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.

SourceResearch connectionFrom yearThrough year

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

At least 649 records · Page 36Linked to original sources

USGS2019

Conservation decisions under pressure: Lessons from an exercise in rapid response to wildlife disease

Novel outbreaks of emerging pathogens require rapid responses to enable successful mitigation. We simulated a 1‐day emergency meeting where experts were engaged to recommend mitigation strategies for a new outbreak of the amphibian fungal pathogen Batrachochytrium salamandrivorans . Despite the inevitable uncertainty, experts suggested and discussed several possible strategies. However, their recommendations were undermined by imperfect initial definitions of the objectives and scope of management. This problem is likely to arise in most real‐world emergency situations. The exercise thus highlighted the importance of clearly defining the context, objectives, and spatial–temporal scale of mitigation decisions. Managers are commonly under pressure to act immediately. However, an iterative process in which experts and managers cooperate to clarify objectives and uncertainties, while collecting more information and devising mitigation strategies, may be slightly more time consuming but ultimately lead to better outcomes.

Conservation Science and Practice↗

USGS2014

Limitations to estimating bacterial cross-speciestransmission using genetic and genomic markers: Inferences from simulation modeling

Cross‐species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. We found that CST estimates are biased for a wide range of parameters when based on VNTRs and a most parsimonious reconstructed phylogeny. However, estimations of CST rates lower than 5% can be achieved with relatively low bias using as low as 250 SNPs. CST estimates are sensitive to several parameters, including the number of mutations accumulated since introduction, stochasticity, the genetic difference of strains introduced, and the sampling effort. Our results suggest that, even with whole‐genome sequences, unbiased estimates of CST will be difficult when sampling is limited, mutation rates are low, or for pathogens that were recently introduced.

Evolutionary Applications↗

USGS2006

Cellular immune response in rainbow trout Salmo gairdneri Richardson to Yersinia ruckeri O-antigen monitored by the passive haemolytic plaque assay test

The specificity and kinetics of the immune response of rainbow trout ( Salmo gairdneri ) to single injections of an O-antigen extracted from the bacterial pathogen Yersinia ruckeri , which causes enteric redmouth in fish, were investigated by the passive haemolytic plaque assay and serum antibody quantitation. Doses ranging from 5 ng to 500 mg in 10-fold increments were injected intraperitoneally into groups of trout held at 17 × 1°5°C. The occurrence of plaque forming cells (PFC) and humoral antibody was followed for 35 days after injection. Trout gave an immune response to doses of 500 ng and above. Seven days after injection no humoral antibody was detected, but PFC were found in the spleen. The maximum PFC numbers occurred 11 days after injection. On day 21, few PFC were found, whereas serum antibody titres were highest. The antibody from immunized trout showed little or no cross-reactions with sheep red blood cells passively labelled With antigens from other fish pathogens.

Journal of Fish Diseases↗

USGS2008

Genetic evidence of intercontinental movement of avian influenza in a migratory bird: The northern pintail (Anas acuta)

The role of migratory birds in the movement of the highly pathogenic (HP) avian influenza H5N1 remains a subject of debate. Testing hypotheses regarding intercontinental movement of low pathogenic avian influenza (LPAI) viruses will help evaluate the potential that wild birds could carry Asian-origin strains of HP avian influenza to North America during migration. Previous North American assessments of LPAI genetic variation have found few Asian reassortment events. Here, we present results from whole-genome analyses of LPAI isolates collected in Alaska from the northern pintail (Anas acuta), a species that migrates between North America and Asia. Phylogenetic analyses confirmed the genetic divergence between Asian and North American strains of LPAI, but also suggested inter-continental virus exchange and at a higher frequency than previously documented. In 38 isolates from Alaska, nearly half (44.7%) had at least one gene segment more closely related to Asian than to North American strains of LPAI. Additionally, sequences of several Asian LPAI isolates from GenBank clustered more closely with North American northern pintail isolates than with other Asian origin viruses. Our data support the role of wild birds in the intercontinental transfer of influenza viruses, and reveal a higher degree of transfer in Alaska than elsewhere in North America. ?? 2008 The Authors.

Alaska↗

USGS2010

Prevention of infectious diseases in aquaculture

Infectious diseases remain one of the most important limitations to the successful propagation of aquatic animals. Most of the losses caused by pathogens in aquaculture could be prevented by health inspection, adequate environment and sound management practices. Effective control measures, mainly based upon 1) avoidance of pathogens 2) modification of the environment 3) improvement of host resistance 4) vaccination and 5) chemoprophylaxis are described.

Journal of Veterinary Medicine, Series B↗

USGS2010

Satellite‐tracking of Northern Pintail Anas acuta during outbreaks of the H5N1 virus in Japan: Implications for virus spread

We fitted Northern Pintail Anas acuta in Japan with satellite transmitters and monitored their spring migration movements relative to locations where the highly pathogenic H5N1 avian influenza virus was detected in Whooper Swans Cygnus cygnus in 2008. Pintails were assumed not to be infected with the H5N1 virus at the time they were marked because capture occurred between 2 and 5 months before reported outbreaks of the virus in Japan. We assessed spatial and temporal overlap between marked birds and occurrence of the virus and tracked Pintails after they departed outbreak locations. Eight of 66 (12.1%) Northern Pintails marked with satellite transmitters used wetlands in Japan where the H5N1 virus was detected in Whooper Swans. Apparent survival did not differ between Pintails that used H5N1 sites and those that did not. However, the proportion of Pintails that migrated from Japan was significantly lower among birds that used H5N1 sites compared with those that did not (0.50 vs. 0.79). Northern Pintails were present at the H5N1 sites from 1 to 88 days, with five birds present at the sites from 0 to 7 days prior to detection of the virus in Swans. The six Pintails observed to depart H5N1 sites did so within 2–77 days of the reported outbreaks and moved between 6 and 1200 km within 4 days of departure. Four Pintails migrated to eastern Russia. After their departure from outbreak sites, Northern Pintails made long‐distance migrations within the period when newly infected ducks would shed the H5N1 virus. This supports a hypothesized mechanism by which a highly pathogenic avian influenza virus could be spread by migratory birds.

Ibis↗

USGS2012

Avian influenza in shorebirds: experimental infection of ruddy turnstones (Arenaria interpres) with avian influenza virus

Background: Low pathogenic avian influenza viruses (LPAIV) have been reported in shorebirds, especially at Delaware Bay, USA, during spring migration. However, data on patterns of virus excretion, minimal infectious doses, and clinical outcome are lacking. The ruddy turnstone (Arenaria interpres) is the shorebird species with the highest prevalence of influenza virus at Delaware Bay. Objectives: The primary objective of this study was to experimentally assess the patterns of influenza virus excretion, minimal infectious doses, and clinical outcome in ruddy turnstones. Methods: We experimentally challenged ruddy turnstones using a common LPAIV shorebird isolate, an LPAIV waterfowl isolate, or a highly pathogenic H5N1 avian influenza virus. Cloacal and oral swabs and sera were analyzed from each bird. Results: Most ruddy turnstones had pre-existing antibodies to avian influenza virus, and many were infected at the time of capture. The infectious doses for each challenge virus were similar (103·6–104·16 EID50), regardless of exposure history. All infected birds excreted similar amounts of virus and showed no clinical signs of disease or mortality. Influenza A-specific antibodies remained detectable for at least 2 months after inoculation. Conclusions: These results provide a reference for interpretation of surveillance data, modeling, and predicting the risks of avian influenza transmission and movement in these important hosts.

Influenza and Other Respiratory Viruses↗

USGS2009

Avian influenza at both ends of a migratory flyway: characterizing viral genomic diversity to optimize surveillance plans for North America

Although continental populations of avian influenza viruses are genetically distinct, transcontinental reassortment in low pathogenic avian influenza (LPAI) viruses has been detected in migratory birds. Thus, genomic analyses of LPAI viruses could serve as an approach to prioritize species and regions targeted by North American surveillance activities for foreign origin highly pathogenic avian influenza (HPAI). To assess the applicability of this approach, we conducted a phylogenetic and population genetic analysis of 68 viral genomes isolated from the northern pintail (Anas acuta) at opposite ends of the Pacific migratory flyway in North America. We found limited evidence for Asian LPAI lineages on wintering areas used by northern pintails in California in contrast to a higher frequency on breeding locales of Alaska. Our results indicate that the number of Asian LPAI lineages observed in Alaskan northern pintails, and the nucleotide composition of LPAI lineages, is not maintained through fall migration. Accordingly, our data indicate that surveillance of Pacific Flyway northern pintails to detect foreign avian influenza viruses would be most effective in Alaska. North American surveillance plans could be optimized through an analysis of LPAI genomics from species that demonstrate evolutionary linkages with European or Asian lineages and in regions that have overlapping migratory flyways with areas of HPAI outbreaks.

Alaska, California↗

USGS2010

Molecular typing of Escherichia coli strains associated with threatened sea ducks and near-shore marine habitats of south-west Alaska

In Alaska, sea ducks winter in coastal habitats at remote, non-industrialized areas, as well as in proximity to human communities and industrial activity. We evaluated prevalence and characteristics of Escherichia coli strains in faecal samples of Steller's eiders ( Polysticta stelleri ; n = 122) and harlequin ducks ( Histrionicus histrionicus ; n = 21) at an industrialized site and Steller's eiders ( n = 48) at a reference site, and compared these strains with those isolated from water samples from near-shore habitats of ducks. The overall prevalence of E. coli was 16% and 67% in Steller's eiders and harlequin ducks, respectively, at the industrialized study site, and 2% in Steller's eiders at the reference site. Based on O and H antigen subtyping and genetic characterization by enterobacterial repetitive intergenic consensus polymerase chain reaction and pulsed-field gel electrophoresis, we found evidence of avian pathogenic E. coli (APEC) strains associated with both species and detected E. coli strains carrying virulence genes associated with mammals in harlequin ducks. Steller's eiders that carried APEC had lower serum total protein and albumin concentrations, providing further evidence of pathogenicity. The genetic profile of two E. coli strains from water matched an isolate from a Steller's eider providing evidence of transmission between near-shore habitats and birds.

Alaska↗

USGS2014

Assessing the potential effects of fungicides on nontarget gut fungi (trichomycetes) and their associated larval black fly hosts

Fungicides are moderately hydrophobic and have been detected in water and sediment, particularly in agricultural watersheds, but typically are not included in routine water quality monitoring efforts. This is despite their widespread use and frequent application to combat fungal pathogens. Although the efficacy of these compounds on fungal pathogens is well documented, little is known about their effects on nontarget fungi. This pilot study, a field survey in southwestern Idaho from April to December 2010 on four streams with varying pesticide inputs (two agricultural and two reference sites), was conducted to assess nontarget impact of fungicides on gut fungi, or trichomycetes. Tissues of larval black flies (Diptera: Simuliidae), hosts of gut fungi, were analyzed for pesticide accumulation. Fungicides were detected in hosts from streams within agricultural watersheds but were not detected in hosts from reference streams. Gut fungi from agricultural sites exhibited decreased percent infestation, density and sporulation within the gut, and black fly tissues had elevated pesticide concentrations. Differences observed between the sites demonstrate a potential effect on this symbiotic system. Future research is needed to parse out the details of the complex biotic and abiotic relationships; however, these preliminary results indicate that impacts to nontarget organisms could have far-reaching consequences within aquatic ecosystems.

Journal of the American Water Resources Associatio↗

USGS2024

Parasite abundance-occupancy relationships across biogeographic regions: Joint effects of niche breadth, host availability and climate

Changing biodiversity and environmental conditions may allow multi-host pathogens to spread among host species and affect prevalence. There are several widely acknowledged theories about mechanisms that may influence variation in pathogen prevalence, including the controversially debated dilution effect and abundance-occupancy relationship hypotheses. Here, we explore such abundance-occupancy relationships for unique lineages of three vector-borne avian blood parasite genera (the avian malaria parasite Plasmodium and the related haemosporidian parasites Parahaemoproteus and Leucocytozoon ) across biogeographical regions.

Journal of Biogeography↗

USGS2013

Polyphasic characterization of Aeromonas salmonicida isolates recovered from salmonid and non-salmonid fish

Michigan's fisheries rely primarily upon the hatchery propagation of salmonid fish for release in public waters. One limitation on the success of these efforts is the presence of bacterial pathogens, including Aeromonas salmonicida, the causative agent of furunculosis. This study was undertaken to determine the prevalence of A. salmonicida in Michigan fish, as well as to determine whether biochemical or gene sequence variability exists among Michigan isolates. A total of 2202 wild, feral and hatchery-propagated fish from Michigan were examined for the presence of A. salmonicida. The examined fish included Chinook salmon, Oncorhynchus tshawytscha (Walbaum), coho salmon, O. kisutcha (Walbaum), steelhead trout, O. mykiss (Walbaum), Atlantic salmon, Salmo salar L., brook trout, Salvelinus fontinalis (Mitchill), and yellow perch, Perca flavescens (Mitchill). Among these, 234 fish yielded a brown pigment-producing bacterium that was presumptively identified as A. salmonicida. Further phenotypic and phylogenetic analyses identified representative isolates as Aeromonas salmonicida subsp. salmonicida and revealed some genetic and biochemical variability. Logistic regression analyses showed that infection prevalence varied according to fish species/strain, year and gender, whereby Chinook salmon and females had the highest infection prevalence. Moreover, this pathogen was found in six fish species from eight sites, demonstrating its widespread nature within Michigan.

Journal of Fish Diseases↗

USGS2015

Effects of temperature on Renibacterium salmoninarum infection and transmission potential in Chinook salmon, Oncorhynchus tshawytscha (Walbaum)

Renibacterium salmoninarum is a significant pathogen of salmonids and the causative agent of bacterial kidney disease (BKD). Water temperature affects the replication rate of pathogens and the function of the fish immune system to influence the progression of disease. In addition, rapid shifts in temperature may serve as stressors that reduce host resistance. This study evaluated the effect of shifts in water temperature on established R. salmoninarum infections. We challenged Chinook salmon with R. salmoninarum at 12°C for 2 weeks and then divided the fish into three temperature groups (8, 12 and 15°C). Fish in the 8°C group had significantly higher R. salmoninarum -specific mortality, kidney R. salmoninarum loads and bacterial shedding rates relative to the fish held at 12 or 15°C. There was a trend towards suppressed bacterial load and shedding in the 15°C group, but the results were not significant. Bacterial load was a significant predictor of shedding for the 8 and 12°C groups but not for the 15°C group. Overall, our results showed little effect of temperature stress on the progress of infection, but do support the conclusion that cooler water temperatures contribute to infection progression and increased transmission potential in Chinook salmon infected with R. salmoninarum .

Journal of Fish Diseases↗

USGS2017

Temporospatial dynamics and public health significance of bacterial flora identified on a major leatherback turtle (Dermochelys coriacea) nesting beach in the Southern Caribbean

Grande Riviere beach, on the island of Trinidad, supports the largest nesting population of leatherback turtles in the Caribbean region. Throughout the nesting season, nests are naturally disturbed by newly nesting females, resulting in egg breakage and loss of some nest viability. This environment is ideal for the growth and proliferation of microorganisms. The range of bacterial flora present in beach sand and egg shells was examined, with emphasis on bacteria that may pose a threat to public and animal health. The extent to which the bacterial load and genera on the beach changed throughout the season was also assessed. Twenty-five genera were identified, with Pseudomonas spp. found to be the most predominant environmental bacteria. Four genera identified possess zoonotic potential, while five additional genera are known to be of public and animal health significance. Distinct shifts in the density and distribution of bacteria were observed along the beach from early to peak nesting season. Shifts were seen across heavily traversed zones, thus highlighting the potential exposure threats posed to beach visitors and animals alike. Further studies aimed at speciating this population of bacteria, as well as isolating potential fungal pathogens may mitigate this threat. Identification of bacterial agents that are specifically pathogenic to leatherback turtles, turtle eggs, hatchlings and those who may interact with these animals will serve to enhance and guide efforts to better conserve this species and protect the health of all who visit this ecologically significant site.

Grande Riviere beach↗

USGS2021

Sin Nombre virus prevalence from 2014–2017 in wild deer mice, Peromyscus maniculatus, on five of the California Channel Islands

Sin Nombre virus (SNV) is a zoonotic virus that is highly pathogenic to humans. The deer mouse, Peromyscus maniculatus , is the primary host of SNV, and SNV prevalence in P . maniculatus is an important indicator of human disease risk. Because the California Channel Islands contain permanent human settlements, receive hundreds of thousands of visitors each year, and can have extremely high densities of P . maniculatus , surveillance for SNV in island P . maniculatus is important for understanding the human risk of zoonotic disease. Despite the importance of surveillance on these heavily utilized islands, SNV prevalence (i.e. the proportion of P . maniculatus that test positive to antibodies to SNV) has not been examined in the last 13–27 years. We present data on 1,610 mice sampled for four consecutive years (2014–2017) on five of the California Channel Islands: East Anacapa, Santa Barbara, Santa Catalina, San Nicolas, and San Clemente. Despite historical data indicating SNV-positive mice on San Clemente and Santa Catalina, we detected no SNV-positive mice on these islands, suggesting very low prevalence or possible loss of SNV. Islands historically free of SNV (East Anacapa, Santa Barbara, and San Nicolas) remained free of SNV, suggesting that rates of pathogen introduction from other islands and/or the mainland are low. Although continued surveillance is warranted to determine whether SNV establishes on these islands, our work helps inform current human disease risk in these locations and suggests that SNV prevalence on these islands is currently very low.

California↗

USGS2024

Developing transmissible vaccines for animal infections

Many emerging and reemerging pathogens originate from wildlife, but nearly all wild species are unreachable using conventional vaccination, which requires capture of and vaccine administration to individual animals. By enabling immunization at scales sufficient to interrupt pathogen transmission, transmissible vaccines (TVs) that spread themselves through wildlife populations by infectious processes could potentially transform the management of otherwise intractable challenges to public health, wildlife conservation, and animal welfare. However, generating TVs likely requires modifying viruses that would be intended to spread in nature, which raises concerns ranging from technical feasibility, to safety and security risks, to regulatory uncertainties ( 1 , 2 ). We propose a series of commitments and strategies for vaccine development—beginning with a priori decisions on vaccine design and continuing through to stakeholder codevelopment [see supplementary materials (SM)]—that we believe increase the likelihood that the potential risks of vaccine transmission are outweighed by benefits to conservation, animal welfare, and zoonosis prevention.

Science↗

USGS2015

Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

Book chapter↗

USGS2017

Phylogenetics of a fungal invasion: Origins and widespread dispersal of white-nose syndrome

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans , a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans . Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia.

mBio↗