Search USGS⌕ Search

Geology topics

Rachel M. Cook

Publications and source records attributed to Rachel M. Cook.

5 recordsLinked to original sources
USGS2025

Detection of viral, bacterial, and protozoan pathogens and microbial source tracking markers in paired large- and small-volume water samples

When sampling for waterborne microbes, researchers may need to diverge from recommended sample volumes due to logistical constraints, novel targets, or challenging matrices, with little guidance about the potential impact on results. In field studies, we measured bacteria, viruses, and protozoa (15 quantitative polymerase chain reaction assays) in paired large- and small-volume samples to evaluate method performance and relevant factors. Concordance between methods was low. Large-volume ultrafiltration yielded more detections than small-volume sampling, especially for pathogens in groundwater. Greater microbial concentrations were associated with more frequent detections in small-volume samples and greater concordance between paired samples. Large-volume samples appeared to be more susceptible to diminished sensitivity from complex sample matrices. In laboratory studies, recovery of microbes was poorer for large- than small-volume methods, although large-volume methods more reliably detected low-concentration targets. Large-volume samples were less stable than small-volume samples during storage. Overall, large-volume sampling was superior for detecting pathogens but may underestimate concentrations; small-volume sampling was more prone to false negatives but was adequate when concentrations were relatively high, like we observed for microbial source tracking in surface waters.

Wisconsin↗
USGS2025

Laboratory assessment for recovery of porcine circovirus 2 and porcine reproductive and respiratory syndrome virus using two types of commercially available hollow-fiber ultrafilters

Groundwater near swine farms is an uninvestigated reservoir for porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circoviruses (PCVs). Enteric microorganisms are often collected from groundwater via dead-end ultrafiltration, but recovery of PRRSV and PCV with this method has not been assessed. We recovered PRRSV2 and PCV2 by dead-end ultrafiltration followed by polyethylene glycol (PEG) precipitation, nucleic acid extraction, and reverse-transcription quantitative real-time PCR. We also compared 2 commercial hemodialysis ultrafilters (Asahi Kasei Rexeed-25A, Nipro Elisio-25H) and compared PRRSV2 recovery in these filters to other waterborne microorganisms. On average, 8 ± 1% of PRRSV2 was recovered by dead-end ultrafiltration and PEG precipitation, compared to 25 ± 6% for adenovirus 41. Full-process recovery of bacteria in the same filters was 5–15%; Cryptosporidium parvum recovery was 42 ± 12%. PCV2 was detected in 4 of 12 replicate filters, but low stock concentrations precluded quantitative recovery estimates. Elisio-25H ultrafilters performed similarly to Rexeed-25A filters for all organisms tested and is an effective replacement for the Rexeed-25A, which is no longer available in the United States. Our recovery of PRRSV2 and PCV2 by dead-end ultrafiltration in the laboratory suggests that PRRSV2 detection limits are as low as 3–50 genomic copies/L in sample volumes of 100–1,500 L. Based on quantitative microbial risk assessment, these concentrations are relevant to PRRSV2 infection rates in the U.S. swine herd.

Journal of Veterinary Diagnostic Investigation↗
USGS2024

Quantitative microbial risk assessment with microbial source tracking for mixed fecal sources contaminating recreational river waters, Iowa, USA

Fecal contamination of surface water can cause acute gastrointestinal illness (AGI) among recreators. AGI risk varies among human, livestock, and wildlife fecal sources, but the prevalence of individual sources is unknown for most recreational sites. We estimated AGI risk for six sites near Des Moines, Iowa, using quantitative microbial risk assessment combined with microbial source-tracking (MST). Water samples ( n = 147) collected over two years were tested for 36 qPCR assays quantifying waterborne pathogens and MST markers specific to avian, bovine, human, and porcine fecal sources. Average swimming risk across all sites was 5 (95% CI: 0.0030–142) to 67 (16–215) AGI cases per 1,000 recreators. Individual fecal sources were rarely associated with swimming exposures where risk was >36 AGI cases per 1,000 recreators; most high-risk exposures were associated with simultaneous occurrence of multiple fecal sources. Iowa’s beach action value for Escherichia coli (235 MPN/100 mL) identified >90% of high-risk exposures at five of six sites, so was generally protective of public health in this setting. For sites influenced by mixed fecal sources, results illustrate that identifying a single dominant source of risk is less important than recognizing the number of unique fecal sources that impact AGI risk.

Iowa↗
USGS2023

Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources

Antimicrobial resistance is a growing public health problem that requires an integrated approach among human, agricultural, and environmental sectors. However, few studies address all three components simultaneously. We investigated the occurrence of five antibiotic resistance genes (ARGs) and the class 1 integron gene ( intI1 ) in private wells drawing water from a vulnerable aquifer influenced by residential septic systems and land-applied dairy manure. Samples ( n = 138) were collected across four seasons from a randomized sample of private wells in Kewaunee County, Wisconsin. Measurements of ARGs and intI1 were related to microbial source tracking (MST) markers specific to human and bovine feces; they were also related to 54 risk factors for contamination representing land use, rainfall, hydrogeology, and well construction. ARGs and intI1 occurred in 5–40% of samples depending on target. Detection frequencies for ARGs and intI1 were lowest in the absence of human and bovine MST markers (1-30%), highest when co-occurring with human and bovine markers together (11-78%), and intermediate when co-occurring with just one type of MST marker (4-46%). Gene targets were associated with septic system density more often than agricultural land, potentially because of the variable presence of manure on the landscape. Determining ARG prevalence in a rural setting with mixed land use allowed an assessment of the relative contribution of human and bovine fecal sources. Because fecal sources co-occurred with ARGs at similar rates, interventions intended to reduce ARG occurrence may be most effective if both sources are considered.

Wisconsin↗