Abstract
Increasing global consumption of seafood and meat products calls for high standards of food safety and stricter regulation. Understanding the level of contamination of foodborne pathogens in food is vital to enhance food safety. This thesis investigated the prevalence of bacterial contamination of food produces and antimicrobial resistance mechanisms of foodborne pathogens in Greater Bay Area, using culture-based and metagenomic approaches.Initially, Vibrio species from food products underwent culture-based analysis, focusing on tetracycline resistance in Vibrio parahaemolyticus. Between 2013 and 2021, 2,342 non-duplicate V. parahaemolyticus strains were isolated from 3,509 food samples, with 530 (21.37%) showing tetracycline resistance, notably 85% from shrimp. tet(A) was the predominant gene (65%), with tet(B) showing high resistance rates. Multiple plasmid types and transposable units harbored tet genes, often linked to multidrug resistance, suggesting frequent horizontal gene transfer.
Metagenomic methods offer a comprehensive analysis of the total microbiome in food samples, providing insights into diverse bacterial communities, antibiotic resistance genes (ARGs), virulence factor genes (VFGs) and mobile genetic elements (MGEs) compared to traditional isolation methods. We initially focused on shrimp, a primary source of Vibrio spp. contamination, by integrating both isolation and metagenomic techniques. Shrimp metagenomes revealed Proteobacteria and Bacteroidetes prevalence, with Firmicutes in some cases key isolated bacteria included Citrobacter portucalensis, Escherichia coli, Salmonella enterica, various Vibrio species, and Klebsiella pneumoniae. Analysis identified clinically significant ARGs blaKPCs, blaNDMs, mcr, and tet(X4). Genomic analysis of bacterial strains revealed ARGs and multidrug-resistant (MDR) plasmids, highlighting resistance gene spread. Examination of VFGs and MGEs showed their complex interplay, impacting bacterial virulence and genetic mobility.
In addition, expanding our research to pork, and chicken skin surfaces, we found diverse microbial communities. Pork from Hong Kong's wet markets showed Firmicutes and Proteobacteria dominance. Clinically significant pathogens like E. coli and K. pneumoniae were detected in pork, raising concerns about foodborne illnesses. In a pioneering study, we analyzed microbial flora on chilled chicken skin using Next-generation sequencing (NGS) and Nanopore sequencing, identifying potential pathogens like Rahnella aquatilis and diverse ARGs, notably beta-lactam resistance genes. Our investigation assembled 49 high-quality metagenome-assembled genomes (MAGs), highlighting identical ARGs in strains from different locations.
We also offer a comprehensive analysis of Biosynthetic Gene Clusters (BGCs) diversity on shrimp, pork, and chicken skin surfaces, highlighting the microbiome's role in habitat-specific secondary metabolisms. Chicken skin microbiomes exhibit remarkable diversity, with 528 clusters, including 17 unique ones. Pork and shrimp skin microbiomes feature distinct BGC profiles, reflecting evolutionary adaptation and biosynthetic potential. The research also explores antibacterial capabilities of chicken skin BGCs, identifying clusters with antibacterial activity and associated resistance marker genes.
In conclusion, our study provides insights into HPBs, ARGs, and BGCs in diverse food sources from China's Greater Bay Area. Stricter regulatory oversight and innovative interventions are needed to mitigate risks to food safety and public health, emphasizing the importance of considering market-sourced in assessing microbial dynamics.
| Date of Award | 6 Aug 2024 |
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| Original language | English |
| Awarding Institution |
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| Supervisor | Runsheng LI (Supervisor), Sheng CHEN (External Co-Supervisor) & Fuyong LI (Co-supervisor) |