Abstract
We report the draft genome sequences of three enteropathogenic Escherichia coli (EPEC) isolates that display the O157 serogroup but do not have the Shiga toxin genes (stx), which are characteristic of O157 enterohemorrhagic E. coli (EHEC). E. coli strain RN587/1 has the O157:H8 serotype and possesses the EAF plasmid characteristic of typical EPEC (J. B. Kaper, J. P. Nataro, and H. L. Mobley, Nat. Rev. Microbiol. 2:123–140, 2004). The other two isolates, strains C844-97 and C639-08, are both O157:H45 and possess the locus of enterocyte effacement (LEE) pathogenicity island; however, they do not contain the EAF plasmid or the stx-carrying phage.
GENOME ANNOUNCEMENT
Attaching and effacing Escherichia coli (AEEC) is characterized by the presence of the locus of enterocyte effacement (LEE) pathogenicity island (1–3) and includes enterohemorrhagic E. coli (EHEC), which expresses Shiga toxins (encoded by stx1 and/or stx2), and typical enteropathogenic E. coli (EPEC), which expresses the EAF plasmid-carried bundle-forming pilus gene (bfp) (1, 4, 5). O157 EHEC has been identified as one of the most frequent agents of severe gastrointestinal illness and hemolytic-uremic syndrome (HUS) in the United States (6–8). O157:H45 EPEC isolates with the genotype bfp+ have been previously associated with an outbreak of diarrhea in Japan (9). Additionally, O157:non-H7 E. coli has been isolated from human, animal, and water sources (10, 11), and a recent study demonstrated that the O157-antigen gene cluster is present in E. coli strains with diverse genetic backgrounds rather than being restricted to O157:H7 EHEC (12), suggesting that the serogroup alone is not indicative of increased virulence.
Genomic DNA was isolated from an overnight culture using the Sigma GenElute kit (Sigma-Aldrich) and was sequenced at the University of Maryland School of Medicine, Institute for Genome Sciences, Genome Resource Center (http://www.igs.umaryland.edu/). The genome sequence of the RN587/1 isolate was generated using 8-kb-insert paired-end libraries on the 454 Titanium system (Roche), and the genome sequences of the C844-97 and C639-08 isolates were generated using paired-end libraries with 300-bp inserts on the Illumina HiSeq2000. The draft genome sequences were assembled using the Celera assembler (13) for 454 sequence data or the Velvet assembly program (14) for the Illumina data. The resulting genome sequences contained an average of 170 contigs per isolate (range, 117 to 243).
These isolates represent the first draft genome sequences of three O157:non-H7 isolates from the EPEC pathotype. Isolate RN587/1 exhibits the O157:H8 serotype and was identified as EPEC by the presence of the LEE and the bfpA gene (15). The other two isolates, C844-97 and C639-08, are isolates from human diarrhea and are serotyped as O157:H45. C844-97 was isolated in Japan and C639-08 was isolated in Denmark. None of these isolates described possess the Shiga toxin genes, stx1 and stx2, which are characteristic of EHEC; thus, they were identified as EPEC. In a whole-genome phylogeny, the genomes from these O157:non-H7 isolates formed a distinct group within the B2 phylogenetic lineage of all E. coli strains and are most similar to the EPEC1 pathotype (data not shown). Furthermore, all three of the O157 EPEC isolates have the alpha intimin type, which is characteristic of EPEC1 and other members of B2 (12). The bundle-forming pilus genes of the EAF plasmid that are characteristic of typical EPEC were identified in RN587/1 but not C844-97 or C639-08. However, the EAF plasmid was originally detected in C844-97, suggesting this isolate has recently lost the virulence plasmid.
To our knowledge, these are among the first O157:non-H7 EPEC genome sequences to be released into the public domain.
Nucleotide sequence accession numbers.
The genome sequence data have been deposited in GenBank with accession numbers ADUS00000000, AIBZ00000000, and AIBH00000000 for isolates RN587/1, C844-97, and C639-08, respectively.
ACKNOWLEDGMENTS
This project was funded in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract number HHSN272200900009C and funds from the State of Maryland.
Footnotes
Citation Hazen TH, Sahl JW, Fraser CM, Donnenberg MS, Scheutz F, Rasko DA. 2013. Draft genome sequences of three O157 enteropathogenic Escherichia coli isolates. Genome Announc. 1(4):e00516-13. doi:10.1128/genomeA.00516-13.
REFERENCES
- 1. Kaper JB, Nataro JP, Mobley HL. 2004. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2:123–140 [DOI] [PubMed] [Google Scholar]
- 2. McDaniel TK, Jarvis KG, Donnenberg MS, Kaper JB. 1995. A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. Proc. Natl. Acad. Sci. U. S. A. 92:1664–1668 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. McDaniel TK, Kaper JB. 1997. A cloned pathogenicity island from enteropathogenic Escherichia coli confers the attaching and effacing phenotype on E. coli K-12. Mol. Microbiol. 23:399–407 [DOI] [PubMed] [Google Scholar]
- 4. Nataro JP, Kaper JB. 1998. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11:142–201 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Donnenberg MS, Kaper JB. 1992. Enteropathogenic Escherichia coli. Infect. Immun. 60:3953–3961 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Banatvala N, Griffin PM, Greene KD, Barrett TJ, Bibb WF, Green JH, Wells JG, Hemolytic Uremic Syndrome Study Collaborators 2001. The United States National Prospective Hemolytic Uremic Syndrome Study: microbiologic, serologic, clinical, and epidemiologic findings. J. Infect. Dis. 183:1063–1070 [DOI] [PubMed] [Google Scholar]
- 7. Bielaszewska M, Köck R, Friedrich AW, von Eiff C, Zimmerhackl LB, Karch H, Mellmann A. 2007. Shiga toxin-mediated hemolytic uremic syndrome: time to change the diagnostic paradigm? PLoS One 2:e1024. 10.1371/journal.pone.0001024 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Tarr PI, Gordon CA, Chandler WL. 2005. Shiga-toxin-producing Escherichia coli and haemolytic uraemic syndrome. Lancet 365:1073–1086 [DOI] [PubMed] [Google Scholar]
- 9. Makino S, Asakura H, Shirahata T, Ikeda T, Takeshi K, Arai K, Nagasawa M, Abe T, Sadamoto T. 1999. Molecular epidemiological study of a mass outbreak caused by enteropathogenic Escherichia coli O157:H45. Microbiol. Immunol. 43:381–384 [DOI] [PubMed] [Google Scholar]
- 10. Feng PC, Keys C, Lacher D, Monday SR, Shelton D, Rozand C, Rivas M, Whittam T. 2010. Prevalence, characterization and clonal analysis of Escherichia coli O157: non-H7 serotypes that carry eae alleles. FEMS Microbiol. Lett. 308:62–67 [DOI] [PubMed] [Google Scholar]
- 11. Stephan R, Borel N, Zweifel C, Blanco M, Blanco JE. 2004. First isolation and further characterization of enteropathogenic Escherichia coli (EPEC) O157:H45 strains from cattle. BMC Microbiol. 4:10. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Iguchi A, Shirai H, Seto K, Ooka T, Ogura Y, Hayashi T, Osawa K, Osawa R. 2011. Wide distribution of O157-antigen biosynthesis gene clusters in Escherichia coli. PLoS One 6:e23250. 10.1371/journal.pone.0023250 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, Lonardi S, Beasley EM, Brandon RC, Chen L, Dunn PJ, Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter JC. 2000. A whole-genome assembly of Drosophila. Science 287:2196–2204 [DOI] [PubMed] [Google Scholar]
- 14. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Blank TE, Lacher DW, Scaletsky IC, Zhong H, Whittam TS, Donnenberg MS. 2003. Enteropathogenic Escherichia coli O157 strains from Brazil. Emerg. Infect. Dis. 9:113–115 [DOI] [PMC free article] [PubMed] [Google Scholar]