Microbial ecology and metagenomics of a foodborne pathogen

Dziegiel, Agata Helena (2024) Microbial ecology and metagenomics of a foodborne pathogen. Doctoral thesis, University of East Anglia.

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Abstract

Foodborne illness represents a major global health burden. Campylobacter is a major bacterial cause of foodborne illness, and chicken meat is a leading source of infection. Outbreaks are rarely reported, though this may partly be due to culturing difficulties and limited isolate sampling from food sources. Culture-independent methods like shotgun metagenomics can facilitate direct investigation of retail chicken microbiomes, potentiating direct Campylobacter characterisation and identification of microbial signatures associated with its presence and absence to inform intervention strategies.

This work utilised a combination of culture approaches, whole genome sequencing (WGS) and shotgun metagenomics to characterise Campylobacter diversity on retail chicken and assess the viability of culture-independent sequencing for pathogen surveillance and detection of microbial signatures associated with Campylobacter persistence.

Campylobacter recovery from individual samples was affected by the culture method, indicating that common approaches and media can fail to recover the pathogen. Within-sample diversity was observed at the species, sequence type (ST), single nucleotide polymorphism and antimicrobial resistance genotype level, with significant implications for public health investigations. Evidence of plasmid sharing between STs indicated that the genomic diversity extends beyond the chromosome.

Detection and characterisation of Campylobacter directly with metagenomics was difficult due to its low abundance, and organisms associated with Campylobacter presence and absence could not be reliably identified. Detection may be less challenging in infection scenarios whereby the pathogen is colonising the host; as a proof-of-concept, this was demonstrated by the identification of Salmonella enterica from faecal samples representing culture-confirmed cases.

While metagenomics is a promising method for microbiome profiling and pathogen identification, optimisation in sequencing, analysis pipelines and databases is needed to improve efficacy for food safety applications, where culture and WGS remains important for Campylobacter typing. In clinical scenarios, metagenomic pathogen detection is more effective, though sample preparation and analysis pipeline development can improve characterisation efficacy.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Zoe White
Date Deposited:	18 Feb 2025 15:31
Last Modified:	18 Feb 2025 15:31
URI:	https://ueaeprints.uea.ac.uk/id/eprint/98541
DOI:

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