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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety & Quality Research » Research » Publications at this Location » Publication #372324

Research Project: Genomic and Metagenomic Differences in Foodborne Pathogens and Determination of Ecological Niches and Reservoirs

Location: Meat Safety & Quality Research

Title: Prophage variation and rearrangements in E. coli O157 and implications for zoonotic threat

item FITZGERALD, STEPHEN - Roslin Institute
item LUPOLOVA, NADEJDA - Roslin Institute
item SHAABAN, SHARIF - Roslin Institute
item LEACH, DAVID - Roslin Institute
item DALLMAN, TIMOTHY - Public Health England (PHE)
item Bono, James - Jim
item GALLY, DAVID - Roslin Institute

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/3/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Escherichia coli O157:H7 is a clonal group of E. coli that is associated with life-threatening disease in humans due to production of Shiga toxins (Stx). Cattle are the main reservoir host in which colonisation is asymptomatic. Different subtypes of Stx are expressed from bacteriophages integrated into the E. coli O157 genome. The United Kingdom has severe human infections due to Lineage I E. coli O157 PT21/28 isolates that usually encode two Stx subtypes, Stx2a and 2c. We have applied both Illumina and Pac Bio sequencing to examine PT21/28 isolates with the aim of understanding their successful emergence in the UK. Stx2a phage integration into Stx2c+ E. coli O157 ancestors is estimated to have occurred approximately 50 years ago in cattle and fits with the timing of emergence of this life-threatening human infection in the UK. While Illumina-based short read sequencing is transforming public health microbiology, long-read sequencing provides further insights into prophage composition and genome configuration. It is evident that E. coli O157 contains multiple large repeated regions that act as the seed sites for extensive genome rearrangements. Previous work has shown that PFGE patterns can change after multiple generations in culture and during animal colonisation and our assemblies show that genomes of PT21/28 isolates are dynamic, undergoing large duplication and inversion events which are continuously occurring as evidenced by optical mapping. We present a model in which double-strand breaks occur in certain prophage regions leading to large duplications that can then produce the inversions. We propose that this genome plasticity acts in an ‘epigenetic’ manner to alter gene expression promoting bacterial growth and survival in different niches. This capacity in E. coli O157 PT21/28 may be an additional factor behind its success in cattle and as a human pathogen.