Award details

Epidemiology and Evolution of Pathogens in the Food Chain

Reference	BBS/E/F/000PR10348
Principal Investigator / Supervisor	Professor Robert Kingsley
Co-Investigators / Co-Supervisors	Professor Ian Charles, Dr Thomas Connor, Dr Matthew Gilmour, Dr Gemma Langridge, Professor Alison Mather, Professor Justin O'Grady, Professor Mark Pallen
Institution	Quadram Institute Bioscience
Department	Quadram Institute Bioscience Department
Funding type	Research
Value (£)	5,374,564
Status	Current
Type	Institute Project
Start date	01/04/2018
End date	31/03/2023
Duration	47 months

Abstract

We will survey of genotypic diversity of Salmonella and E. coli in the food chain to gain new insights into pathogen biology and evolution and exploit genome sequences in risk assessment. Two parallel projects will be employed to deliver this objective, a structured epidemiological investigation for the comparison of Salmonella and E. coli from domestic and imported food, and an intensive batch enrichment approach aimed at the isolation of as greater diversity of Salmonella from pork and poultry food at retail. Samples from the structured epidemiological set will undergo enrichment and culture for Salmonella and E. coli. The AMR phenotype of isolates will be determined and DNA extracted for WGS on the Illumina platform. We will determine bacterial population structure and investigate phylogenetic signals and AMR genes in isolates from imported and domestic food. Using the diversity sample set, we will investigate the population structure of isolates from the pork and poultry by whole genome sequencing (WGS) and phylogenetic reconstruction. We will make comparisons with all Salmonella genomes in public databases using the BBSRC-funded Enterobase (http://enterobase.warwick.ac.uk) and with S. Typhimurium genomes collected from ten European countries by the Compare Consortium (http://www.compare-europe.eu) in collaboration with APHA, a consortium member. We will also develop and validate methods to detect and characterise pathogens and AMR genes in food without the need for culture by optimising protocols for metagenomic long-read nanopore sequencing. We will characterise microbial populations of three sentinel bacteria (Campylobacter, E. coli, Salmonella) found in animals and in the environment across multiple farms in the Wye Valley to develop a comprehensive framework for source attribution of E. coli recovered from animals, the farm and the wider environment and assay survival and gene expression in relevant environments. A subset of 160 isolates will be subjected to long-read sequencing to investigate mobile elements relevant to virulence and AMR. We will determine the population structures and core/pan genome of Campylobacter, Salmonella and E. coli from linked environments. On a subset of environmental isolates attributed to animals, we will assay survival and gene expression in relevant environments, examining changes in gene expression via RNA-Seq. We will use state-of-the-art bacterial GWAS to evaluate L. monocytogenes genetic variation in food and clinical isolates. Furthermore, we will investigate the phylogenetic distribution of putative essential genes for survival in the food chain identified in functional genomics experiments. Identify AMR genes/mutations and mobile genetic elements within L. monocytogenes genomes and evaluate temporal trends. We will use Oxford nanopore long-read sequencing, building on the techniques developed by O’Grady, to obtain finished L. monocytogenes genomes directly from food and identify to the sub-species level.

Summary

unavailable

Committee	Not funded via Committee
Research Topics	Microbial Food Safety, Microbiology
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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