A partnership between PHF Science's Māori Impact and Genomics and Bioinformatics teams has developed a rapid, low-cost Vibrio test - a colour-changing assay that can detect dangerous Vibrio bacteria in seawater and kaimoana, returning a result in under an hour with no lab required.
For hapū and iwi managing customary fisheries, one question comes up again and again: is our kai safe to eat right now?
It's a question Georgia Bell, Technical Lead in PHF Science's Māori Impact team, has spent years working to help answer. Her connection to this is personal. "As a kid I was in the estuary every day, observing creatures in the taiao and taking kai home to my nan and my aunties and uncles," she says. "Mahinga kai is our food cupboard - a key source of sustenance for iwi and hapū."
PHF Science's mahinga kai food safety work grew out of a request from Ngāi Tahu customary fisheries managers - the people who authorise harvesting in areas governed by tikanga, and who need good information to keep their people safe. Mahinga kai, the customary gathering of traditional foods, was a cornerstone of the Ngāi Tahu Treaty settlement, recognised as central to cultural identity, wellbeing and rangatiratanga.
That need is growing more urgent. Māori are at higher risk of foodborne illness from kaimoana, and official disease notification data likely understates the true impact: barriers to healthcare access mean many cases of gastroenteritis are never captured, and Vibrio infections are only notifiable during a recognised outbreak. Meanwhile, harbours and estuaries collect contamination from stormwater, wastewater and agricultural runoff, and filter-feeding kaimoana such as mussels, cockles and pāua concentrate that contamination well above the levels found in the surrounding water.
Vibrio species are a growing concern worldwide. The World Health Organisation and the Food and Agriculture Organisation list Vibrio cholerae, V. parahaemolyticus and V. vulnificus as key human pathogens, and warn that climate change is helping more dangerous strains spread further. New Zealand recorded no Vibrio-related seafood outbreaks before 2019. Since then, there have been several: around 30 cases linked to Coromandel mussels in 2019, a further outbreak in mussels in 2020 involving a different strain, and an even larger outbreak in Canterbury over the summer of 2022-2023, with roughly 50 reported cases across a range of kaimoana. Warmer water and heavier rainfall, both linked to climate change, create ideal conditions for Vibrio to thrive.
Getting sick from V. parahaemolyticus, the species most often behind these outbreaks, usually means sudden watery diarrhoea, stomach cramps, nausea and vomiting, often with a fever - typically starting within a day of eating contaminated kaimoana and lasting up to a week. Most people recover without treatment, but it can hit harder and last longer for people with liver disease or a weakened immune system, and in rare cases leads to a serious bloodstream infection.
Testing for it the traditional way is slow. Culturing samples, followed by qPCR (quantitative polymerase chain reaction) and genetic sequencing, can take days, need a fully equipped lab, and only ever give a retrospective snapshot rather than the real-time answer a harvesting decision actually needs.
That gap is what brought Bell together with Vinko Besic, Senior Scientist in PHF Science's Genomics and Bioinformatics team, who leads development of the assay. Besic's background is in rapid diagnostic techniques, and the pair set out to build a test that worked directly from seawater, in the field, without a lab.
It took several attempts to get right. The team's first method, a quantitative technique called padlock RCA, could distinguish incredibly fine differences in DNA quantity, but converting it into a simple colour-change test wasn't sensitive enough to pick up the low numbers of bacteria found in seawater that are still potentially able to cause infection. They switched to a different chemistry called LAMP (loop-mediated isothermal amplification), which hit the sensitivity they needed within an hour, while still running at a single, low temperature - simple enough for a small, battery-powered heat block in the field. To make results visible without any equipment needed to read the resulting outputs at all, the team paired the reaction with a pH-sensitive dye: as the target DNA amplifies, the chemistry shifts the solution's pH just enough to flip the dye's colour, a change visible to the naked eye. “It’s similar to performing a pH test for measuring chlorine in a pool” Georgia says.
The team validated the assay against a commercial laboratory test, and Besic ran a blinded trial using live samples supplied by Ernest Williams, Senior Scientist in PHF Science's Enteric Reference Laboratory. "He wouldn't tell me what the bacteria were," Besic says. "It was going to have to be a blinded study - that was exciting at the time." It correctly identified every sample.
Field testing followed at Akaroa Harbour, where the team runs an ongoing Vibrio surveillance programme alongside the Department of Conservation and Environment Canterbury Regional Council, who help collect water samples monthly. The test picked up background levels of Vibrio parahaemolyticus at one of three sites tested, at concentrations low enough to be easily missed by standard culturing methods. A more detailed follow-up analysis of the original culture plates confirmed the result was real - a useful demonstration that the new test can detect background contamination that traditional methods can sometimes miss.
Since then, the team has expanded the assay to cover more targets, including a species marker for V. cholerae and two genes linked to more severe V. parahaemolyticus infections, each paired with its own coloured dye so several tests could eventually run side by side as one panel - with some of the newer dyes detecting concentrations up to ten times lower than the original. The finished assay takes 10 to 15 minutes of hands-on time and delivers a result within an hour.
The project has also drawn on genomics and sequencing expertise from PHF Science colleagues Jackie Wright, Jing Wang and David Winter. The team recently presented this work at Queenstown Research Week, New Zealand's largest annual science conference, and directly to customary fisheries partners at Akaroa Harbour.
The next steps are about making the test even easier to use; freeze-drying the reagents to remove the need for pipetting and refrigeration, pairing the test with a phone application so communities can read and share results in real time, and working out the safety thresholds that turn a colour change into clear food safety advice. The team also wants to test a much wider set of samples from around Aotearoa, to make sure the test performs just as well wherever it's used, and to keep building its Vibrio isolate library from ongoing sampling in Akaroa Harbour. Now that there's a working prototype, they also want to spend more time with customary fisheries communities themselves, to hear what ideas they have for making it more user-friendly.
For more information, please contact Georgia Bell at Georgia.Bell@phfscience.nz or Vinko Besic at Vinko.Besic@phfscience.nz.