Volume 23, Number 12—December 2017
Research
Evolutionary Context of Non–Sorbitol-Fermenting Shiga Toxin–Producing Escherichia coli O55:H7
Table 1
Name | Accession no. | Serotype | STX | SOR | GUD | Reference |
---|---|---|---|---|---|---|
USDA 5905 | SRS702210 | O55 | – | + | + | (7) |
3256–97–1 | AEUA01000000 | O55 | – | + | + | (7) |
RM12579–1 | CP003109 | O55 | – | + | + | (7) |
CB9615 | NC_013941 | O55 | – | + | + | (10) |
ZH-1141 | Pending | O55:H7 | – | + | + | (14) |
2013C-4465 | GCA_001644745.1 | O55 | Stx1a | + | + | (15) |
Sakai | O157:H7 | Stx1a and 2a | – | – | (16) | |
155 | CP018237 | O157:H7 | Stx2a | – | – | (17) |
TL-000142 | ERR180875 | O55 | – | + | + | This study |
SRR3578942 | SRR3578942 | O55:H7 | Stx2d | + | + | This study |
TL-000132 | ERR197199 | O55 | – | + | + | This study |
3041–1_85 | ERR197201 | O55 | – | + | + | This study |
100446 | ERR178176 | O55:H7 | – | + | + | This study |
*GUD, β-glucuronidase; SOR, sorbitol; Stx, Shiga toxin; –, negative; +, positive.
References
- McFarland N, Bundle N, Jenkins C, Godbole G, Mikhail A, Dallman T, et al. Recurrent seasonal outbreak of an emerging serotype of Shiga toxin-producing Escherichia coli (STEC O55:H7 Stx2a) in the south west of England, July 2014 to September 2015. Euro Surveill. 2017;22:30610. DOIPubMedGoogle Scholar
- Whittam TS, Wolfe ML, Wachsmuth IK, Orskov F, Orskov I, Wilson RA. Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect Immun. 1993;61:1619–29.PubMedGoogle Scholar
- Feng P, Lampel KA, Karch H, Whittam TS. Genotypic and phenotypic changes in the emergence of Escherichia coli O157:H7. J Infect Dis. 1998;177:1750–3. DOIPubMedGoogle Scholar
- Iguchi A, Ooka T, Ogura Y, Asadulghani , Nakayama K, Frankel G, et al. Genomic comparison of the O-antigen biosynthesis gene clusters of Escherichia coli O55 strains belonging to three distinct lineages. Microbiology. 2008;154:559–70. DOIPubMedGoogle Scholar
- Wick LM, Qi W, Lacher DW, Whittam TS. Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7. J Bacteriol. 2005;187:1783–91. DOIPubMedGoogle Scholar
- Zhou Z, Li X, Liu B, Beutin L, Xu J, Ren Y, et al. Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One. 2010;5:e8700. DOIPubMedGoogle Scholar
- Kyle JL, Cummings CA, Parker CT, Quiñones B, Vatta P, Newton E, et al. Escherichia coli serotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage. J Bacteriol. 2012;194:1885–96. DOIPubMedGoogle Scholar
- Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, Adak G, et al. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin Infect Dis. 2015;61:305–12. DOIPubMedGoogle Scholar
- Jenkins C, Lawson AJ, Cheasty T, Willshaw GA. Assessment of a real-time PCR for the detection and characterization of verocytotoxigenic Escherichia coli. J Med Microbiol. 2012;61:1082–5. DOIPubMedGoogle Scholar
- Persson S, Olsen KE, Ethelberg S, Scheutz F. Subtyping method for Escherichia coli shiga toxin (verocytotoxin) 2 variants and correlations to clinical manifestations. J Clin Microbiol. 2007;45:2020–4. DOIPubMedGoogle Scholar
- Stevens MP, Frankel GM. The locus of enterocyte effacement and associated virulence factors of enterohemorrhagic Escherichia coli. Microbiol Spectr. 2014;2:EHEC-0007–2013. http://dx.doi.org: DOIGoogle Scholar
- Feng P, Lampel KA. Genetic analysis of uidA expression in enterohaemorrhagic Escherichia coli serotype O157:H7. Microbiology. 1994;140:2101–7. DOIPubMedGoogle Scholar
- Lim JY, Yoon J, Hovde CJ. A brief overview of Escherichia coli O157:H7 and its plasmid O157. J Microbiol Biotechnol. 2010;20:5–14.PubMedGoogle Scholar
- Mainda G, Lupolova N, Sikakwa L, Bessell PR, Muma JB, Hoyle DV, et al. Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle. Sci Rep. 2016;6:26589. DOIPubMedGoogle Scholar
- Lindsey RL, Rowe L, Garcia-Toledo L, Loparev V, Knipe K, Stripling D, et al. High-quality draft genome sequences for five non-o157 Shiga toxin-producing Escherichia coli strains generated with PacBio sequencing and optical maps. Genome Announc. 2016;4:e00626–16. DOIPubMedGoogle Scholar
- Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 2001;8:11–22. DOIPubMedGoogle Scholar
- Shaaban S, Cowley LA, McAteer SP, Jenkins C, Dallman TJ, Bono JL, et al. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing. Microb Genom. 2016;2:e000096.PubMedGoogle Scholar
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77. DOIPubMedGoogle Scholar
- Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. DOIPubMedGoogle Scholar
- Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5:e11147. DOIPubMedGoogle Scholar
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. DOIPubMedGoogle Scholar
- Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39(suppl):W347-52. DOIPubMedGoogle Scholar
- Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. DOIPubMedGoogle Scholar
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20. DOIPubMedGoogle Scholar
- Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95. DOIPubMedGoogle Scholar
- McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303. DOIPubMedGoogle Scholar
- Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3. DOIPubMedGoogle Scholar
- Ingle DJ, Tauschek M, Edwards DJ, Hocking DM, Pickard DJ, Azzopardi KI, et al. Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nat Microbiol. 2016;1:15010. DOIPubMedGoogle Scholar
- Dallman TJ, Ashton PM, Byrne L, Perry NT, Petrovska L, Ellis R, et al. 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. DOIPubMedGoogle Scholar
- Feng PC, Jinneman K, Scheutz F, Monday SR. Specificity of PCR and serological assays in the detection of Escherichia coli Shiga toxin subtypes. Appl Environ Microbiol. 2011;77:6699–702. DOIPubMedGoogle Scholar
- Monday SR, Whittam TS, Feng PC. Genetic and evolutionary analysis of mutations in the gusA gene that cause the absence of beta-glucuronidase activity in Escherichia coli O157:H7. J Infect Dis. 2001;184:918–21. DOIPubMedGoogle Scholar
- Sánchez S, Llorente MT, Herrera-León L, Ramiro R, Nebreda S, Remacha MA, et al. Mucus-activatable Shiga toxin genotype stx2d in Escherichia coli O157:H7. Emerg Infect Dis. 2017;23:1431–3. DOIPubMedGoogle Scholar
- Byrne L, Jenkins C, Launders N, Elson R, Adak GK. The epidemiology, microbiology and clinical impact of Shiga toxin-producing Escherichia coli in England, 2009-2012. Epidemiol Infect. 2015;143:3475–87. DOIPubMedGoogle Scholar
- Feng PC, Monday SR, Lacher DW, Allison L, Siitonen A, Keys C, et al. Genetic diversity among clonal lineages within Escherichia coli O157:H7 stepwise evolutionary model. Emerg Infect Dis. 2007;13:1701–6. DOIPubMedGoogle Scholar
- Maurelli AT. Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens. FEMS Microbiol Lett. 2007;267:1–8. DOIPubMedGoogle Scholar
- Matthews L, Reeve R, Gally DL, Low JC, Woolhouse ME, McAteer SP, et al. Predicting the public health benefit of vaccinating cattle against Escherichia coli O157. Proc Natl Acad Sci U S A. 2013;110:16265–70. DOIPubMedGoogle Scholar
- See comment in PubMed Commons belowPersad AK, LeJeune JT. Animal reservoirs of Shiga toxin-producing Escherichia coli. Microbiol Spectr. 2014;2:EHEC-0027–2014.
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