In-Situ Detection of Fecal Indicators Enables Advanced Ocean Safety Forecasting.

This NOAA funded project is a collaboration between the University of Hawaiʻi, the Surfrider Foundation, Amato Science, and multiple community volunteers on Oʻahu aims to develop multiple in-situ fecal indicator methods that enable real-time forecasting of fecal indicator bacteria in Waikiki waters. These methods will also be tested during extreme tidal and rain events with the help of trained “Extreme Teams” of citizen scientists in multiple communities on Oʻahu, Hawaii. I can’t say too much more about it until the funding announcement is released in early January of 2023.

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

UPDATE 1/5/23

I welcomed a new PhD student Nic Storie to the team to manage the day to day work in the lab.  We will begin testing onsite sample prep methods this spring on Oahu. Phase II was completed in Fall 2022. 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! 

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 (, 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