USGS Science⌕ Search

SEARCH · USGS Science

Results for “Pathogens”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55Linked to original sources
USGS2024

Naegleria fowleri detected in Grand Teton National Park hot springs

The free-living thermophilic amoeba Naegleria fowleri ( N. fowleri ) causes the highly fatal disease primary amoebic meningoencephalitis. The environmental conditions that are favorable to the growth and proliferation of N. fowleri are not well-defined, especially in northern regions of the United States. In this study, we used culture-based methods and multiple molecular approaches to detect and analyze N. fowleri and other Naegleria spp. in water, sediment, and biofilm samples from five hot spring sites in Grand Teton National Park, Wyoming, U.S.A. These results provide the first detections of N. fowleri in Grand Teton National Park and provide new insights into the distribution of pathogenic N. fowleri and other nonpathogenic Naegleria spp. in natural thermal water systems in northern latitudes.

Wyoming↗
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↗
USGS2003

Escherichia coli and enterococci at beaches in the Grand Traverse Bay, Lake Michigan: Sources, characteristics, and environmental pathways

This study quantified Escherichia coli(EC) and enterococci (ENT) in beach waters and dominant source materials, correlated these with ambient conditions, and determined selected EC genotypes and ENT phenotypes. Bathing-water ENT criteria were exceeded more frequently than EC criteria, providing conflicting interpretations of water quality. Dominant sources of EC and ENT were bird feces (108/d/bird), storm drains (107/d), and river water (1011/d); beach sands, shallow groundwater and detritus were additional sources. Beach-water EC genotypes and ENT phenotypes formed clusters with those from all source types, reflecting diffuse inputs. Some ENT isolates had phenotypes similar to those of human pathogens and/or exhibited high-level resistance to human-use antibiotics. EC and ENT concentrations were influenced by collection time and wind direction. There was a 48-72-h lag between rainfall and elevated EC concentrations at three southern shoreline beaches, but no such lag at western and eastern shoreline beaches, reflecting the influence of beach orientation with respect to cyclic (3-5 d) summer weather patterns. In addition to local contamination sources and processes, conceptual or predictive models of Great Lakes beach water quality should consider regional weather patterns, lake hydrodynamics, and the influence of monitoring method variables (time of day, frequency).

Grand Traverse Bay↗
USGS2007

Incidence of the enterococcal surface protein ( esp ) gene in human and animal fecal sources

The occurrence of the enterococcal surface protein ( esp ) gene in the opportunistic pathogens Enterococcus faecalis and E. faecium is well-documented in clinical research. Recently, the esp gene has been proposed as a marker of human pollution in environmental waters; however, information on its relative incidence in various human and animal fecal sources is limited. We have determined the occurrence of the esp gene in enterococci from human ( n = 64) and animal ( n = 233) fecal samples by polymerase chain reaction using two primer sets: one presumably specific for E. faecium ( esp fm ) and the other for both E. faecalis and E. faecium ( esp fs/fm ). We believe that this research is the first to explore the use of esp fs/fm for the detection of human waste in natural environmental settings. The incidence in human sources was 93.1% esp fm and 100% esp fs/fm in raw sewage influent; 30% for both esp fm and esp fs/fm in septic waste; and 0% esp fm and 80% esp fs/fm in active pit toilets. The overall occurrence of the gene in animal feces was 7.7% ( esp fs/fm ) and 4.7% ( esp fm ); animal types with positive results included dogs (9/43, all esp fm ), gulls (10/34, esp fs/fm ; 2/34, esp fm ), mice (3/22, all esp fs/fm ), and songbirds (5/55, all esp fs/fm ). The esp gene was not detected in cat (0/34), deer (0/4), goose (0/18), or raccoon (0/23) feces. The inconsistent occurrence, especially in septic and pit toilet sewage, suggests a low statistical power of discrimination between animal and human sources, which means a large number of replicates should be collected. Both esp fm and esp fs/fm were common in raw sewage, but neither one efficiently differentiated between animal and other human sources.

Environmental Science & Technology↗
USGS2007

Human enteric viruses in groundwater from a confined bedrock aquifer

Confined aquifers are overlain by low-permeability aquitards that are commonly assumed to protect underlying aquifers from microbial contaminants. However, empirical data on microbial contamination beneath aquitards is limited. This study determined the occurrence of human pathogenic viruses in well water from a deep sandstone aquifer confined by a regionally extensive shale aquitard. Three public water-supply wells were each sampled 10 times over 15 months. Samples were analyzed by reverse transcription−polymerase chain reaction (RT-PCR) for several virus groups and by cell culture for infectious enteroviruses. Seven of 30 samples were positive by RT-PCR for enteroviruses; one of these was positive for infectious echovirus 18. The virus-positive samples were collected from two wells cased through the aquitard, indicating the viruses were present in the confined aquifer. Samples from the same wells showed atmospheric tritium, indicating water recharged within the past few decades. Hydrogeologic conditions support rapid porous media transport of viruses through the upper sandstone aquifer to the top of the aquitard 61 m below ground surface. Natural fractures in the shale aquitard are one possible virus transport pathway through the aquitard; however, windows, cross-connecting well bores, or imperfect grout seals along well casings also may be involved. Deep confined aquifers can be more vulnerable to contamination by human viruses than commonly believed.

Wisconsin↗
USGS2011

Effects of sediment-associated extractable metals, degree of sediment grain sorting, and dissolved organic carbon upon Cryptosporidium parvum removal and transport within riverbank filtration sediments, Sonoma County, California

Oocysts of the protozoan pathogen Cryptosporidium parvum are of particular concern for riverbank filtration (RBF) operations because of their persistence, ubiquity, and resistance to chlorine disinfection. At the Russian River RBF site (Sonoma County, CA), transport of C. parvum oocysts and oocyst-sized (3 μm) carboxylate-modified microspheres through poorly sorted (sorting indices, σ 1 , up to 3.0) and geochemically heterogeneous sediments collected between 2 and 25 m below land surface (bls) were assessed. Removal was highly sensitive to variations in both the quantity of extractable metals (mainly Fe and Al) and degree of grain sorting. In flow-through columns, there was a log–linear relationship ( r 2 = 0.82 at p < 0.002) between collision efficiency (α, the probability that colloidal collisions with grain surfaces would result in attachment) and extractable metals, and a linear relationship ( r 2 = 0.99 at p < 0.002) between α and σ 1 . Collectively, variability in extractable metals and grain sorting accounted for ∼83% of the variability in α (at p < 0.0002) along the depth profiles. Amendments of 2.2 mg L –1 of Russian River dissolved organic carbon (DOC) reduced α for oocysts by 4–5 fold. The highly reactive hydrophobic organic acid (HPOA) fraction was particularly effective in re-entraining sediment-attached microspheres. However, the transport-enhancing effects of the riverine DOC did not appear to penetrate very deeply into the underlying sediments, judging from high α values (∼1.0) observed for oocysts being advected through unamended sediments collected at ∼2 m bls. This study suggests that in evaluating the efficacy of RBF operations to remove oocysts, it may be necessary to consider not only the geochemical nature and size distribution of the sediment grains, but also the degrees of sediment sorting and the concentration, reactivity, and penetration of the source water DOC.

California↗
USGS2013

Choices in recreational water quality monitoring: new opportunities and health risk trade-offs

With the recent release of new recreational water quality monitoring criteria, there are more options for regulatory agencies seeking to protect beachgoers from waterborne pathogens. Included are methods that can reduce analytical time, providing timelier estimates of water quality, but the application of these methods has not been examined at most beaches for expectation of health risk and management decisions. In this analysis, we explore health and monitoring outcomes expected at Lake Michigan beaches using protocols for indicator bacteria including culturable Escherichia coli (E. coli; EC), culturable enterococci (ENT), and enterococci as analyzed by qPCR (QENT). Correlations between method results were generally high, except at beaches with historically high concentrations of EC. The “beach action value” was exceeded most often when using EC or ENT as the target indicator; QENT exceeded the limit far less frequently. Measured water quality between years was varied. Although methods with equivalent health expectation have been established, the lack of relationship among method outcomes and annual changes in mean indicator bacteria concentrations complicates the decision-making process. The monitoring approach selected by beach managers may be a combination of available tools that maximizes timely health protection, cost efficiency, and collaboration among beach jurisdictions.

Environmental Science & Technology↗
USGS2008

Investigation of bioaerosols released from swine farms using conventional and alternative waste treatment and management technologies

Microbial air pollution from concentrated animal feeding operations (CAFOs) has raised concerns about potential public health and environmental impacts. We investigated the levels of bioaerosols released from two swine farms using conventional lagoon-sprayfield technology and ten farms using alternative waste treatment and management technologies in the United States. In total, 424 microbial air samples taken at the 12 CAFOs were analyzed for several indicator and pathogenic microorganisms, including culturable bacteria and fungi, fecal coliform, Escherichia coli, Clostridium perfringens, bacteriophage, and Salmonella. At all of the investigated farms, bacterial concentrations at the downwind boundary were higher than those at the upwind boundary, suggesting that the farms are sources of microbial air contamination. In addition, fecal indicator microorganisms were found more frequently near barns and treatment technology sites than upwind or downwind of the farms. Approximately 4.5% (19/424), 1.2% (5/424), 22.2% (94/424), and 12.3% (53/424) of samples were positive for fecal coliform, E. coli, Clostridium, and total coliphage, respectively. Based on statistical comparison of airborne fecal indicator concentrations at alternative treatment technology farms compared to control farms with conventional technology, three alternative waste treatment technologies appear to perform better at reducing the airborne release of fecal indicator microorganisms during on-farm treatment and management processes. These results demonstrate that airborne microbial contaminants are released from swine farms and pose possible exposure risks to farm workers and nearby neighbors. However, the release of airborne microorganisms appears to decrease significantly through the use of certain alternative waste management and treatment technologies. ?? 2008 American Chemical Society.

Environmental Science & Technology↗
USGS2004

Characterization of aerosolized bacteria and fungi from desert dust events in Mali, West Africa

Millions of metric tons of African desert dust blow across the Atlantic Ocean each year, blanketing the Caribbean and southeastern United States. Previous work in the Caribbean has shown that atmospheric samples collected during dust events contain living microbes, including plant and opportunistic human pathogens. To better understand the potential downwind public health and ecosystem effects of the dust microbes, it is important to characterize the source population. We describe 19 genera of bacteria and 3 genera of fungi isolated from air samples collected in Mali, a known source region for dust storms, and over which large dust storms travel.

Aerobiologia↗
USGS2011

Dust: Small-scale processes with global consequences

Desert dust, both modern and ancient, is a critical component of the Earth system. Atmospheric dust has important effects on climate by changing the atmospheric radiation budget, while deposited dust influences biogeochemical cycles in the oceans and on land. Dust deposited on snow and ice decreases its albedo, allowing more light to be trapped at the surface, thus increasing the rate of melt and influencing energy budgets and river discharge. In the human realm, dust contributes to the transport of allergens and pathogens and when inhaled can cause or aggravate respiratory diseases. Dust storms also represent a significant hazard to road and air travel. Because it affects so many Earth processes, dust is studied from a variety of perspectives and at multiple scales, with various disciplines examining emissions for different purposes using disparate strategies. Thus, the range of objectives in studying dust, as well as experimental approaches and results, has not yet been systematically integrated. Key research questions surrounding the production and sources of dust could benefit from improved collaboration among different research communities. These questions involve the origins of dust, factors that influence dust production and emission, and methods through which dust can be monitored.

Eos, Transactions, American Geophysical Union↗
USGS2019

Improving predictions of fine particle immobilization in streams

Fine particles are critical to stream ecosystem functioning, influencing in-stream processes from pathogen transmission to carbon cycling, all of which depend on particle immobilization. However, our ability to predict particle immobilization is limited by: (1) availability of combined solute and particle tracer data and (2) identifying parameters that appropriately represent fine particle immobilization, due to the myriad of objective functions and model formulations. We found that improved predictions of the full distribution of possible fine particle residence times requires using an objective function that assesses both the peak and tailing together with solute tracers to constrain in-stream transport processes. The representation of immobilization processes was significantly improved when solute tracer data were combined with a particle model, starkly contrasting the common assumption that fine particles transport as washload. We develop a clear strategy for improving fine particle transport predictions, reshaping the potential role of fine particles in water quality management.

Geophysical Research Letters↗
USGS2021

Estimating and forecasting time-varying groundwater recharge in fractured rock: A state-space formulation with preferential and diffuse flow to the water table

Rapid infiltration following precipitation may result in groundwater contamination from surface contaminants or pathogens. In fractured rock, contaminants can migrate rapidly to points of groundwater withdrawals. In contrast to the temporal availability of groundwater quality chemical indicators, meteorological and groundwater level observations are available in real-time to estimate time-varying recharge, which can act as a surrogate to identify periods of rapid infiltration that may indicate contamination susceptibility. Estimating recharge using methods, such as base-flow recession, unsaturated infiltration models, or Water-Table Fluctuations (WTF), cannot capitalize on currently available technologies and telecommunication infrastructure to conduct real-time recharge estimation at scales relevant to characterizing rapid infiltration. We present a linear, physics-based State-Space (SS) model of one-dimensional infiltration to estimate recharge, which includes preferential and diffuse-flow to the water table. The model can take advantage of real-time data for water-table altitude, precipitation, and evapotranspiration. Model parameters are calibrated over an observation period, and the Kalman Filter (KF) is subsequently applied to continuously update the observed (water-table altitude) and unobserved (groundwater recharge) system states and predict future states as new data become available. The SS/KF algorithm is demonstrated at the Masser Groundwater Recharge Site in Pennsylvania, USA and comparisons are made with recharge estimates from WTF methods. Model results indicate that the frequency of observations (daily versus sub-daily) dictates the allocation between preferential and diffuse flow. Additionally, because infiltration processes encompass many nonlinearities, model parameters estimated from observation periods need to be updated at least seasonally to account for changing recharge conditions.

Water Resources Research↗
USGS2023

Hawaiian volcanic ash, an airborne fomite for nontuberculous mycobacteria

Nontuberculous mycobacteria (NTM) are environmentally acquired opportunistic pathogens that can cause chronic lung disease. Within the U.S., Hawai'i shows the highest prevalence rates of NTM lung infections. Here, we investigated a potential role for active volcanism at the Kīlauea Volcano located on Hawai'i Island in promoting NTM growth and diversity. We recovered NTM that are known to cause lung disease from plumbing biofilms and soils collected from the Kīlauea environment. We also discovered viable Mycobacterium avium, Mycobacterium abscessus , and Mycobacterium intracellulare subsp. chimaera on volcanic ash collected during the 2018 Kīlauea eruption. Analysis of soil samples showed that NTM prevalence is positively associated with bulk content of phosphorus, sulfur, and total organic carbon. In growth assays, we showed that phosphorus utilization is essential for proliferation of Kīlauea-derived NTM, and demonstrate that NTM cultured with volcanic ash adhere to ash surfaces and remain viable. Ambient dust collected on O'ahu concurrent with the 2018 eruption contained abundant fresh volcanic glass, suggestive of inter-island ash transport. Phylogenomic analyses using whole genome sequencing revealed that Kīlauea-derived NTM are genetically similar to respiratory isolates identified on other Hawaiian Islands. Consequently, we posit that volcanic eruptions could redistribute environmental microorganisms over large scales. While additional studies are needed to confirm a direct role of ash in NTM dispersal, our results suggest that volcanic particulates harbor and can redistribute NTM and should therefore be studied as a fomite for these burgeoning, environmentally acquired respiratory infections.

Hawaii↗
USGS2016

Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (B3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.

Nature Communications↗
USGS2014

Respiratory transmission of an avian H3N8 influenza virus isolated from a harbour seal

The ongoing human H7N9 influenza infections highlight the threat of emerging avian influenza viruses. In 2011, an avian H3N8 influenza virus isolated from moribund New England harbour seals was shown to have naturally acquired mutations known to increase the transmissibility of highly pathogenic H5N1 influenza viruses. To elucidate the potential human health threat, here we evaluate a panel of avian H3N8 viruses and find that the harbour seal virus displays increased affinity for mammalian receptors, transmits via respiratory droplets in ferrets and replicates in human lung cells. Analysis of a panel of human sera for H3N8 neutralizing antibodies suggests that there is no population-wide immunity to these viruses. The prevalence of H3N8 viruses in birds and multiple mammalian species including recent isolations from pigs and evidence that it was a past human pandemic virus make the need for surveillance and risk analysis of these viruses of public health importance.

Nature Communications↗
USGS2019

Fluorescent biomarkers demonstrate prospects for spreadable vaccines to control disease transmission in wild bats

Vaccines that autonomously transfer among individuals have been proposed as a strategy to control infectious diseases within inaccessible wildlife populations. However, rates of vaccine spread and epidemiological efficacy in real-world systems remain elusive. Here, we investigate whether topical vaccines that transfer among individuals through social contacts can control vampire bat rabies—a medically and economically important zoonosis in Latin America. Field experiments in three Peruvian bat colonies, which used fluorescent biomarkers as a proxy for the bat-to-bat transfer and ingestion of an oral vaccine, revealed that vaccine transfer would increase population-level immunity up to 2.6 times beyond the same effort using conventional, non-spreadable vaccines. Mathematical models showed that observed levels of vaccine transfer would reduce the probability, size and duration of rabies outbreaks, even at low but realistically achievable levels of vaccine application. Models further predicted that existing vaccines provide substantial advantages over culling bats—the policy currently implemented in North, Central and South America. Linking field studies with biomarkers to mathematical models can inform how spreadable vaccines may combat pathogens of health and conservation concern before costly investments in vaccine design and testing.

Nature Ecology and Evotution↗
USGS2019

Towards common ground in the biodiversity–disease debate

The disease ecology community has struggled to come to consensus on whether biodiversity reduces or increases infectious disease risk, a question that directly affects policy decisions for biodiversity conservation and public health. Here, we summarize the primary points of contention regarding biodiversity–disease relationships and suggest that vector-borne, generalist wildlife and zoonotic pathogens are the types of parasites most likely to be affected by changes to biodiversity. One synthesis on this topic revealed a positive correlation between biodiversity and human disease burden across countries, but as biodiversity changed over time within these countries, this correlation became weaker and more variable. Another synthesis—a meta-analysis of generally smaller-scale experimental and field studies—revealed a negative correlation between biodiversity and infectious diseases (a dilution effect) in various host taxa. These results raise the question of whether biodiversity–disease relationships are more negative at smaller spatial scales. If so, biodiversity conservation at the appropriate scales might prevent wildlife and zoonotic diseases from increasing in prevalence or becoming problematic (general proactive approaches). Further, protecting natural areas from human incursion should reduce zoonotic disease spillover. By contrast, for some infectious diseases, managing particular species or habitats and targeted biomedical approaches (targeted reactive approaches) might outperform biodiversity conservation as a tool for disease control. Importantly, biodiversity conservation and management need to be considered alongside other disease management options. These suggested guiding principles should provide common ground that can enhance scientific and policy clarity for those interested in simultaneously improving wildlife and human health.

Nature Ecology & Evolution↗
USGS2020

Multiple elements of soil biodiversity drive ecosystem functions across biomes

The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Here, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes.

Nature Ecology and Evolution↗