains and 75.9% of the bovine isolates. The molecular characterization of human STEC O157 strains allows us to conclude that the particular situation previously described for Neuquén Province, may actually be a characteristic of the whole country. These genetic features are quite similar to those observed in the bovine reservoir and may be derived from it. This data confirms that, unlike the rest of the world, in Argentina most of the STEC O157 strains present in cattle may cause human infections of varying severity and the marked virulence described for these strains may be related to the high incidence of HUS in our country.
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Affiliation(s)
- L Pianciola
- Laboratorio Central, Subsecretaría de Salud de Neuquén, Gregorio Martínez 65, 8300 Neuquén, Argentina.
| | - B A D'Astek
- Servicio Fisiopatogenia, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, 1281 Buenos Aires, Argentina
| | - M Mazzeo
- Laboratorio Central, Subsecretaría de Salud de Neuquén, Gregorio Martínez 65, 8300 Neuquén, Argentina
| | - I Chinen
- Servicio Fisiopatogenia, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, 1281 Buenos Aires, Argentina
| | - M Masana
- Instituto Nacional de Tecnología Agropecuaria, Centro de Investigación de Agroindustria, Instituto Tecnología de Alimentos, Morón, Pcia, de Buenos Aires, Argentina
| | - M Rivas
- Servicio Fisiopatogenia, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Vélez Sarsfield 563, 1281 Buenos Aires, Argentina
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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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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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