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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Publications at this Location » Publication #336742
Research Project: Genomic and Metagenomic Differences in Foodborne Pathogens and Determination of Ecological Niches and Reservoirs

Location: Meat Safety and Quality

Title: Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic E. coli O157 by long-read sequencing

Author
item SHAABAN, SHARIF - ROSLIN INSTITUTE
item DALLMAN, TIMOTHY - PUBLIC HEALTH ENGLAND (PHE)
item MCATEER, SEAN - ROSLIN INSTITUTE
item COWLEY, LAUREN - PUBLIC HEALTH ENGLAND (PHE)
item JENKINS, CLAIRE - PUBLIC HEALTH ENGLAND (PHE)
item Bono, James - Jim
item GALLY, DAVID - ROSLIN INSTITUTE

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 2/1/2017
Publication Date: 4/3/2017
Citation: Shaaban, S., Dallman, T., McAteer, S., Cowley, L., Jenkins, C., Bono, J.L., Gally, D. 2017. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic E. coli O157 by long-read sequencing. [Abstract]. Microbiology Society Annual Conference 2017, Edinburgh, UK. No. 561.

Interpretive Summary:

Technical Abstract: Enterohaemorrhagic Escherichia Coli (EHEC) is a zoonotic pathogen known to be potentially lethal in humans. Its main animal reservoir is ruminants, specifically cattle, and yearly outbreaks occur worldwide with the most prevalent serotype being EHEC O157:H7. Most virulence factors of EHEC O157, including Shiga toxin (stx) genes, have been acquired through horizontal gene transfer, mostly as the integration of bacteriophages (prophages), which complicate genome assembly using the more prevalent short-read sequencing platforms. For our analysis selected representative strains from the EHEC O157 SNP phylogeny were sequenced using the long-read Pacific Biosciences platform. This has allowed an analysis of complete genomes from EHEC O157 strains, including the extraction, and comparison of their fully assembled prophage content. We observed different levels of variation across the prophage population which could be representative of the timing of acquisition events. Stx2c prophages exhibited minimal sequence variation compared to Stx2a- and Stx1a-encoding prophages, supporting the hypothesis that a Stx2c prophage acquisition event lead to the founder EHEC O157 clone. Acquisition of a specific type of Stx2a prophage into the Stx2c background resulted in conversion of the isolate from Phage Type (PT) 32 to PT21/28, the PT associated with the most serious EHEC O157 human infections in the UK over the last decade. By comparing the gene content of all prophages, it was evident that certain functional groups were over-represented or under-represented dependent on the size of the prophage. Recombinational activity was retained while phage structural genes were lost in the smaller and presumably cryptic prophage regions.