Multi-dimensional assessment of aquaculture health based on environmental nucleic acid (eNA) characterization using a high-throughput qPCR platform

The rapid global expansion of aquaculture is vital important in meeting the increasing demand for aquatic products, making it the fastest-growing animal food production sector. However, the intensification of aquaculture practices, particularly in recirculating aquaculture systems (RAS), has inescapably introduced complex ecological and health challenges. These include the proliferation of infectious agents (IAs) under high-density systems leading to disease outbreak, the accumulations of off-flavour compounds compromising aquatic product quality, difficulties of timely and non-invasive health monitoring, and the widespread dissemination of antibiotic resistance genes (ARGs) driven by antibiotic use in routine disease management practices. Collectively, these factors not only threaten fish welfare and productivity but also pose potential risks to ecological and public health. Consequently, there is a pressing need to improve disease prevention, strengthen biosecurity measures, and enhance early health monitoring in aquaculture systems. Traditional monitoring methods primarily relied on invasive sampling and pathogen-specific detection, which have limitations in terms of scalability and unable to capture real-time IA dynamics in surrounding environment for early monitoring. Moreover, these methods overlook the functional impacts of pathogens on host physiology, thus impeding effective management strategies.

Addressing these systemic gaps requires a paradigm shift toward more integrative approaches, environmental nucleic acid (eNA)-based technologies offer a promising, non-invasive alternative for comprehensive aquatic health monitoring. eNA-based approaches enable the non-invasive and sensitive identification of infectious agents and off-flavour producers directly from environmental samples (e.g., water, air), offering early risk warnings of disease outbreaks before clinical symptoms occur. In complementary, environmental RNA (eRNA) analysis enable captures transcriptional level dynamics from host-derived transcripts, such as stress and immune-related genes, thus linking pathogen presence to host physiological responses, improving infection assessment and enhances disease prediction capabilities. Additionally, the surveillance of ARGs and mobile genetic elements (MGEs) using eNA allows for the evaluation of antimicrobial resistance dynamics and potential transmission pathways within and beyond aquaculture systems.

Centred on the theme “How eNA-based molecular tools could empower aquatic health monitoring and promote sustainable aquaculture management”, this thesis comprises three interrelated studies focusing on infectious agents monitoring, host health assessment, and resistance risk profiling based on high-throughput qPCR (HT-qPCR) platform.