A rapid DNA-based test for Enterococcus enables onsite detection of fecal indicators in coastal waters of Hawai‘i

UPDATE 1/20/22

Phase II completed in Fall 2021. Initial characterization of our LAMP protocol was successful. Both phosphate buffer and coastal water sample spikes yielded great LAMP reactions with little inhibition using two different types of filters. Thanks our lab manager Lena Diaz and Surfrider Volunteers (Simone Ray and Sherine Blooma) for your help! Our first paper detailing methods and results is in progress with publication expected Fall 2022. I am currently looking for a Graduate Assistant to take over for Lena (she is graduating with her PHD Spring 2022). The position has 2 years of support for tuition, salary, and research expenses. Email me with a CV if interested at dwamato@hawaii.edu

Project Goal: The objective of this project is to refine a novel protocol that allows for the detection of FIB and an indication of associated risk of illness in near-real time using DNA amplification in the field. The recently developed BioRanger (http://diagenetix.com/), which is capable of detecting Enterococcus within minutes, is a handheld device controlled from a phone or tablet. Using a relatively new low-cost technology for DNA quantification, the BioRanger employs Loop mediated isothermal amplification (LAMP) to quantify genetic sequences.

Intro to problem:
For decades, federal, state, and local governments have been using the fecal indicator bacteria (FIB) Enterococcus to monitor the risk of illness to users of the Nation’s coastal recreation waters as stipulated in the USEPA BEACH Act (33 U.S.C. §§ 1251 et seq.). Despite this effort, an estimated 90 million people become sick after contact with waterborne illnesses in the US each year at a cost of $2.2- $3.7 billion annually (DeFlorio-Barker et al., 2018). The EPA recommended method for testing the concentration of Enterococcus in water samples involves an incubation period of 24 hours before the results are available. In practice, this typically means that there is a minimal lag time of around 2 days between the time the sample was taken and closing of a public beach due to high FIB levels. It is clear that alternative methods of FIB monitoring that drastically minimize this lag time are required to reduce the public’s risk of swimming related illness (Byappanahalli et al., 2012). The future of water quality science needs to include real-time assessments of risk that are easily available to the public.

Handheld BioRanger used to detect fecal indicator bacteria in the field