Microbial Water Quality Research Plan

View SCCWRP’s full thematic Research Plan for Microbial Water Quality (PDF)

2021-2022 Executive Summary

Microbial water quality is a focused area of aquatic microbiology dedicated to minimizing the risk of human exposure to waterborne pathogens. Whether swimming and surfing at the beach, or consuming shellfish harvested from coastal waters, the public depends on rigorous, fully vetted science to rapidly detect aquatic microbial contamination and to inform remediation strategies. Advances in molecular microbiology are enabling the water-quality management community to develop incrementally stronger, more effective solutions for protecting public health. SCCWRP is working to improve methods for evaluating microbial water quality and assessing risks to public health from waterborne pathogen exposure. SCCWRP’s goal is not only to improve the speed at which microbial contamination can be detected, but also to develop molecular methods for tracing contamination back to its source and pinpoint its origin point. SCCWRP also is focused on helping water-quality managers better understand how field measures of microbial contamination correspond to specific levels of health risk.

SCCWRP’s microbial water quality research is focused around three major areas: (1) Rapid methods for microbial contamination detection, which involves validating the accuracy, sensitivity and applicability of DNA and RNA-based methods for measuring microbial contamination; (2) microbial source tracking, which involves using molecular methods to identify whether humans vs. various individual animal species are responsible for observed contamination – and to identify where in a watershed the contamination is coming from and potentially which specific type of stormwater or wastewater infrastructure is responsible; and (3) microbial risk assessment, which involves quantifying health risk for Southern California’s beachgoing population through epidemiological studies, as well as through health risk modeling approaches such as Quantitative Microbial Risk Assessment (QMRA) that estimate illness risk based on site-specific considerations.

This year, SCCWRP will continue to focus on human fecal source tracking, a revisit of risk-based water quality objectives for recreational shellfish waters, and quantitative surveillance in wastewater of the SARS-CoV-2 virus that causes COVID-19. SCCWRP’s focus for 2021-22 will be on:

  • Identifying human sources of fecal contamination during wet weather: SCCWRP is working to identify specific sources of human fecal contamination in Southern California waterways during wet weather by tracking and quantifying the relative contributions of public sewers, private laterals, septic systems, illicit connections and illegal discharges, and individuals experiencing homelessness.  This work, which includes quantifying both relative contributions and the factors that control these contributions, is a reflection of the fact that human fecal sources appear to be widespread in Southern California waterways during wet weather. During these short but dynamic storm events, source tracking is incredibly difficult when so many possible human sources are mixed together in stormwater runoff. These source-tracking investigations build on previous SCCWRP research that has found that the risk of gastrointestinal illness from body contact recreation during wet weather is greater than the risk illness during dry weather, and that genetic markers of human fecal contamination (i.e., HF183) and human pathogens are commonly found in wet-weather discharges. Related research this year will start to establish relationships between HF183 and human pathogens, utilizing QMRA to establish health risk thresholds for wet-weather discharges. With managers no longer asking “Are human fecal sources found in wet weather?” but rather “What are the human source(s) found in wet weather?” the goal of this research is to help managers most efficiently and effectively remediate human fecal sources to protect the public health of beachgoers following storm events.
  • Evaluating the SHEL water-quality standard: SCCWRP and its partners are continuing to investigate whether a water-quality standard designed to protect the health of people who consume shellfish from Newport Bay in Orange County has been appropriately set. The study’s goal is to examine whether California’s existing standard for permissible fecal coliform bacterial levels in the water correlates to potentially unsafe levels of pathogens in the tissue of bivalve shellfish harvested from Newport Bay. If the water-column bacterial measurements of indicators positively correlate with pathogen levels found in the shellfish, researchers would conclude that California’s existing standard for recreational shellfish harvesting is working as designed. However, if there is no relationship between water-quality indicators and pathogens found in the shellfish, the study could provide a scientific basis for developing a site-specific standard for Newport Bay, or trigger follow-up studies examining the appropriateness of using a fecal coliform-based standard to protect California shellfish.
  • Coronavirus surveillance of sewersheds: SCCWRP is part of a national research team that is investigating the use of wastewater treatment plant influent as a more comprehensive COVID-19 surveillance system, given that infected people are known to shed the SARS-CoV-2 virus in their fecal material. The study will involve quantifying presence of COVID genetic markers in wastewater treatment plant influent, along with quantifying shedding rates and decay during transport to the facility. The study is intended to help address the existing lack of clear information about magnitude and trends in infection rates, as existing insights about infection rates are based on measuring infection in a small percentage of the population – and therefore slanted toward measuring individuals already showing illness symptoms. When completed, the project will provide decision-makers with a rapid, cost-effective tool for estimating pervasiveness of infections and for assessing the effectiveness of government-mandated behavior restrictions and business closures. The tool also will provide early-warning signs of future waves of infection, including from COVID-19 variants. The study is ongoing at about 50 sites nationally, with SCCWRP leading the effort for seven of them in Southern California.