Metagenomic insights into foodborne pathogenic bacterial community and their antibiotic resistance genes in food samples from Kinta Valley, Perak

Quek, Jerrald Jia Weai (2026) Metagenomic insights into foodborne pathogenic bacterial community and their antibiotic resistance genes in food samples from Kinta Valley, Perak. Master dissertation/thesis, UTAR.

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Abstract

Foodborne diseases represent an increasing worldwide threat, primarily originating from contamination of bacteria. Despite of a rising prevalence rate in Malaysia, there exists a significant lack of thorough investigations employing metagenomic methodologies to examine foodborne pathogens. This study aimed to determine the feasibility of using shotgun metagenomics to investigate the bacterial community and potential presence of foodborne pathogens, as well as to characterise antibiotic resistance genes (ARGs) present in foodborne pathogens found in food samples, including meats, fruits and vegetables. Shotgun metagenomics revealed the highest DNA sequence reads in vegetables, followed by meats and fruits. Metagenomics analysis of the mock community consisting of Escherichia coli ATCC BAA-197, Campylobacter jejuni ATCC 33560, Shigella flexneri ATCC 29903, Salmonella enterica subspecies enterica serovar Typhimurium ATCC 700408 and Shigella flexneri ATCC 29903 and Listeria monocytogenes ATCC 19115 showed that L. monocytogenes was undetectable in vegetable and meat samples. ARGs from the mock community such as aac(3)-lle, sul1, sco-1, floR and aph(3’)-la were detected in three spiked samples. Dominant bacterial phyla of Pseudomonadota occurred across all 27 samples except for deli meat sample collected from Gopeng. Vegetable samples showed high presence of Proteobacterium, Pseudomonas, Pectobacterium, and lactic acid bacteria. Meat samples contained spoilage and pathogenic bacteria such as Aeromonas, Pseudomonas, and Lactococcus. Fruits had Leuconostoc and Enterobacter. The prevalence of pathogens found in food items varied between locations due to factors like hygiene practices, retail environments, and transport distances. Metagenomics detected pathogens in samples, though some pathogens were not detected when compared to culture methods. Cephalosporin and penam resistance genes were frequent, while deli meat and some fruits showed a lower presence of ARGs compared to vegetables. This suggests that the deli meats underwent processing and that the curing procedure could lower the survival chances of these AMR pathogens while fruits have protective skin or peel. This study demonstrated metagenomics' utility in pathogen detection, microbial profiling, and ARGs prediction, highlighting its potential in enhancing food safety.

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