Search USGS⌕ Search

SEARCH · Search USGS

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 955 records · Page 53Linked to original sources
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↗
USGS2025

Sea star wasting disease mystery finally solved

A decade after a marine epidemic killed off sea stars and triggered ecosystem-wide effects along the Pacific Coast of North America, researchers have identified the bacterial pathogen that is responsible for sea star wasting disease.

Nature Ecology and Evolution↗
USGS2025

Vibrio pectenicida strain FHCF-3 is a causative agent of sea star wasting disease

More than 10 years following the onset of the sea star wasting disease (SSWD) epidemic, affecting over 20 asteroid species from Mexico to Alaska, the causative agent has been elusive. SSWD killed billions of the most susceptible species, sunflower sea stars ( Pycnopodia helianthoides ), initiating a trophic cascade involving unchecked urchin population growth and the widespread loss of kelp forests. Identifying the causative agent underpins the development of recovery strategies. Here we induced disease and subsequent mortality in exposure experiments using tissue extracts, coelomic fluid and effluent water from wasting sunflower sea stars, with no mortality in controls. Deep sequencing of diseased sea star coelomic fluid samples from experiments and field outbreaks revealed a dominant proportion of reads assigned to the bacterium Vibrio pectenicida . Fulfilling Koch’s postulates, V. pectenicida strain FHCF-3, cultured from the coelomic fluid of a diseased sunflower sea star, caused disease and mortality in exposed sunflower sea stars, demonstrating that it is a causative agent of SSWD. This discovery will enable recovery efforts for sea stars and the ecosystems affected by their decline by facilitating culture-based experimental research and broad-scale screening for pathogen presence and abundance in the laboratory and field.

Nature Ecology & Evolution↗
USGS2026

Rapid expansion of genotype D1.1 A(H5N1) influenza viruses in wild birds across North America during the 2024 migratory season

In late 2021, high pathogenicity avian influenza A(H5N1) clade 2.3.4.4b viruses entered North America and reassorted rapidly with local avian influenza viruses. In September 2024, we detected a new reassortant later classified as genotype D1.1. Using active and passive avian influenza surveillance across Canada and the USA, we tracked the emergence and rapid spread of D1.1 viruses in wild birds during the 2024 fall migration. Phylodynamic analysis showed that D1.1 viruses formed a monophyletic group and displaced earlier A(H5) genotypes across several flyways. Their expansion coincided with detections in other hosts, including 17 human cases, 4 of which were severe or fatal. None of the mammalian-adaptive markers detected in human cases were found in wild bird viruses, and candidate vaccine viruses retained antigenic cross-reactivity with D1.1 strains.

Nature medicine↗
USGS2018

Acquisition and dissemination of cephalosporin-resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

Antimicrobial resistance (AMR) in bacterial pathogens threatens global health, though the spread of AMR bacteria and AMR genes between humans, animals, and the environment is still largely unknown. Here, we investigated the role of wild birds in the epidemiology of AMR Escherichia coli. Using next-generation sequencing, we characterized cephalosporin-resistant E. coli cultured from sympatric gulls and bald eagles inhabiting a landfill habitat in Alaska to identify genetic determinants conferring AMR, explore potential transmission pathways of AMR bacteria and genes at this site, and investigate how their genetic diversity compares to isolates reported in other taxa. We found genetically diverse E. coli isolates with sequence types previously associated with human infections and resistance genes of clinical importance, including blaCTX-M and blaCMY. Identical resistance profiles were observed in genetically unrelated E. coli isolates from both gulls and bald eagles. Conversely, isolates with indistinguishable core-genomes were found to have different resistance profiles. Our findings support complex epidemiological interactions including bacterial strain sharing between gulls and bald eagles and horizontal gene transfer among E. coli harboured by birds. Results suggest that landfills may serve as a source for AMR acquisition and/or maintenance, including bacterial sequence types and AMR genes relevant to human health.

Alaska↗
USGS2019

A novel host-adapted strain of Salmonella Typhimurium causes disease in olive ridley turtles (Lepidochelys olivacea) in the Pacific.

Salmonella spp. are frequently shed by wildlife including turtles, but S. enterica subsp. enterica serovar Typhimurium or lesions associated with Salmonella are rare in turtles. Between 1996 and 2016, we necropsied 127 apparently healthy pelagic olive ridley turtles ( Lepidochelys olivacea ) that died from drowning bycatch in fisheries and 44 live or freshly dead stranded turtles from the west coast of North and Central America and Hawaii. Seven % (9/127) of pelagic and 47% (21/44) of stranded turtles had renal granulomas associated with S. Typhimurium. Stranded animals were 12 times more likely than pelagic animals to have Salmonella -induced nephritis suggesting that Salmonella may have been a contributing cause of stranding. S. Typhimurium was the only Salmonella serovar detected in L. olivacea , and phylogenetic analysis from whole genome sequencing showed that the isolates from L. olivacea formed a single clade distinct from other S. Typhimurium. Molecular clock analysis revealed that this novel clade may have originated as recently as a few decades ago. The phylogenetic lineage leading to this group is enriched for non-synonymous changes within the genomic area of Salmonella pathogenicity island 1 suggesting that these genes are important for host adaptation.

California, Hawaii, Oregon, Washington↗
USGS2020

Models with environmental drivers offer a plausible mechanism for the rapid spread of infectious disease outbreaks in marine organisms

The first signs of sea star wasting disease (SSWD) epidemic occurred in just few months in 2013 along the entire North American Pacific coast. Disease dynamics did not manifest as the typical travelling wave of reaction-diffusion epidemiological model, suggesting that other environmental factors might have played some role. To help explore how external factors might trigger disease, we built a coupled oceanographic-epidemiological model and contrasted three hypotheses on the influence of temperature on disease transmission and pathogenicity. Models that linked mortality to sea surface temperature gave patterns more consistent with observed data on sea star wasting disease, which suggests that environmental stress could explain why some marine diseases seem to spread so fast and have region-wide impacts on host populations.

Baja California, British Columbia, California, Ore↗
USGS2021

Feral swine as sources of fecal contamination in recreational waters

Recreational waters are primary attractions at many national and state parks where feral swine populations are established, and thus are possible hotspots for visitor exposure to feral swine contaminants. Microbial source tracking (MST) was used to determine spatial and temporal patterns of fecal contamination in Congaree National Park (CONG) in South Carolina, U.S.A., which has an established population of feral swine and is a popular destination for water-based recreation. Water samples were collected between December 2017 and June 2019 from 18 surface water sites distributed throughout CONG. Host specific MST markers included human (HF183), swine (Pig2Bac), ruminant (Rum2Bac), cow (CowM3), chicken (CL), and a marker for shiga toxin producing Escherichia coli (STEC; stx2 ). Water samples were also screened for culturable Escherichia coli ( E. coli ) as part of a citizen science program. Neither the cow nor chicken MST markers were detected during the study. The human marker was predominantly detected at boundary sites or could be attributed to upstream sources. However, several detections within CONG without concurrent detections at upstream external sites suggested occasional internal contamination from humans. The swine marker was the most frequently detected of all MST markers, and was present at sites located both internal and external to the Park. Swine MST marker concentrations ≥ 43 gene copies/mL were associated with culturable E. coli concentrations greater than the U.S. Environmental Protection Agency beach action value for recreational waters. None of the MST markers showed a strong association with detection of the pathogenic marker ( stx2 ). Limited information about the health risk from exposure to fecal contamination from non-human sources hampers interpretation of the human health implications.

South Carolina↗
USGS2023

Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha)

Pacific salmon experience prolonged elevation in corticosteroid hormones during important life history events including migration, reproduction, and senescence. These periods of elevated corticosteroids correspond with changes to immunity and energy metabolism; therefore, fish may be particularly vulnerable to mortality at these times. Recent studies found that stress-induced cortisol release associated with microbial community shifts in salmonids, raising the question of how longer-term corticosteroid dynamics that accompany life history transitions affect salmonid microbiomes. In this work, we experimentally evaluated the relationships between gut microbiome composition, chronically elevated corticosteroids, and mortality in juvenile Chinook salmon ( Oncorhynchus tshawytscha) . We found that treatment with slow-release implants of the corticosteroids cortisol or dexamethasone resulted in persistent changes to the gut microbiome. Morbidity was also associated with microbiome composition, suggesting that the gut microbiome reflects individual differences in susceptibility to opportunistic pathogens. Additionally, we analyzed a small number of samples from adult fish at various stages of senescence. Results from these samples suggest that microbiome composition associated with gut integrity, and that the microbial communities of corticosteroid treated juveniles shift in composition toward those of senescent adults. Overall, findings from this work suggest that the gut microbiome associates with mortality risk during periods of chronic corticosteroid elevation.

Scientific Reports↗
USGS2023

Environmental transmission of Pseudogymnoascus destructans to hibernating little brown bats

Pathogens with persistent environmental stages can have devastating effects on wildlife communities. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has caused widespread declines in bat populations of North America. In 2009, during the early stages of the WNS investigation and before molecular techniques had been developed to readily detect P. destructans in environmental samples, we initiated this study to assess whether P. destructans can persist in the hibernaculum environment in the absence of its conclusive bat host and cause infections in naive bats. We transferred little brown bats ( Myotis lucifugus ) from an unaffected winter colony in northwest Wisconsin to two P. destructans contaminated hibernacula in Vermont where native bats had been excluded . Infection with P. destructans was apparent on some bats within 8 weeks following the introduction of unexposed bats to these environments, and mortality from WNS was confirmed by histopathology at both sites 14 weeks following introduction. These results indicate that environmental exposure to P. destructans is sufficient to cause the infection and mortality associated with WNS in naive bats, which increases the probability of winter colony extirpation and complicates conservation efforts.

Nature↗
USGS2025

Independent and interactive effects of disease and methylmercury on demographic rates across multiple amphibian populations

Disease, alone or combined with other stressors such as habitat loss and contaminants, affects wildlife populations worldwide. However, interactions among stressors and how they affect demography and populations remain poorly understood. The amphibian chytrid fungus ( Batrachochytrium dendrobatidis ; Bd) is a sometimes-lethal pathogen linked with population declines and extirpations of amphibians globally. Laboratory evidence shows ubiquitous contaminants like methylmercury (MeHg) can reduce vigor and survival of amphibians, but population-level effects remain unclear. We used non-lethal sampling to assess how Bd and MeHg affected survival of juvenile and adult amphibians in 20 populations across the USA. Survival of several species declined with increasing Bd loads, including some species previously considered resistant to Bd (e.g., eastern newt [ Notophthalmus viridescens ]). Although our sampling for MeHg was less intensive than for Bd, we found MeHg can both directly reduce survival and synergistically magnify the effects of Bd infection. For a population of foothill yellow-legged frogs ( Rana boylii ), the estimated reduction in survival from MeHg exceeded that from Bd. Although effects varied widely among populations and species, our results help clarify the potential for synergistic effects of disease and contaminants and emphasize the complexity of identifying and quantifying the population-level effects of interactions among stressors.

Scientific Reports↗
USGS2001

Biochemical and molecular typing of Streptococcus iniae isolated from fish and human cases

Streptococcus iniae is an important bacterial pathogen of fish, causing up to 50% mortality in stocks, which has recently been associated with human infections. To determine whether S. iniae isolates from humans and fish are similar, the present authors examined the biochemical profiles and genetic relatedness of these isolates by random amplified polymorphic DNA (RAPD) analysis and repetitive primer polymerase chain reaction(REP PCR). The biochemical profiles differentiated between the human and fish isolates of S. iniae using pyrrolidonyl arylamidase, arginine dehydrogenase, ribose, β-glucoronidase and glycogen as markers. These biochemical results suggest that the fish and human S. iniae isolates are genetically different. However, RAPD and REP PCR do not have the discriminatory power to differentiate between these streptococcus isolates using five different RAPD primers and BoxA primer.

Journal of Fish Diseases↗
USGS2002

Puerto Rican parrots and potential limitations of the metapopulation approach to species conservation

Population viability analyses for a number of endangered species have incorporated a metapopulation approach. The risk assessments of these viability analyses have indicated that some extant populations should be subdivided into numerous subgroups with exchange of individuals among them in order to reduce the chance of catastrophic loss of the species. However, routine application of a policy of extensive subdivision may have detrimental consequences for certain endangered species. We examine the Puerto Rican Parrot as a case history in which this policy is ill-advised. In 1989, a population viability analysis was conducted for the parrot. The document recommended subdivision of the existing small captive flock into three groups. One of these captive flocks would consist of individuals transferred to a multi-species facility in the continental United States. Subsequently, individuals from this facility would be exchanged with the insular captive population(s) and the relict wild flock. For two reasons, implementation of this recommendation might have led to serious repercussions. First, this parrot, like many endangered species, has gone through a genetic bottleneck and may have a heightened susceptibility to disease. Multi-species facilities are a high-risk environment favoring the transmission of pathogens, especially when the facilities are located outside the natural ranges of a particular species. Second, the parrot is a K-selected species for which mate selection is idiosyncratic. This type of species often proves difficult to breed in captivity in small groups. Part of the problem in mate selection may be reduced by a policy allowing frequent transfers of individuals among facilities, but such movements increase the chances of spreading disease in the metapopulation. Thus, population viability analyses need to acknowledge that proliferation of captive subgroups accompanied by exchanges of individuals can in themselves carry substantial risks that must be weighed against the presumed benefits of subdivision.

Puerto Rico↗
USGS2010

Emerging viral diseases of fish and shrimp

The rise of aquaculture has been one of the most profound changes in global food production of the past 100 years. Driven by population growth, rising demand for seafood and a levelling of production from capture fisheries, the practice of farming aquatic animals has expanded rapidly to become a major global industry. Aquaculture is now integral to the economies of many countries. It has provided employment and been a major driver of socio-economic development in poor rural and coastal communities, particularly in Asia, and has relieved pressure on the sustainability of the natural harvest from our rivers, lakes and oceans. However, the rapid growth of aquaculture has also been the source of anthropogenic change on a massive scale. Aquatic animals have been displaced from their natural environment, cultured in high density, exposed to environmental stress, provided artificial or unnatural feeds, and a prolific global trade has developed in both live aquatic animals and their products. At the same time, over-exploitation of fisheries and anthropogenic stress on aquatic ecosystems has placed pressure on wild fish populations. Not surprisingly, the consequence has been the emergence and spread of an increasing array of new diseases. This review examines the rise and characteristics of aquaculture, the major viral pathogens of fish and shrimp and their impacts, and the particular characteristics of disease emergence in an aquatic, rather than terrestrial, context. It also considers the potential for future disease emergence in aquatic animals as aquaculture continues to expand and faces the challenges presented by climate change.

Veterinary Research↗
USGS2016

Anticipating environmental and environmental-health implications of extreme storms: ARkStorm scenario

The ARkStorm Scenario predicts that a prolonged winter storm event across California would cause extreme precipitation, flooding, winds, physical damages, and economic impacts. This study uses a literature review and geographic information system-based analysis of national and state databases to infer how and where ARkStorm could cause environmental damages, release contamination from diverse natural and anthropogenic sources, affect ecosystem and human health, and cause economic impacts from environmental-remediation, liability, and health-care costs. Examples of plausible ARkStorm environmental and health concerns include complex mixtures of contaminants such as petroleum, mercury, asbestos, persistent organic pollutants, molds, and pathogens; adverse physical and contamination impacts on riverine and coastal marine ecosystems; and increased incidences of mold-related health concerns, some vector-borne diseases, and valley fever. Coastal cities, the San Francisco Bay area, the Sacramento-San Joaquin River Delta, parts of the Central Valley, and some mountainous areas would likely be most affected. This type of screening analysis, coupled with follow-up local assessments, can help stakeholders in California and disaster-prone areas elsewhere better plan for, mitigate, and respond to future environmental disasters.

Natural Hazards Review↗