E. coli serotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage

Authors: Kyle, Jennifer; CUMMINGS, CRAIG - Life Technologies Corporation; Parker, Craig; Quinones, Beatriz; VATTA, PAOLO - Life Technologies Corporation; NEWTON, ELIZABETH - Life Technologies Corporation; Huynh, Steven; Swimley, Michelle; DEGORICIJA, LOVORKA - Life Technologies Corporation; BARKER, MELISSA - Life Technologies Corporation; Walker, Samarpita; Nguyen, Kimberly; Patel, Ronak; FANG, RIXUN - Life Technologies Corporation; TEBBS, ROBERT - Life Technologies Corporation; PETRAUSKENE, OLGA - Life Technologies Corporation; FURTADO, MANOHAR - Life Technologies Corporation; Mandrell, Robert

Submitted to: Journal of Bacteriology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2012
Publication Date: 3/28/2012
Citation: Kyle, J.L., Cummings, C.A., Parker, C., Quinones, B., Vatta, P., Newton, E., Huynh, S., Swimley, M.S., Degoricija, L., Barker, M., Fontanoz, S., Nguyen, K.M., Patel, R.N., Fang, R., Tebbs, R., Petrauskene, O., Furtado, M., Mandrell, R.E. 2012. E. coli serotype O55:H7 diversity supports parallel acquisition of bacteriophage at Shiga toxin phage insertion sites during evolution of the O157:H7 lineage. Journal of Bacteriology. 194:1885-1896.

Interpretive Summary: Enteropathogenic Escherichia coli (EPEC) is a leading cause of infant mortality and morbidity in developing countries. The EPEC O55:H7 serotype has been established as a recent precursor to the virulent, food-borne enterohemorrhagic E. coli serotype O157:H7. We determined the DNA sequence RM12579 an O55:H7 strain from a California to help elucidate the close evolutionary relationship to the O157:H7 serotype. We utilized two state of the art second generation sequencing technologies were used to ensure complete and accurate DNA sequencing. The EPEC O55:H7 genome is approximately 5.3 million base pairs and includes five plasmids. Three plasmids show similarity to those sequenced from other EPEC strains; the remaining two appear to be small, cryptic plasmids. A total of 18 prophage or integrated virus elements were identified, including 16 shared with the previously completed EPEC O55:H7 strain CB9615. The overall pattern of bacteriophage insertion elements appears genetically intermediate between the previously sequenced O157:H7 and O55:H7 strains. Thus, analysis of the complete sequence of this clone permits further insight into the evolution and emergence of the deadly O157:H7 serotype.

Technical Abstract: Insights into Evolution of Escherichia coli O157:H7 from Complete Genome Sequence of Closely Related O55:H7 Precursor Enteropathogenic Escherichia coli (EPEC) continues to be a leading cause of mortality and morbidity in children around the world. The O55:H7 serotype is a recent precursor to the virulent enterohemorrhagic E. coli (EHEC) serotype O157:H7. To explore this diversity, we fully sequenced EPEC O55:H7 str. RM12579 from California, collected one year before the first US isolate of O157:H7 was identified in 1975 in California. The RM12579 chromosome was 5,263,980 bp and possessed five plasmids, two of which encoded resistance to ampicillin and streptomycin antibiotics. Phage-related sequences accounted for nearly all differences between the two fully sequenced O55:H7 strains. Mobile genomic islands encode the majority of virulence factors in pathogenic E. coli, and we also examined the genetic diversity of 14 other O55:H7 by testing for key virulence genes. Additionally, O55:H7 and O157:H7 strains were tested for the presence and insertion site of Shiga toxin gene (stx)-containing bacteriophages. Although separate analysis of non-phage-associated genes supported core elements of previous O157:H7 evolutionary models, phage composition and insertion analyses suggested a key refinement. Specifically, the placement and presence of stx-containing bacteriophages should not be considered a stable evolutionary marker, nor a requirement for placing O55:H7 and O157:H7 strains within the stepwise evolutionary model. Exploration of O55:H7 diversity improved our understanding of the evolution of the E. coli O157:H7 pathogen, and further suggested that new configurations of stx-containing E. coli will continue to appear in the future.