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1 JB Accepts, published online ahead of print on February 0 J. Bacteriol. doi:./jb.00- Copyright 0, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved. 1 Draft genome sequences of six Escherichia coli isolates from the stepwise model emergence of Escherichia coli O1:H Rump L. V. 1,, Strain E. A. 1, Cao G., Allard M. W. 1, Fischer M., Brown E. W. 1 and Gonzalez-Escalona N. 1* 1 Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, 0 Paint Branch Parkway, College Park, MD 00, USA, Joint Institute for Food Safety and Applied Nutrition (JIFSAN) University of Maryland and Institute of Food Chemistry, University of Hamburg, Hamburg, Germany Key words: Escherichia coli O1:H, EHEC, EPEC, genome sequencing, Running title: Escherichia coli draft genome sequences *Corresponding author. Mailing address: FDA, CFSAN, 0 Paint Branch Parkway HFS-1, College Park, MD 00. Phone: (01) -1. Fax: (01) -. E- mail: narjol.gonzalez-escalona@fda.hhs.gov. Downloaded from on December, 01 by guest 1

2 Abstract Enterohemorrhagic Escherichia coli (EHEC) of serotype O1:H has been implicated in foodborne illnesses worldwide. An evolutionary model was proposed in which the highly pathogenic EHEC O1:H arose from its ancestor enteropathogenic E. coli (EPEC) O:H [sorbitol fermenting (SOR+) and β-glucuronidase positive (GUD+)] through sequential gain of virulence, phenotypic traits, and serotype change. Here we report six draft genomes of strains belonging to this evolutionary model: two EPEC O:H (SOR+/GUD+) strains, two non-motile EHEC O1:H- strains (SOR+/GUD+) containing plasmid psfo1, one EHEC O1:H (SOR-/GUD+) strain, and one O1:H strain containing plasmid psfo1 (SOR+/GUD+). Downloaded from on December, 01 by guest

3 Enterohemorrhagic Escherichia coli (EHEC) O1:H has become a significant worldwide cause of food-borne illness since its discovery about 0 years ago. It frequently causes large outbreaks of severe enteric infections including bloody diarrhoea, hemorrhagic colitis (HC) and haemolytic uremic syndrome (HUS) (1,). This serotype expresses the somatic (O) 1 and flagellar (H) antigens, so these traits are extensively used in clinical analysis to identify this highly pathogenic serotype (1). A stepwise evolutionary model has been proposed in which the highly pathogenic enterohemorrhagic E. coli (EHEC) O1:H arose from its ancestor enteropathogenic E. coli (EPEC) O:H belonging to clonal complex (CC) A1/A (SOR+/GUD+) through sequential acquisition of virulence and phenotypic traits and serotype change (,,). After the somatic antigen change from O to O1 gave rise to a probably extinct intermediary (CC A), two separate O1 CCs evolved splitting into two diverging clonal groups. One was composed of sorbitol fermenting (SF) non-motile O1:H- strains containing plasmid psfo1 (CC A) (SOR+/GUD+). The other was composed of non-sorbitol fermenting (NSF) O1:H strains containing plasmid po1 (CC A) (SOR-/GUD+). The latter by a mutational inactivation of the uida gene lost its β-glucuronidase activity which is the most typical O1:H phenotype at present (CC A) (). These CC A strains expanded and spread geographically and account for most of the diseases caused by EHEC (). So far, only four complete genomes sequences for pathogenic E. coli O1:H belonging to the CC A have been reported and deposited in GenBank: Sakai (NC_00) (), EDL (AE001) (), TW1 (CP001) () and EC (NC_0). Recently, the genome of an ancestral O:H strain CB1 Downloaded from on December, 01 by guest

4 (NC_0) was made available (). In the present publication we announce the availability of six draft genome sequences for other enteropathogenic E. coli strains belonging to the stepwise model emergence of E. coli O1:H (). The strains sequenced are: EPEC O:H - (CC A) and USDA 0 (CC A), O1:H LSU-1 (CC A unknown), EHEC O1:H- / (CC A) and H (CC A), and EHEC O1:H G1 (CC A) (). Genomic DNA from each strain was isolate from overnight cultures using DNeasy Blood & Tissue Kit (QIAGEN). The genomes were sequenced using Titanium pyrosequencing (Roche), according to manufacter s instructions at a 0X coverage. Genomic sequence contigs for strains - and USDA 0 were assembled with the Life Sciences Newbler software package version. (Roche) using the complete E. coli O:H strain CB1 genome (see above for accession number) as a reference. Genomic sequence contigs for strains LSU-1, /, H and G1, were assembled using the complete E. coli O1:H strain Sakai genome as a reference. Sequences were annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline ( (). A detailed report of a full comparative analysis between the genomes of these six isolates will be included in a future publication. Nucleotide sequence accession numbers. The draft genome sequences for six E. coli strains are available in GenBank under accession numbers: AEUB , AEUA , AETY , AETZ , AEUC , and AETX Downloaded from on December, 01 by guest

5 Acknowledgements and Funding This project was supported by an appointment to the Research Fellowship Program for the Center for Food Safety and Applied Nutrition administered by the Oak Ridge Associated Universities through a contract with the FDA. References 1. Feng P. 1. Escherichia coli serotype O1:H: novel vehicles of infection and emergence of phenotypic variants. Emerg. Infect. Dis 1:-.. Feng P, Lampel KA, Karch H, and Whittam TS. 1. Genotypic and phenotypic changes in the emergence of Escherichia coli O1:H. J. Infect. Dis. 1:-1.. Feng PC, Monday SR, Lacher DW, Allison L, Siitonen A, Keys C, Eklund M, Nagano H, Karch H, Keen J, and Whittam TS. 00. Genetic diversity among clonal lineages within Escherichia coli O1:H stepwise evolutionary model. Emerg. Infect. Dis. 1:1-.. Griffin PM and Tauxe RV.. The epidemiology of infections caused by Escherichia coli O1:H, other enterohemorrhagic E. coli, and the associated hemolytic uremic syndrome. Epidemiol. Rev. 1:0-. Downloaded from on December, 01 by guest 1. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H,

6 Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, and Shinagawa H Complete genome sequence of enterohemorrhagic Escherichia coli O1:H and genomic comparison with a laboratory strain K-1. DNA. Res. :-.. Klimke, W., R. Agarwala, A. Badretdin, S. Chetvernin, S. Ciufo, B. Fedorov, B. Kiryutin, K. O'Neill, W. Resch, S. Resenchuk, S. Schafer, I. Tolstoy, and T. Tatusova. 00. The National Center for Biotechnology Information's Protein Clusters Database. Nucleic Acids Res. :D1-D.. Kulasekara, B. R., M. Jacobs, Y. Zhou, Z. Wu, E. Sims, C. Saenphimmachak, L. Rohmer, J. M. Ritchie, M. Radey, M. McKevitt, T. L. Freeman, H. Hayden, E. Haugen, W. Gillett, C. Fong, J. Chang, V. Beskhlebnaya, M. K. Waldor, M. Samadpour, T. S. Whittam, R. Kaul, M. Brittnacher, and S. I. Miller. 00. Analysis of the genome of the Escherichia coli O1:H 00 spinach-associated outbreak isolate indicates candidate genes that may enhance virulence. Infect. Immun. :1-1.. Perna, N. T., G. Plunkett, III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner Genome sequence of enterohaemorrhagic Escherichia coli O1:H. Nature 0:-. Downloaded from on December, 01 by guest

7 . Whittam, T. S., M. L. Wolfe, I. K. Wachsmuth, F. Orskov, I. Orskov, and R. A. Wilson. 1. Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect. Immun. 1:-1.. Wick, L. M., W. Qi, D. W. Lacher, and T. S. Whittam. 00. Evolution of genomic content in the stepwise emergence of Escherichia coli O1:H. J. Bacteriol. 1:1-.. Zhou, Z., X. Li, B. Liu, L. Beutin, J. Xu, Y. Ren, L. Feng, R. Lan, P. R. Reeves, and L. Wang. 0. Derivation of Escherichia coli O1:H from its O:H precursor. PLoS One :e00. Downloaded from on December, 01 by guest