John F. Griffith
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View article: Evaluation of a modified IDEXX method for antimicrobial resistance monitoring of extended Beta-lactamases-producing Escherichia coli in impacted waters near the U.S.-Mexico border
Evaluation of a modified IDEXX method for antimicrobial resistance monitoring of extended Beta-lactamases-producing Escherichia coli in impacted waters near the U.S.-Mexico border Open
As part of a One Health approach, the World Health Organization (WHO) has deemed extended beta-lactamases-producing Escherichia coli (ESBL-Ec) as an appropriate proxy for antimicrobial resistance (AMR) in human, animal, and environmental s…
View article: Towards quantifying exfiltration from in situ sanitary sewer pipes
Towards quantifying exfiltration from in situ sanitary sewer pipes Open
Exfiltration from sanitary sewers has been researched for many years because of its potential impact on shallow groundwater or surface water, but measurements of exfiltration in situ are rare. Most previous measurements of sanitary sewer e…
View article: Extrapolating empirical measurements of wastewater exfiltration from sanitary sewers to estimate watershed-scale fecal pollution loading in urban stormwater runoff
Extrapolating empirical measurements of wastewater exfiltration from sanitary sewers to estimate watershed-scale fecal pollution loading in urban stormwater runoff Open
Inflow and infiltration are well-known issues for sanitary sewer collection systems, but exfiltration is understudied and rarely empirically quantified. The goal of this study is to estimate the potential human fecal contribution from wast…
View article: Correction: Health risks to children from exposure to fecally-contaminated recreational water
Correction: Health risks to children from exposure to fecally-contaminated recreational water Open
[This corrects the article DOI: 10.1371/journal.pone.0266749.].
View article: Using HF183 to Estimate Watershed-Wide Annual Loadings of Human Fecal Pollution from Onsite Wastewater Treatment Systems
Using HF183 to Estimate Watershed-Wide Annual Loadings of Human Fecal Pollution from Onsite Wastewater Treatment Systems Open
Onsite wastewater treatment systems (OWTSs or septic systems), when properly sited, designed, operated, and maintained, treat domestic wastewater to reduce impacts on and maintain sustainability of aquatic resources. However, when OWTSs ar…
View article: Universal microbial indicators provide surveillance of sewage contamination in harbours worldwide
Universal microbial indicators provide surveillance of sewage contamination in harbours worldwide Open
Human population pressures and activities pose unprecedented challenges to water resources in urban environments. However, standard methods of assessing microbial water quality have relied on the same cultured organisms for decades. We sho…
View article: Longitudinal Sequencing and Variant Detection of SARS-CoV-2 across Southern California Wastewater
Longitudinal Sequencing and Variant Detection of SARS-CoV-2 across Southern California Wastewater Open
Wastewater-based epidemiology (WBE) is useful for detecting pathogen prevalence and may serve to effectively monitor diseases across broad scales. WBE has been used throughout the COVID-19 pandemic to track disease burden through quantifyi…
View article: Assessing the defecation practices of unsheltered individuals and their contributions to microbial water quality in an arid, urban watershed
Assessing the defecation practices of unsheltered individuals and their contributions to microbial water quality in an arid, urban watershed Open
Outdoor defecation by people experiencing homelessness is frequently perceived as a potentially large source of human fecal pollution and a significant source of health risk in urban waterbodies with recreational contact. The goal of this …
View article: Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters
Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters Open
Bacteria in the marine environment cause thousands of human illnesses annually. Bivalves are a popular seafood source and are important in coastal ecology, but their ability to concentrate pathogens from the water can cause human illness, …
View article: Dry and Wet Weather Survey for Human Fecal Sources in the San Diego River Watershed
Dry and Wet Weather Survey for Human Fecal Sources in the San Diego River Watershed Open
State and federal agencies regulate fecal indicator bacteria (FIB), such as E. coli or Enterococcus, in order to manage public health risks at swimming beaches. Despite these goals, watershed managers are challenged in terms of how to best…
View article: Toward a national <scp>eDNA</scp> strategy for the United States
Toward a national <span>eDNA</span> strategy for the United States Open
Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use‐cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an op…
View article: Longitudinal sequencing and variant detection of SARS-CoV-2 across Southern California wastewater from April 2020 – August 2021
Longitudinal sequencing and variant detection of SARS-CoV-2 across Southern California wastewater from April 2020 – August 2021 Open
Wastewater based epidemiology (WBE) is a useful method to detect pathogen prevalence and may serve to effectively monitor diseases at a broad scale. WBE has been used throughout the COVID-19 pandemic to track localized and population-level…
View article: Host and Water Microbiota are Differentially Linked to Potential Human Pathogen Accumulation in Oysters
Host and Water Microbiota are Differentially Linked to Potential Human Pathogen Accumulation in Oysters Open
Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering …
View article: Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes
Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes Open
Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically-important…
View article: Health risks to children from exposure to fecally-contaminated recreational water
Health risks to children from exposure to fecally-contaminated recreational water Open
Background Children may be at higher risk for swimming-associated illness following exposure to fecally-contaminated recreational waters. We analyzed a pooled data set of over 80,000 beachgoers from 13 beach sites across the United States …
View article: Assessing cross-laboratory performance for quantifying coliphage using EPA Method 1642
Assessing cross-laboratory performance for quantifying coliphage using EPA Method 1642 Open
Aims Widespread adoption of the new U.S. Environmental Protection Agency (USEPA) Method 1642 for enumeration of coliphage in recreational water requires demonstration that laboratories consistently meet internal method performance goals an…
View article: SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works
SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works Open
We compared SARS-CoV-2 RNA concentrations in primary settled solids and raw wastewater samples matched in date to investigate the relationship between the two matrices.
View article: SARS-CoV-2 RNA is enriched by orders of magnitude in solid relative to liquid wastewater at publicly owned treatment works
SARS-CoV-2 RNA is enriched by orders of magnitude in solid relative to liquid wastewater at publicly owned treatment works Open
Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Methods have been developed using both the liquid and the solid fraction of wastewater, w…
View article: RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants
RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants Open
Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is …
View article: SARS-CoV-2 Wastewater Surveillance for Public Health Action
SARS-CoV-2 Wastewater Surveillance for Public Health Action Open
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has garnered extensive public attention during the coronavirus disease pandemic as a proposed complement to existing disease surveillance systems. Ove…
View article: A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border
A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border Open
Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multipl…
View article: RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants
RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants Open
Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early…
View article: Pathogenic <i>Vibrio</i> Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes
Pathogenic <i>Vibrio</i> Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes Open
Many species of coastal vibrio bacteria can infect humans, representing a growing health threat linked to increasing seawater temperatures. However, their interactions with surrounding microbes in the environment, especially eukaryotic org…
View article: Sources of variability in methods for processing, storing, and concentrating SARS-CoV-2 in influent from urban wastewater treatment plants
Sources of variability in methods for processing, storing, and concentrating SARS-CoV-2 in influent from urban wastewater treatment plants Open
The rapid emergence of wastewater based surveillance has led to a wide array of SARS-CoV-2 RNA quantification methodologies being employed. Here we compare methods to store samples, inactivate viruses, capture/concentrate viruses, and extr…
View article: Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater Surveillance
Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater Surveillance Open
Wastewater surveillance for pathogens using the reverse transcription-polymerase chain reaction (RT-PCR) is an effective, resource-efficient tool for gathering additional community-level public health information, including the incidence a…