Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7

Authors: Sharma, Vijay; Akavaram, Surya Tej; SCHAUT, ROBERT - Orise Fellow; Bayles, Darrell

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2019
Publication Date: 3/8/2019
Citation: Sharma, V.K., Akavaram, S.N., Schaut, R.G., Bayles, D.O. 2019. Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7. BMC Genomics. 20:196. https://doi.org/10.1186/s12864-019-5568-6.
DOI: https://doi.org/10.1186/s12864-019-5568-6

Interpretive Summary: Escherichia coli O157:H7 (O157) is a serious foodborne bacteria capable of causing sporadic outbreaks of diarrheal illnesses in humans. However, these illnesses in children and the elderly coluld lead to kidney failure, neurological complications, and even death. Humans become infected with O157 by consuming undercooked and contaminated ground beef, vegetables, and water contaminated with O157 bacteria. The major sources for the contamination of these foods and water are cattle feces or manure containing O157 bacteria. These bacteria colonize cattle intestines, colonized animals shed these bacteria in their feces, a major risk factor in the contamination of cattle carcasses and meats. Run-off water from cattle production facilities also poses the down-stream risk to the contamination of vegetables and other produce. The genetic mechanisms promoting colonization and persistence of O157 in cattle intestines are not fully understood. Newer technologies to unravel the entire genetic make-up of bacterial populations are becoming increasingly valuable to identify genetic features of bacteria enhancing colonization of a susceptible host animal. By using one of these technologies we determined the complete genetic make-up of an O157 bacterial strain. Fine-tune analysis of the genetic make-up, allowed identification of genetic features that could potentially enhance survival of O157 in cattle and the environment outside the cattle. The practical field applications of having detailed genetic fingerprints would be to use these as reference tools to identify how these genetic fingerprints and the genetic information produced by these fingerprints change during the course of colonization of O157 in cattle or during survival in the environment, such as feces and manure. In addition, these fingerprints would be important in identifying genetic features that could be used as O157-specific biomarkers and as targets in vaccine candidates.

Technical Abstract: Background: Escherichia coli O157:H7 (O157) has been linked to numerous foodborne outbreaks since early 1980s. Ability to rapidly sequence and compare genomes are important for understanding outbreak strain epidemiology, virulence, environmental survival, evolutionary divergence and identifying genetic markers suitable for developing vaccines to control carriage of O157 in reservoir animals. In the current study, we performed comparative genomics of a foodborne O157 strain NADC 6564 to identify genetic features unique to this strain, infer its evolutionary relationship, and assess if the newly identified features directly or indirectly impact its virulence and environmental survival. Results: The chromosome of NADC 6564 contained 5,466 kb compared to reference strains Sakai (5,498 kb) and EDL933 (5,547 kb) and shared 41 of its 43 Linear Conserved Blocks (LCB) with the reference strains. However, 18 of 41 LCB were inverted in their orientation compared to that in the reference strains. NADC 6564 and the reference strains shared 18 of 19 bacteriophages with some occupying similar and others dissimilar sites on their chromosomes. The additional phage-like element (P19) of NADC 6564 was located on a 39 kb insertion element (IE) encoding several hypothetical proteins, an integrase, transposases, transcriptional regulators, an adhesion, and a phosphoethanolamine transferase (PEA). The complete homologs of the 39 kb IE were found in a few E. coli strains, including E. coli PCN061 of porcine origin. The additional PEA transferase showed 32 - 33 percent homology to mobilizable colistin resistance genes and four other PEA transferases present in NADC 6564, but exhibited 95 percent homology to a PEA transferase present in strains of uropathogenic, avian pathogenic, and enteroaggregative E. coli. NADC 6564 showed slight increase in the minimum inhibitory concentration of colistin compared to the reference strains. The IE also contained dndBCDE and dptFGH operons encoding DNA S-modification and a restriction pathway, linked to oxidative stress tolerance and self-defense against foreign DNA, respectively. Evolutionary tree analysis grouped NADC 6564 with lineage I strains. Conclusions: These results indicated that varied phage and genomic islands count and their chromosomal distribution could account for the altered chromosomal organization of NADC 6564 via specific recombination events. In addition, IE-encoded novel genes could potentially enhance tolerance of NADC 6564 to various stressors.