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USGS2012

The effect of swab sample choice on the detection of avian influenza in apparently healthy wild ducks

Historically, avian influenza viruses have been isolated from cloacal swab specimens, but recent data suggest that the highly pathogenic avian influenza (HPAI) H5N1 virus can be better detected from respiratory tract specimens. To better understand how swab sample type affects the detection ability of low pathogenic avian influenza (LPAI) viruses we collected and tested four swab types: oropharyngeal swabs (OS), cloacal swabs (CS), the two swab types combined in the laboratory (LCS), and the two swab types combined in the field (FCS). A total of 1968 wild waterfowl were sampled by each of these four methods and tested for avian influenza virus using matrix gene reverse-transcription (RT)-PCR. The highest detection rate occurred with the FCS (4.3%) followed by the CS (4.0%). Although this difference did not achieve traditional statistical significance, Bayesian analysis indicated that FCS was superior to CS with an 82% probability. The detection rates for both the LCS (2.4%) and the OS (0.4%) were significantly different from the FCS. In addition, every swab type that was matrix RT-PCR positive was also tested for recovery of viable influenza virus. This protocol reduced the detection rate, but the ordering of swab types remained the same: 1.73% FCS, 1.42% CS, 0.81% LCS, and 0% OS. Our data suggest that the FCS performed at least as well as any other swab type for detecting LPAI viruses in the wild ducks tested. When considering recent studies showing that HPAI H5N1 can be better detected in the respiratory tract, the FCS is the most appropriate sample to collect for HPAI H5N1 surveillance while not compromising LPAI studies.

California, Colorado, North Dakota↗

USGS2024

Abiotic and demographic drivers of flea parasitism on deer mice in a recovering mixed-conifer forest a decade postfire

With the intensity and frequency of wildfires increasing rapidly, the need to study the ecological effects of these wildfires is also growing. An understudied aspect of fire ecology is the effect fires have on parasite–host interactions, including ectoparasites that might be pathogen vectors. Although some studies have examined the impacts of fire on ticks, studies on other ectoparasites, including pathogen vectors, are rare. To help address this knowledge gap, we examined the abiotic and biotic factors that predict the likelihood and extent of parasitism of deer mice ( Peromyscus maniculatus ) by fleas within a landscape of unburned and recovering burned (>9 yr postfire) mixed conifer forests. We sampled 227 individual deer mice across 27 sites within the Jemez Mountains of northern New Mexico in 2022 and quantified measures of parasitism by fleas (primarily Aetheca wagneri ). These sites were distributed in both unburned areas (n = 15) and recovering burned areas (n = 12), with the latter derived from 2 large fires, the Las Conchas fire (2011) and the Thompson Ridge fire (2013). Using these data, we tested for differences in prevalence, mean abundance, and mean intensity of fleas on deer mice, focusing on the predictive importance of host sex and fire history. We also created generalized linear mixed-effects models to investigate the best host and environmental predictors of parasitism by fleas. Approximately a decade postfire, we found minimal evidence to suggest that fire history influenced either the presence or intensity of fleas on deer mice. Rather, at the current forest-regeneration stage, the extent of parasitism by fleas was best predicted by measures of host sex, body condition, and the trapline's ability to accumulate water, as measured through topography. As host body condition increased, the probability of males being parasitized increased, whereas the opposite pattern was seen for females. Male mice also had significantly greater flea loads. Among potential abiotic predictors, the topographic wetness index or compound topographic index (a proxy for soil moisture) was positively related to flea intensity, suggesting larger flea populations in burrows with higher relative humidity. In summary, although fire may potentially have short-term impacts on the likelihood and extent of host parasitism by fleas, in this recovering study system, host characteristics and topographic wetness index are the primary predictors of parasitism by fleas.

New Mexico↗

USGS2020

Effects of snowpack, temperature, and disease on the demography of a wild population of amphibians

Understanding the demographic consequences of interactions among pathogens, hosts, and weather conditions is critical in determining how amphibian populations respond to disease and in identifying site-specific conservation actions that can be developed to bolster persistence of amphibian populations. We investigated population dynamics in Boreal Toads ( Anaxyrus boreas ) relative to abiotic (fall temperatures and snowpack) and biotic (the abundance of another anuran host and disease) characteristics of the local environment in Wyoming, USA. We used capture–recapture data and a multistate model where state was treated as a hidden Markov process to incorporate disease state uncertainty and assess our a priori hypotheses. Our results indicated that snowpack during the coldest week of winter is more influential to toad survival, disease transition probabilities, and the population-level prevalence of the amphibian chytrid fungus ( Batrachochytrium dendrobatidis ) in the spring, than temperatures in the fall or the presence of another host. As hypothesized, apparent survival at low (i.e., <25 cm) snowpack (0.22; confidence interval [CI] = 0.15–0.31) was lower than apparent survival at high snowpack (90.65; CI = 0.50–0.78). Our findings highlight the potential for local environmental factors, like snowpack, to influence disease and host persistence, and demonstrate the ecological complexity of disease effects on population demography in natural environments. This work further emphasizes the need for improved understanding of how climate change may influence the relationships among pathogens, hosts, and their environment for wild animal populations challenged by disease.

Wyoming↗

USGS2024

Predicted occurrence of Eastern Newts (Notophthalmus viridescens viridescens) across the northeastern United States

Effective conservation is becoming more difficult as threats to wildlife increase. Natural resource managers are pressured to make difficult decisions with limited resources, and in many instances, large uncertainty. Scientists and managers tasked with the conservation of a species need tools to help guide efficient decision-making. Often, information for management decisions is insufficient. Tools that help to inform decision makers and address uncertainty are invaluable to effective conservation initiatives. The objective of our study was to create a model to best predict Eastern Newt (Notophthalmus viridescens viridescens) breeding occurrence across the northeastern United States. We estimated relationships between breeding newt field survey data and landscape-level covariates while accounting for imperfect detection. We then used those relationships to map expected newt breeding site occupancy across the northeastern United States. We find that newt breeding occupancy is inversely correlated to the amount of human influence in a landscape, highlighting a key existing threat to Eastern Newts that may be exacerbated by the introduction of novel pathogens, such as the fungal pathogen Batrachochytrium salamandrivorans.

Herpetologica↗

USGS2010

Rice production systems and avian influenza: Interactions between mixed-farming systems, poultry and wild birds

Wild waterfowl are the reservoir for avian influenza viruses (AIVs), a family of RNA viruses that may cause mild sickness in waterbirds. Emergence of H5N1, a highly pathogenic avian influenza (HPAI) strain, causing severe disease and mortality in wild birds, poultry and humans, had raised concerns about the role of wild birds in possible transmission of the disease. In this review, the link between rice production systems, poultry production systems, and wild bird ecology is examined to assess the extent to which these interactions could contribute towards the persistence and evolution of HPAI H5N1. The rice (Oryza sativa) and poultry production systems in Asia described, and then migration and movements of wild birds discussed. Mixed farming systems in Asia and wild bird movement and migration patterns create opportunities for the persistence of low pathogenic AIVs in these systems. Nonetheless, there is no evidence of long-term persistence of HPAI viruses (including the H5N1 subtype) in the wild. There are still significant gaps in the understanding of how AIVs circulate in rice systems. A better understanding of persistence of AIVs in rice farms, particularly of poultry origins, is essential in limiting exchange of AIVs between mixed-farming systems, poultry and wild birds.

Waterbirds↗

USGS2014

Wildlife health in a rapidly changing North: focus on avian disease

Climate-related environmental changes have increasingly been linked to emerging infectious diseases in wildlife. The Arctic is facing a major ecological transition that is expected to substantially affect animal and human health. Changes in phenology or environmental conditions that result from climate warming may promote novel species assemblages as host and pathogen ranges expand to previously unoccupied areas. Recent evidence from the Arctic and subarctic suggests an increase in the spread and prevalence of some wildlife diseases, but baseline data necessary to detect and verify such changes are still lacking. Wild birds are undergoing rapid shifts in distribution and have been implicated in the spread of wildlife and zoonotic diseases. Here, we review evidence of current and projected changes in the abundance and distribution of avian diseases and outline strategies for future research. We discuss relevant climatic and environmental factors, emerging host–pathogen contact zones, the relationship between host condition and immune function, and potential wildlife and human health outcomes in northern regions.

Frontiers in Ecology and the Environment↗

USGS2015

The dynamics of avian influenza in western Arctic snow geese: implications for annual and migratory infection patterns

Wild water birds are the natural reservoir for low-pathogenic avian influenza viruses (AIV). However, our ability to investigate the epizootiology of AIV in these migratory populations is challenging, and despite intensive worldwide surveillance, remains poorly understood. We conducted a cross-sectional, retrospective analysis in Pacific Flyway lesser snow geese Chen caerulescens to investigate AIV serology and infection patterns. We collected nearly 3,000 sera samples from snow geese at 2 breeding colonies in Russia and Canada during 1993-1996 and swab samples from > 4,000 birds at wintering and migration areas in the United States during 2006-2011. We found seroprevalence and annual seroconversion varied considerably among years. Seroconversion and infection rates also differed between snow goose breeding colonies and wintering areas, suggesting that AIV exposure in this gregarious waterfowl species is likely occurring during several phases (migration, wintering and potentially breeding areas) of the annual cycle. We estimated AIV antibody persistence was longer (14 months) in female geese compared to males (6 months). This relatively long period of AIV antibody persistence suggests that subtype-specific serology may be an effective tool for detection of exposure to subtypes associated with highly-pathogenic AIV. Our study provides further evidence of high seroprevalence in Arctic goose populations, and estimates of annual AIV seroconversion and antibody persistence for North American waterfowl. We suggest future AIV studies include serology to help elucidate the epizootiological dynamics of AIV in wild bird populations.

Ecological Applications↗

USGS2009

Gene and antigen markers of Shiga-toxin producing E. coli from Michigan and Indiana river water: Occurrence and relation to recreational water quality criteria

The relation of bacterial pathogen occurrence to fecal indicator bacteria (FIB) concentrations used for recreational water quality criteria (RWQC) is poorly understood. This study determined the occurrence of Shiga-toxin producing Escherichia coli (STEC) markers and their relation to FIB concentrations in Michigan and Indiana river water. Using 67 fecal coliform (FC) bacteria cultures from 41 river sites in multiple watersheds, we evaluated the occurrence of five STEC markers: the Escherichia coli (EC) O157 antigen and gene, and the STEC virulence genes eae A, stx 1, and stx 2. Simple isolations from selected FC cultures yielded viable EC O157. By both antigen and gene assays, EC O157 was detected in a greater proportion of samples exceeding rather than meeting FC RWQC ( P < 0.05), but was unrelated to EC and enterococci RWQC. The occurrence of all other STEC markers was unrelated to any FIB RWQC. The eaeA , stx2, and stx1 genes were found in 93.3, 13.3, and in 46.7% of samples meeting FC RWQC and in 91.7, 0.0, and 37.5% of samples meeting the EC RWQC. Although not statistically significant, the percentage of samples positive for each STEC marker except stx1 was lower in samples that met, as opposed to exceeded, FIB RWQC. Viable STEC were common members of the FC communities in river water throughout southern Michigan and northern Indiana, regardless of FIB RWQC. Our study indicates that further information on the occurrence of pathogens in recreational waters, and research on alternative indicators of their occurrence, may help inform water-resource management and public health decision-making.

Journal of Environmental Quality↗

USGS2013

Surveillance theory applied to virus detection: a case for targeted discovery

Virus detection and mathematical modeling have gone through rapid developments in the past decade. Both offer new insights into the epidemiology of infectious disease and characterization of future risk; however, modeling has not yet been applied to designing the best surveillance strategies for viral and pathogen discovery. We review recent developments and propose methods to integrate viral and pathogen discovery and mathematical modeling through optimal surveillance theory, arguing for a more targeted approach to novel virus detection guided by the principles of adaptive management and structured decision-making.

Future Virology↗

USGS1941

Blood parasites of birds of the District of Columbia and Patuxent Research Refuge vicinity

Recently a number of surveys of blood parasites of birds have been made in different parts of this country by different workers, the general purpose of which was to further the knowledge of the distribution and pathogenicity of these protozoa. This paper treats the distribution of parasites found in sampling miscellaneous birds of the District of Columbia and vicinity and contains a preliminary report on the more important phase of the problem of pathogenicity.

Maryland↗

USGS1963

Disease and infection in the Tetraonidae

Disease is one of many factors advanced to explain the fluctuations of grouse populations, but no profound study of natural disease losses in Tetraonidae exists. The literature contains frequent references to THE grouse disease, although many potential pathogens are listed in numerous surveys and limited investigations, and the relevant data indicate that no single etiologic agent is universally responsible for disease in grouse. Few experimental infections or related studies on parasite biology have been attempted. Well-trained personnel and specialized facilities are required for research and analysis (1) to develop new methods of interpretation to be used with existing census techniques, (2) to conduct intensive studies of ecological factors of host and habitat, and (3) to establish base lines for recognition of deviations from the norm. Disease in wildlife can be controlled only through management procedures based on information concerning the biology of pathogens, hosts, and environments. It cannot be studied as a separate entity if its impact on survival or population fluctuations of grouse is to be correctly assessed.

Journal of Wildlife Management↗

USGS1987

Microbial infections in a declining wild turkey population in Texas

A survey was conducted at 5 locations in Texas for avian pathogens that might adversely affect wild turkey ( Meleagris gallopavo ) productivity and survival. At 1 site, the Rob and Bessie Welder Wildlife Refuge (WWR), turkeys have declined precipitously in recent years. During the winters of 1983-85, 442 wild turkeys were caught with cannon and drop nets, 161 of these on WWR. Blood samples were drawn for serologic evaluation, and cloacal and tracheal swabs were collected for isolation attempts. Salmonella spp. bacteria, Newcastle disease virus (NDV), and avian influenza virus (AIV) were not detected in any samples tested. Serologic tests for antibodies to NDV and AIV also were negative. Many mycoplasma isolates were recovered from turkeys from every location. Characterization of these isolates indicated that several species were present. None were species typically associated with mycoplasmosis in domestic turkeys, such as Mycoplasma gallisepticum (MG), M. meleagridis (MM), or M. synoviae (MS), although antibodies to these pathogens were detected in turkeys at every location sampled. There was no evidence to link any of these disease causing agents to the decline observed in the population of wild turkeys on the WWR.

Texas↗

USGS2007

Improved husbandry to control an outbreak of rainbow trout fry syndrome caused by infection with Flavobacterium psychrophilum

Case Description - A cohort of 35,200, 13-week-old, female rainbow trout at a fish farm was evaluated because of a 2-week history of anorexia and lethargy and a mortality rate of approximately 100 fish/d. Clinical Findings - Affected fish were lethargic and thin and had disequilibrium, bilateral exophthalmia, pale red gills and kidneys, red-tinged coelomic fluid, and pale brown livers. Some fish were differentially pigmented bilaterally. The presumptive diagnosis was bacterial or viral septicemia. The definitive diagnosis was rainbow trout fry syndrome caused by infection with Flavobacterium psychrophilum. Treatment and Outcome - A strategy for controlling the outbreak based on reducing pathogen numbers in affected tanks and reducing pathogen spread among tanks was developed. The option of treating with antimicrobial-medicated feed was discussed with the farmer, but was declined. After changes were made, mortality rate declined quickly, with no more deaths within 10 days after the initial farm visit. Clinical Relevance - Bacterial coldwater disease is the most common manifestation of infection with F psychrophilum in fingerling and adult rainbow trout. However, the organism can also cause rainbow trout fry syndrome. This condition should be included on a list of differential diagnoses for septicemia in hatchery-reared rainbow trout fry.

Journal of the American Veterinary Medical Associa↗

USGS2019

Screening and biosecurity for White-nose Fungus Pseudogymnoascus destructans (Ascomycota: Pseudeurotiaceae) in Hawai‘i

Introduced pathogens causing emerging infectious diseases (EIDs) are serious contemporary threats to animal, plant, and ecosystem health. The invasive fungus, Pseudogymnoascus destructans , has established populations of European origin in North America, resulting in mass mortality of several hibernating bat species. Extensive monitoring for this pathogen exists in Europe and North America, but limited screening is taking place elsewhere. We report results from cave surveys on Hawai‘i Island. Substrates in 10 lava-tube caves with elevations up to 3,045 m were swabbed providing samples for screening P. destructans . Interior cave air temperatures spanned temperatures suitable for the growth and survival of P. destructans . Using quantitative PCR, all 85 samples tested were negative for the presence of P. destructans . The biology of the Hawaiian hoary bat ( Lasiurus cinereus semotus ) in relation to its unusual use of high elevation caves is discussed because these bats could come into contact with P. destructans should it arrive in Hawai‘i. Large numbers of cave enthusiasts visit Hawaiian caves from across the world after having been inside caves elsewhere including areas with P. destructans . Thus, resource managers in Hawai‘i and other remote areas may want to consider the potential for P. destructans to arrive unintentionally via human activities. Biosecurity measures and periodic screening for P. destructans are especially important in Hawai‘i given the presence of high elevation caves with suitable temperatures for its growth. If P. destructans was introduced to Hawaiian caves, it could affect the local fauna but also act as a source population for colonisations elsewhere.

Hawaii↗

USGS2019

Selected water-quality data from the Cedar River and Cedar Rapids well fields, Cedar Rapids, Iowa, 2008–17

The Cedar River alluvial aquifer is the primary source of municipal water in Cedar Rapids, Iowa. Municipal wells are completed in the alluvial aquifer about 40 to 80 feet below land surface. The City of Cedar Rapids and the U.S. Geological Survey have led a cooperative study of the groundwater-flow system and water quality of the aquifer since 1992. Cooperative reports between the City of Cedar Rapids and the U.S. Geological Survey have documented hydrologic and water-quality data, geochemistry, and groundwater models. Water-quality samples were collected for studies involving well field monitoring, trends, source-water protection, groundwater geochemistry, surface-water–groundwater interaction, and pesticides in groundwater and surface water. Water-quality analyses were completed for major ions (boron, bromide, calcium, chloride, fluoride, iron, magnesium, manganese, potassium, silica, sodium, and sulfate), nutrients (ammonia as nitrogen, ammonia plus organic nitrogen as nitrogen, nitrite plus nitrate as nitrogen, nitrite as nitrogen, orthophosphate as phosphorus, and phosphorus), dissolved organic carbon, selected pesticides, bacteria, and viral pathogens. Physical characteristics (alkalinity, dissolved oxygen, pH, specific conductance, and water temperature) were measured onsite and recorded for each water sample collected. This report presents the results of routine water-quality data-collection activities from water years 2010 through 2017, and additional viral pathogen data from May 2008 to August 2017. A water year is the period from October 1 to September 30 and is designated by the year in which it ends; for example, water year 2015 was from October 1, 2014, to September 30, 2015. Methods of data collection, quality assurance, water-quality analyses, and statistical procedures are presented. Data include the results of water-quality analyses from quarterly sampling from monitoring wells, municipal wells, two water treatment plants, and the Cedar River, as well as monthly nutrient sampling from the Cedar River.

Iowa↗

USGS1998

How do we determine when the beaches are safe for swimming?

The use of Lake Erie and other public waters for swimming is a valuable recreational resource for the people of Ohio and elsewhere in the United States. Water-resource managers and the scientific community have recognized the need for rapid methods to determine the quality of these recreational waters to adequately protect public health. Fecal-indicator bacteria, such as Escherichia coli ( E. coli ) and fecal coliforms, are used to determine the risk of contracting waterborne disease from fecal-contaminated recreational waters. Fecal-indicator bacteria are not necessarily pathogens ( disease-causing organisms), but their presence can indicate the possible presence of pathogens. Although improvements to existing sewage treatment systems are continuously being made in many areas, fecal contamination is still a possibility. Therefore, findings from carefully designed monitoring programs are needed to inform the public on the risk of swimming in fecal-contaminated waters. Current methods to assess the concentrations of fecal indicators-that is, the number of bacteria in a certain volume of water-take at least 24 hours to complete. Due to the long time frame, some scientists have suggested using other water-quality or environmental surrogates (substitutes) to determine these concentrations. The U.S. Geological Survey (USGS) is working to address this concern in a study conducted at three Lake Erie beaches in the Cleveland, Ohio, area. The study has shown that turbidity (the amount of light scattered or absorbed by suspended materials in a water sample), rainfall, and wave height could be used in a statistical model to predict E. coli concentrations.

Ohio↗

USGS2006

Surveillance for Asian H5N1 avian influenza in the United States

Increasing concern over the potential for migratory birds to introduce the Asian H5N1 strain of avian influenza to North America prompted the White House Policy Coordinating Committee for Pandemic Influenza Preparedness to request that the U.S. Departments of Agriculture (USDA) and Interior (DOI) develop a plan for the early detection of highly pathogenic avian influenza (HPAI) in the United States. To promote coordination among wildlife, agriculture, and human health agencies on HPAI surveillance efforts, the two Departments worked with representatives from the U.S. Department of Health and Human Services, the International Association of Fish and Wildlife Agencies, and the Alaska Department of Fish and Game to develop the U.S. Interagency Strategic Plan for Early Detection of Asian H5N1 Highly Pathogenic Avian Influenza in Wild Migratory Birds.

Fact Sheet↗

USGS2007

Avian influenza surveillance of wild birds

The President's National Strategy for Pandemic Influenza directs federal agencies to expand the surveillance of United States domestic livestock and wildlife to ensure early warning of hightly pathogenic avian influenza (HPAI) in the U.S. The immediate concern is a potential introduction of HPAI H5N1 virus into the U.S. The presidential directive resulted in the U.S. Interagency Strategic Plan for Early Detection of H5N1 Highly Pathogenic Avian Influenza in Wild Migratory Birds (referred to as the Wild Bird Surveillance Plan or the Plan).

Fact Sheet↗