Aquaculture is the world’s fastest-growing food sector and is recognized for its potential to alleviate poverty and hunger in small-scale systems. However, progress is limited by diseases and a lack of knowledge and tools to identify fish pathogens, track their origin and manage their spread.
Whole-genome sequencing informs how pathogens change and move through environments, permitting the implementation of evidence-based biosecurity to minimize disease impact. Offsite sequencing services are expensive and cause prohibitive delays.
A team of researchers led by WorldFish in collaboration with the University of Queensland and Wilderlab have developed a compact “lab-in-a-backpack” for pond-side identification and quantitation of pathogens affecting tilapia. Equipped with a portable DNA-extraction system, a hand-held DNA sequencer (MinION), a battery-operated minicomputer (MinIT), and an intuitive purpose-built software package, users without experience in molecular biology or bioinformatics can identify fish pathogens from both water samples and infected tissues remotely and in real-time, with limited electricity and internet connectivity.
These low-cost tools will enable tilapia breeding, quarantine, and biosecurity centers, as well as academics and vets, to identify causal agents of disease outbreaks in a fraction of the time and cost required for external laboratory analysis. The project’s tests give results in hours rather than weeks or months and cost roughly 40 USD as opposed to more than 100 USD.
The project was undertaken in the framework of the CGIAR Research Program on Fish Agri-Food Systems (FISH) and received additional funding by the CGIAR Antimicrobial Resistance Hub on AMR-related activities and from the CGIAR Platform for Big Data in Agriculture as part of the 2019 Inspire Challenge prize.