Rapid qPCR-Based Water Quality Monitoring in New York State Recreational Waters

Abstract

Public swimming beaches often rely on culture-based methods to determine if fecal indicator bacteria (FIB) levels are greater than health risk-based beach action values (BAV). The slow turnaround time of culture-based assays can prevent effective beach closure and reopening decisions. Faster testing methods that can be completed on-site are needed. Additionally, beach closures are currently based on high FIB levels, but at-present there are no tools to examine the health risks to bathers from myriad pathogens (e.g., bacteria, viruses, protozoa) that may be present in recreational waters. Twelve New York State beaches (n = 9 freshwater and n = 3 marine) were monitored over the course of summer 2018, and two of the freshwater beaches were monitored in fall 2017 as part of a preliminary study. A rapid, in-field workflow for detecting fecal enterococci in water samples was tested using four assays on two Biomeme handheld devices. All Biomeme-based workflows involved in-field DNA extractions and qPCR using portable devices. Beach water samples were also analyzed using EPA-approved or EPA-based qPCR methods: two culture-based methods, Enterolert (targeting enterococci at freshwater and marine beaches) and Colilert (targeting E. coli at freshwater beaches); and one qPCR method based on EPA 1611.1. For low abundance pathogen quantification, nanoscale-qPCR was conducted in 2018 using the Pathogen Panel which targeted 12 viral, bacterial, and protozoal pathogens. In fall 2017, the qPCR-based methods performed similarly to Enterolert (r2 from 0.537 to 0.687) and correctly classified 62.5–75.0% of water samples for a BAV of 104 MPN per 100 ml. In summer 2018, the correlation between Enterococcus levels based on Biomeme qPCR and Enterolert varied substantially between the 12 beaches. Inclusion of diverse regions and beach types may have confounded the Biomeme qPCR results. The EPA 1611.1-based method showed a weak, significant correlation (r2 = 0.317, p = 0.00012) with Enterolert. Nanoscale-qPCR showed low-levels of pathogens present at all beach sites; but only three showed up with any substantial frequency, E. coli eae (25% of samples), norovirus (31.4%), and Giardia lamblia (11.4%). Preliminary studies to establish beach-specific correlation curves between rapid qPCR and Enterolert methods are needed before any qPCR assay is used to inform beach decisions.

Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach

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Non-Linear Analyses of Fish Behaviours in Response to Aquatic Environmental Pollutants—A Review

“…New methods are being developed for the fast screening of known drugs, pesticides, toxins, and microorganisms [39][40][41]. Unfortunately, there are still additional stressors that remain unknown and/or whose real effect is not easily measurable particularly when the net effect is the results of several interacting chemicals in the environment [42].…”

Structural equation models suggest that on-farm non-crop vegetation removal is not associated with improved food safety outcomes but is linked to impaired water quality

“…Datasets. This study used historical data from 16 peer-reviewed papers and two citizen science databases where the original source was willing to share the complete dataset (12,(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46). Specifically, we compiled data from the Northeastern USA that reported (i) the presence or absence of foodborne pathogens in soil, water, vegetation, or wildlife feces, or (ii) dissolved oxygen, fecal indicator bacteria, chloride, conductivity, nutrient, salinity, or sediment levels in streams.…”