A pilot study to analyze whether changes in bacteria microbial community using flow cytometry and pathogen eDNA can be employed to monitor and predict disease outbreaks in commercial fish farms in Singapore
Role
Collaborator
Description
AIM: Can changes in bacteria microbial community using flow cytometry and pathogen eDNA be used as a proxy for predicting disease outbreaks in commercial fish farms in Singapore? CONTEXT: The aquaculture industry is constantly jeopardized by diseases which can result in insignificant economic losses due to poor growth performance and mortality. Fish diseases are caused by a wide range of infectious organisms, including viruses, bacteria, fungi, protozoan, and metazoan parasites. Microbial communities can change rapidly in aquatic environments and adversely impact fish health and water quality such that efficient and reliable monitoring methods are needed to inform the management of aquaculture production. Conventional total bacteria plate counts are commonly used to monitor bacteria load and serve as an indicator for managing water exchange, but this is a tedious technique for large sample sizes. Flow cytometry (FCM) and eDNA monitoring are fast gaining traction for fast and reliable high throughput analysis of large sample sizes. Environmental DNA sampling methodology represents the new frontier of research, where water, soil, and biofilms are collected for DNA analysis of potential environmental pathogens. Total bacteria counts are an indicator of water quality and microbial loads are highly correlated with suspended solids from land runoffs that can harbor aquatic pathogens (sea snow). This study will compare whether eDNA molecular analysis with FCM for total viable bacteria counts is a rapid, reliable, and efficient tool to improve disease monitoring to predict the presence of pathogens that may cause an outbreak. METHODOLOGY: Representative water samples will be collected once weekly from selected farm sites ( Singapore Aquaculture Technologies SAT) for analysis using FCM and eDNA, for 6 months. Fish samples will be examined using histopathology to provide an overview of general fish health and the presence of any significant disease. Depending on an initial site visit assessment and interview with farms, a panel of up to 5 significant pathogens of interest to fish farms may be included in the eDNA monitoring panel. The final sampling design will be developed based on issues that partner farms wish to investigate. Up to 6 water and 6 fish samples will be collected each week for analysis, giving an overall total of 144 water and 144 fish samples. A monthly report will be made available to partner farms to assist them in making management decisions. Trends in viable bacteria counts and pathogen loads will be correlated to farm production data and general fish health.
Date
04 Apr 2024 - 04 Apr 2025
Project Type
N/A
Keywords
eDNA research study
Funding Body
JCU Singapore, QIAGEN Singapore Pte. Ltd., KYTOS
Amount
0
Project Team
Susan Kueh;Jose Domingos