Paper-based platform for onsite, rapid and multiplexed pathogen detection in shrimp farms

The aquaculture industry in South Asia, and in particular shrimp farming in India, has been growing rapidly and now has significant potential to alleviate poverty within low-income regions and communities. In these settings, farms are often small (90% of the shrimp farmers in India use <2ha of land) and are run by poor families. However, they can generate benefits across a large portion of the local population, through improved employment, increased income (from jobs associated with the industry and its supply-chain, as well as through export for example). These benefits can flow to wider community, locally, alleviating poverty.

However, these benefits are generally not realised, as the production from these farms is not sustainable, mainly due to the high frequency and impact of outbreaks of infectious diseases, which destroy crops and yield slow growth, resulting in significant impact on the farms themselves but also on the wider communities and economy. At a national level, this translates into ca. 50,000 Metric Tonne (MT) losses (ca. £1B) and loss of employment of 2.15 million man days per annum.

In this project, we will translate a novel, low-cost, battery-powered handheld platform for the early, multiplexed detection of pathogens at the farm or hatchery, to empower local farmers and communities to control and reduce the occurrence and impact of disease outbreaks. We will work with our partners Ananda (a well-established, seafood company, based in the hub of Indian shrimp farming in Andhra Pradesh), ICAR-Central Institute of Fisheries Technology, (in Cochin), Mologic (a provider of rapid diagnostic tests), Epigem (a manufacturer of low-cost devices) and the Centre for Environment, Fisheries and Aquaculture Sciences Cefas (aworld leader in marine science and technology in the UK), to design, validate and deploy the tests in the field in India.

The current diagnostic tests, which are used in India and elsewhere in South Asia, are based on nucleic acid-based detection, which takes a few hours to perform, in a well-resourced laboratory, using sophisticated equipment. This has two major consequences: (i) the tests are not available to poor farmers (the majority), either at all, or at a frequency that would allow to monitor the production reliably and detect potential outbreaks timely; and (ii) when they are carried out (e.g. at Ananda), they require the samples to be transported to where expertise is available, which leads to significant delays in results (often many days). These delays can result in mis-timed inaction (and the potential to lose the crop), emergency harvesting (leading to decreased economic output), or, in some cases, the mis-use of antibiotic or chemical treatment, which has the potential to increase drug resistance and contaminate the environment.

In this project, we will deliver a step-change in the farmer's abilty to reduce the impact of production-based losses and the burden associated with ineffective treatments. The platform relies upon the enrichment of pathogens from shrimp tissue using a combination of paper-based filtration and magnetic beads, onto a paper-based biosensor. By folding the paper, in a process akin to origami, the genetic material of the pathogens is purified and distributed into specific areas, where nucleic acids are amplified. This amplification (performed using a small hand-held heater, with low power at around 60oC, but which could also be performed in a thermos flask) is then detected using either direct visualisation of a colour change, as in pregnancy tests, or using a mobile phone to quantify the response, within 45min.

By developing and deploying a low-cost, point-of-use detection device, we will empower small-scale farmers with the ability to identify pathogens early, thus allowing them to take remedial actions as well as liaise with the community to ensure outbreaks are contained.

The project aims to create impact within low-resource settings, by enabling the rapid, multiplexed detection and identification of pathogens within shrimp farms and hatcheries in India. In these coastal regions, whilst there are some large commercial organisations, the majority of farms are small-scale (90% <2ha), family-run operations, who are generally low-income. Their economic sustainability, mostly through export sales, is very important for the community, providing a virtuous cycle of development in local infrastructure, to enhance local livelihoods. This economic benefit is constantly under threat from infectious disease outbreaks, which destroy harvests and reduce growth rates, resulting in significant economic impact for poor families and their communities. It should also be noted that the shrimp farming industry is underpinned by the work of women throughout the value chain of processing, such that improvements in farming have the potential to directly impact upon their well-being and lead to increased gender equality.

The platform to be developed during this project aims to rapidly detect pathogens in fish farms and hatcheries, and promises to deliver significant impact in enabling direct testing at the site, thus mitigating the effects of disease outbreaks, including as an early warning system of contamination events, to alert other farmers. In India, small scale producers are often organised into mutually beneficial societies/associations (clusters of ca. 20 - 75 farms) based within specific geographical areas (around 19,000 in India), which will benefit from increased (and timely) awareness of pathogen levels in the area.

The project will be conducted in close collaboration with non-academic partners, including a large scale shrimp farming industry in India, as well as providers and manufacturers of rapid diagnostic tests in the UK. Their input in the project will ensure that the technologies developed will be efficiently translated into practical use during this project, with a clear route to commercialisation in India. In practice, this impact will be realised through the development of commercial devices and intellectual property, the delivery of which will have additional economic impacts.

Academics and commercial organisations will benefit in the short term. Academics involved in the immediate environment of the Investigators will benefit from the improved capabilities of this technology and its demonstration including: Professor R. Zadocks (Moredun Institute and Life Sciences Glasgow, University of Sydney); Professor Elise Cartmell (Scottish Water), and Professor Marian Scott (Maths and Stats - Glasgow). Other collaborators of the investigators, in Thailand and Vietnam for example, will also benefit from increased knowledge of the how to translate user-centred requirements into practical device designs.

This research is widely multi-disciplinary at the intersection of molecular biology, aquaculture, microfluidics, and biosensing. A broad range of other academics will benefit, including those involved in biological assays, sensor instrumentation, microfluidics and microsystems, and environmental monitoring, as the new capabilities of rapid pathogen detection is delivered. Commercial organisations, including fisheries (especially small-scale family-owned production) and testing laboratories will also benefit in the short term, through the availability of new tools for testing.