Clade analysis of enterohemorrhagic Escherichia coli serotype O157: H7/H- strains and hierarchy of their phylogenetic relationships

Infection, Genetics and Evolution

Volumn 12, Issue 8, 2012, Pages 1724-1728

  Yokoyama, Eiji ^a   Hirai, Shinichiro ^a   Hashimoto, Ruiko ^a   Uchimura, Masako ^a  

^a CHIBA PREFECTURAL INSTITUTE OF PUBLIC HEALTH   (Japan)

Author keywords

Clade; Cluster; Enterohemorrhagic Escherichia coli serotype O157:H7 H ; Evolutionary model; Lineage specific polymorphism assay 6 (LSAP6); Subgroup

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CLADISTICS; ENTEROHEMORRHAGIC ESCHERICHIA COLI; ESCHERICHIA COLI O157; GENE CLUSTER; GENE INSERTION; GENE LOCUS; GENETIC ANALYSIS; GENETIC VARIABILITY; JAPAN; MOLECULAR EVOLUTION; NONHUMAN; PARAPHYLY; PHYLOGENY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STX GENE; STX2C GENE;

ESCHERICHIA COLI INFECTIONS; ESCHERICHIA COLI O157; GENES, BACTERIAL; HUMANS; JAPAN; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE;

ESCHERICHIA COLI;

EID: 84865834805     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2012.07.003     Document Type: Article

References (23)

1. Bono J.L., Smith P.L., Keen J.E., Harhay G.P., McDaneld T.G., Mandrell R.E., Jung W.K., Besser T.E., Gerner-Smidt P., Nielaszewska M., Karch H., Clawson M.L. Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans. Mol. Biol. Evol 2012, 29:2047-2062.
2. Dowd S.E., Williams J.B. Comparison of Shiga-like toxin II expression between two genetically diverse lineages of Escherichia coli O157:H7. J. Food Prot. 2008, 71:1673-1678.
3. Eppinger M., Mammel M.K., Leclerc J.E., Ravel J., Cebula T.A. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proc. Natl. Acad. Sci. USA 2011, 108:20142-20147.
4. Franz E., van Hoek A.H.A.M., van der Wal F.J., de Boer A., Zwartkruis-Nahuis A., van der Zwaluw K., Aarts H.J.M., Heuvelink A.E. Genetic features differentiating bovine, food, and human isolates of Shiga toxin-producing Escherichia coli O157 in the Netherlands. J. Clin. Microbiol. 2012, 50:772-780.
5. Hirotsu N., Murakami N., Kashiwagi T., Ujiie K., Ishimaru K. Protocol: a simple gel-free method for SNP genotyping using allele-specific primers in rice and other plant species. Plant Methods 2010, 6:12.
6. Hunson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
7. Kim J., Nietfeldt J., Ju J., Wise J., Fegan N., Desmarchelier P., Benson A.K. Ancestral divergece, genome diversification, and phylogeographic variation in subpopulation of sorbitole-negative, β-glucuronidase-negative enterohemorrhagic Escherichia coli O157. J. Bacteriol. 2001, 183:6885-6897.
8. Kyle, J.L., Cummings, C.A., Parker, C.T., Quiñones, B., Vatta, P., Newton, Elizabeth, Huynh, S., Swimley, M., Degoricija, L., Barker, M., Fontanoz, S., Nguyen, K., Patel, R., Fang, R., Tebbs, R., Petrauskene, O., Furtado, M., Mandrell, R.E., 2012. Escherichia coli serotype O55:H7 diversity supports pararell acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of O157:H7 lineage. J. Bacteriol., 1885-1896.
9. Lee K.-I., French L.N., Jones G., Hara-Kudo Y., Iyoda S., Koyabashi H., Sugita-Konishi Y., Tsubone H., Kumagai S. Variation in stress resistance patterns among stx genotypes and genetic lineages of Shiga toxin-producing Escherichia coli O157. Appl. Environ. Microbiol. 2012, 78:3361-3368.
10. Leopold S.R., Magrini V., Holt N.J., Shaikh N., Mardis E.R., Cagno J., Ogura Y., Iguchi A., Hayashi T., Mellmann A., Karch H., Besser T.E., Sawyer S.A., Whittam T.S., Tarr P.I. A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis. Proc. Natl. Acad. Sci. USA 2009, 106:8713-8718.
11. Liu K., Knabel S.J., Dudley E.G. Rhs genes are potential markers for multilocus sequence typing of Escherichia coli O157:H7 strains. Appl. Environ. Microbiol. 2009, 75:5853-5862.
12. Manning S.D., Motiwala A.S., Springman A.C., Qi W., Lacher D.W., Ouellette L.M., Mladonicky J.M., Somsel P., Rudrik J.T., Dietrich S.E., Zhang W., Swaminathan B., Alland D., Whittam T.S. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc. Nat. Acad. Sci. USA 2008, 105:4868-4873.
13. Newton C.R., Graham A., Heptinstall L.E., Powell S.J., Summers C., Kalsheker N., Smith J.C., Markham A.F. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989, 17:2503-2516.
14. Riordan J.T., Viswanath S.B., Manning S.D., Whittam T.S. Genetic differentiation of Escherichia coli O157:H7 clades associated with human disease by real-time PCR. J. Clin. Microbiol. 2008, 46:2070-2073.
15. Sharma R., Stanford K., Louie M., Munns K., John S.J., Zhang Y., Gannon V., Chui L., Read R., Topp E., McAllister T. Escherichia coli O157:H7 lineages in healthy beef and dairy cattle and clinical human cases in Alberta. Canada J. Food Prot. 2009, 72:601-607.
16. Shaikh N., Tarr P.I. Escherichia coli O157:H7 Shiga toxin-producing bacteriophages: integrations, excisions, truncations, and evolutionary implications. J. Bacteriol. 2003, 185:3596-3605.
17. Whittam, T., Manning, S., Alland, D., Motiwala, A. 2010. Methods of detecting and genotyping Escherichia coli O157:H7. United States Patent Application Publication. US 2010/0279294 A1.
18. Whittam T.S., Wilson R.A. Genetic relationships among pathogenic Escherichia coli of serogroup O157. Infect. Immun. 1988, 56:2467-2473.
19. Whitworth J., Zhang Y., Bono J., Pleydell E., French N., Besser T. Diverse genetic markers concoedantly identified bovine origin Escherichia coli O157 genotypes underrepresented in human disease. Appl. Environ. Microbiol. 2010, 76:361-365.
20. Yang Z., Kovar J., Kim J., Nietfeldt J., Smith D.R., Moxley R.A., Olson M.E., Fey P.D., Benson A.K. Identification of common subpopulations of non-sorbitol-fermenting, beta-glucuronidase-negative Escherichia coli O157:H7 from bovine production environments and human clinical samples. Appl. Environ. Microbiol. 2004, 70:6846-6854.
21. Yokoyama E., Etoh Y., Ichihara S., Horikawa K., Konishi N., Kai A., Matsumoto Y., Kurosaki M., Kasahara H., Kurazono T., Yoda K. Emergence of enterohemorrhagic Escherichia coli serovar O157 strains in clade 8 with highly similar pulsed-field gel electrophoresis patterns. J. Food Prot. 2011, 74:1324-1327.
22. Yokoyama E., Hashimoto R., Etoh Y., Ichihara S., Horikawa K., Uchimura M. Biased distribution of IS629 among strains in different lineages of enterohemorrhagic Escherichia coli serovar O157. Infect. Genet. Evol. 2011, 11:78-82.
23. Zhang Y., Laing C., Steele M., Ziebell K., Johnson R., Benson A.K., Taboada E., Gannon V.P.J. Genome evolution in major Escherichia coli O157:H7 lineages. BMC Genomics 2006, 8:121.