Abstract: 

Antibiotics represent a cornerstone of modern medicine, yet their widespread use has driven the rapid emergence and environmental dissemination of antibiotic resistance genes (ARGs), creating a major public health threat recognized under the One Health framework. Despite documented antibiotic contamination in the Pearl River Estuary and ARG-carrying pathogens in Hong Kong's coastal waters, no systematic metagenomic study has characterized the resistome profiles of farmed and wild-caught fish within this region, leaving critical gaps in understanding how aquaculture practices, environmental pollution, and food chain exposure intersect to shape ARG carriage in locally consumed seafood. This thesis addresses these gaps by deploying metagenomic sequencing across water, sediments, and host-associated tissues (skin, gill, and gut) to profile ARG abundance, diversity, and mobility potential in Hong Kong's marine fish and their surrounding habitats. Sampling was conducted during the dry (March) and wet (August) seasons at two major Fish Culture Zones (Ma Wan in the west and Tai Tau Chau in the east), encompassing both environmental and host-associated samples. Our findings demonstrate that sediments function as permanent resistance reservoirs with quantitative stability across seasons, while monsoon-driven runoff enriches clinical resistance traits in western estuarine zones, particularly beta-lactam and sulfonamide classes, and that host physiological strain correlates with elevated gill-associated ARG burdens under estuarine influence. Building on these findings, future work will extend to wild-caught specimens representing the five most landed fish families for trophic-level comparisons, and will employ controlled mesocosms to investigate whether ARGs persist in the fish microbiome without antibiotic exposure despite fitness costs, and whether depuration in uncontaminated environments can reduce ARG carriage. Together, this research establishes a baseline of fish-associated resistomes in Hong Kong waters, elucidates the ecological and physiological drivers of ARG accumulation with data-driven evidence to inform One Health risk assessment and seafood safety management in this densely populated coastal metropolis.