Geology topics
Publications and source records attributed to Andrew M. Ramey.
Highly pathogenic avian influenza (HPAI) is an ecologically and economically significant avian disease that is quickly spreading among wild and domestic birds throughout North America. In this blog post, we provide information and resources that can help you to be informed, be prepared, and be ready to take appropriate action should you observe wild birds that may be affected by HPAI.
In this chapter, we provide an overview of antimicrobial resistant (AMR) bacteria in wildlife through the presentation of general trends of occurrence among both captive and free-ranging wild animal populations, discussion of importance to human health and wildlife conservation, and identification of priority areas for future research and monitoring efforts. Once most commonly identified in humans and domestic animals, AMR bacteria have now been reported to be widespread among free-ranging and captive wildlife and the broader environment. Antimicrobial resistance has been identified in wildlife inhabiting nearly every country, region, and habitat type from which samples have been obtained, although occurrence may be more common in animals that occupy anthropogenically impacted environments. Though AMR bacteria identified in free-ranging wildlife have generally not been associated with direct health impacts to the host, specific bacteria and types of resistance found in wildlife may be clinically relevant to humans. Furthermore, AMR bacteria harbored by captive or free-ranging animals may complicate veterinary treatment of captive, rare, or vulnerable wildlife provided care. Future investigations may obtain important information on the acquisition and dissemination of AMR bacteria by wildlife through the comparison of resistance harbored by bacteria from wildlife and the environments they occupy. The identification of specific environmental pathways through which resistance may be acquired would help to guide the development of intervention strategies to interrupt further spread of antimicrobial resistance to, from, and among wildlife. Implications of such strategies may also extend more broadly to promote domestic animal, human, and environmental health.
1. Migratory waterfowl facilitate long distance dispersal of zoonotic pathogens and are increasingly recognized as contributing to the geographic spread of avian influenza viruses (AIV). AIV are globally distributed and have the potential to produce highly contagious poultry disease, economically impact both large-scale and backyard poultry producers, and raise the specter of epidemics and pandemics in human populations. 2. Because migratory waterfowl behavior varies across multiple spatial and temporal scales, the timing and distribution of wild bird AIV introductions to poultry are also heterogeneous in time and space. To help reduce economic impacts to the poultry industry and enable poultry producers to better anticipate when and where poultry outbreaks may occur, it is critically important to consider the movement ecology of the waterfowl species transporting and transmitting AIV. 3. We used telemetry for a geographically widespread and common AIV host, blue-winged teal ( Spatula discors ; BWTE), to model reservoir host movement states with respect to backyard and commercial poultry facilities in the United States. Our modeling framework enabled us to estimate wild bird proximity to poultry facilities while concurrently assessing the influence of poultry facilities on BWTE movement state transition. Our primary objective was to estimate the likelihood of duck and poultry overlap by estimating when and where BWTE were geographically closest to poultry. 4. Synthesis and applications . Migratory waterfowl facilitate dispersal of the avian influenza viruses that cause highly contagious poultry disease. Movement analysis of blue-winged teal indicates that spatio-temporal overlap between wild birds and poultry facilities varies by season, the poultry type produced (e.g., turkey, chicken), and if the facility is a commercial or backyard operation. These findings are broadly applicable to disease ecology research and can be applied by poultry producers to improve bio-security, enhance poultry management, and prioritize disease surveillance efforts.
Prior assessments support wildlife as indicators of anthropogenically influenced antimicrobial resistance across the landscape. A ground-breaking new study suggests that wildlife may also provide information on antimicrobial resistance in the environment through time.
Emperor Geese ( Anser canagicus ) are iconic waterfowl endemic to Alaska and adjacent areas of northeastern Russia that are considered to be near threatened by the International Union for Conservation. This species has been identified as harboring diverse viruses and parasites which have, at times, been associated with disease in other avian taxa. To better assess if disease represents a vulnerability for Emperor Geese breeding on the Yukon-Kuskokwim Delta, Alaska, we evaluated if haemosporidian parasites were associated with decreased mass or survival among adult female nesting birds captured during 2006–2016. Through molecular analyses, we detected genetically diverse Leucocytozoon , Haemoproteus , and Plasmodium parasites in 28%, 1%, and 1% of 607 blood samples screened in triplicate, respectively. Using regression analysis, we found evidence for a small effect of Leucocytozoon infection on the mass of incubating adult female Emperor Geese. The estimated mass of infected individuals was approximately 43 g (95% CI: 20–67 g), or approximately 2%, less than uninfected birds when captured during the second half of incubation (days 11–25). We did not, however, find support for an effect of Leucocytozoon infection on survival of adult female nesting Emperor Geese using a multi-state hidden Markov framework to analyze mark-resight and recapture data. Using parasite mitochondrial DNA cytochrome b sequences, we identified 23 haplotypes among infected Emperor Geese. Leucocytozoon haplotypes clustered into three phylogenetically supported clades designated as ‘ L. simondi clade A’, ‘ L. simondi clade B’, and ‘other Leucocytozoon ’. We did not find evidence that parasites assigned to any of these clades were associated with differential mass measures among nesting adult female Emperor Geese. Collectively, our results provide negligible evidence for Leucocytozoon parasites as causing detrimental effects to adult female Emperor Geese breeding on the Yukon-Kuskokwim Delta.
Objectives Wildlife may harbor clinically important antimicrobial resistant (AMR) bacteria, but the role of wildlife in the epidemiology of AMR bacterial infections in humans is largely unknown. In this study, we aimed to assess dissemination of the bla KPC carbapenemase gene among humans and gulls in Alaska. Methods We performed whole genome sequencing to determine the genetic context of bla KPC in bacterial isolates from all four human carbapenemase-producing Enterobacteriaceae (CPE) infections reported in Alaska between 2013–2018 and to compare sequences to seven previously reported CPE isolates from gull feces within the same region and time period. Results Genomic analysis of CPE isolates suggested independent acquisition events among humans with no evidence for direct transmission of bla KPC between people and gulls. However, some isolates shared conserved genetic elements surrounding bla KPC , suggesting possible exchange between species. Conclusions Our results highlight the genomic plasticity associated with bla KPC and demonstrate that sampling of wildlife may be useful for identifying clinically relevant antimicrobial resistance not observed through local passive surveillance in humans.
Anthropogenic inputs into the environment may serve as sources of antimicrobial resistant bacteria and alter the ecology and population dynamics of synanthropic wild animals by providing supplemental forage. In this study, we used a combination of phenotypic and genomic approaches to characterize antimicrobial resistant indicator bacteria, animal telemetry to describe host movement patterns, and a novel modeling approach to combine information from these diverse data streams to investigate the acquisition and long-distance dispersal of antimicrobial resistant bacteria by landfill-foraging gulls. Our results provide evidence that gulls acquire antimicrobial resistant bacteria from anthropogenic sources, which they may subsequently disperse across and between continents via migratory movements. Furthermore, we introduce a flexible modeling framework to estimate the relative dispersal risk of antimicrobial resistant bacteria in western North America and adjacent areas within East Asia, which may be adapted to provide information on the risk of dissemination of other organisms and pathogens maintained by wildlife through space and time.
We sequenced the coding-complete genome of an avian orthoavulavirus serotype 16 (AOAV-16) isolate recovered from emperor goose ( Anser canagicus ) feces collected in Alaska. The detection of AOAV-16 in North America and genomic sequencing of the resultant isolate confirms that the geographic distribution of this virus extends beyond Asia.
Haemosporidian parasites may impact avian health and are subject to shifts in distribution and abundance with changing ecologic conditions. Therefore, understanding variation in parasite prevalence is important for evaluating biologically meaningful changes in infection patterns and associated population level impacts. Previous research in western Alaska, US, indicated a possible increase in Leucocytozoon spp. infection between Emperor Geese ( Anser canagicus ) sampled in 1996 (<1%, n =134) and during 2011–12 (19.9%, 95% confidence interval [CI]: 3.0–36.8%, n =77); however, different detection methods were used for these estimates. Prior research in this same region identified a lack of Leucocytozoon spp. parasites (0%, n =117) in sympatrically breeding Cackling Geese ( Branta hutchinsii minima ) in 2011. We molecularly screened blood samples collected from sympatrically breeding Emperor and Cackling Geese in western Alaska during additional breeding seasons to better assess temporal and species-specific variation in the prevalence of blood parasites. We found similar prevalence estimates for Leucocytozoon spp. parasites in Emperor Goose blood samples collected in 1998 and 2014, suggesting consistent infection of Emperor Geese with blood parasites at these time points. Using samples from sympatric geese sampled during 2014, we found evidence for a higher incidence of parasites among Emperor Geese (20.3%, 95% CI: 11.8–32.7%) compared to Cackling Geese (3.6%, 95% CI: 1.1–11.0%), reinforcing the previous finding of species-specific differences in infection. Furthermore, we detected Leucocytozoon , Haemoproteus , and Plasmodium spp. blood parasites in unflighted goslings of both species, supporting the possible transmission of these parasites at western Alaska breeding grounds. Our results help to clarify that prevalence of Leucocytozoon spp. parasites have probably remained consistent among Emperor Geese breeding in western Alaska since the late 1990s and that this species may disproportionally harbor Leucocytozoon spp. compared to sympatrically breeding Cackling Geese.
In this investigation, we used a combination of field- and laboratory-based approaches to assess if influenza A viruses (IAVs) shed by ducks could remain viable for extended periods in surface water within three wetland complexes of North America. In a field experiment, replicate filtered surface water samples inoculated with duck swabs were tested for IAVs upon collection and again after an overwintering period of approximately 6–7 months. Numerous IAVs were molecularly detected and isolated from these samples, including replicates maintained at wetland field sites in Alaska and Minnesota for 181–229 days. In a parallel laboratory experiment, we attempted to culture IAVs from filtered surface water samples inoculated with duck swabs from Minnesota each month during September 2018–April 2019 and found monthly declines in viral viability. In an experimental challenge study, we found that IAVs maintained in filtered surface water within wetlands of Alaska and Minnesota for 214 and 226 days, respectively, were infectious in a mallard model. Collectively, our results support surface waters of northern wetlands as a biologically important medium in which IAVs may be both transmitted and maintained, potentially serving as an environmental reservoir for infectious IAVs during the overwintering period of migratory birds.
Highly pathogenic avian influenza (HPAI) viruses of the H5 A/goose/Guangdong/1/96 lineage can cause severe disease in poultry and wild birds, and occasionally in humans. In recent years, H5 HPAI viruses of this lineage infecting poultry in Asia have spilled over into wild birds and spread via bird migration to countries in Europe, Africa, and North America. In 2016/2017, this spillover resulted in the largest HPAI epidemic on record in Europe and was associated with an unusually high frequency of reassortments between H5 HPAI viruses and cocirculating low-pathogenic avian influenza viruses. Here, we show that the seven main H5 reassortant viruses had various combinations of gene segments 1, 2, 3, 5, and 6. Using detailed time-resolved phylogenetic analysis, most of these gene segments likely originated from wild birds and at dates and locations that corresponded to their hosts’ migratory cycles. However, some gene segments in two reassortant viruses likely originated from domestic anseriforms, either in spring 2016 in east China or in autumn 2016 in central Europe. Our results demonstrate that, in addition to domestic anseriforms in Asia, both migratory wild birds and domestic anseriforms in Europe are relevant sources of gene segments for recent reassortant H5 HPAI viruses. The ease with which these H5 HPAI viruses reassort, in combination with repeated spillovers of H5 HPAI viruses into wild birds, increases the risk of emergence of a reassortant virus that persists in wild bird populations yet remains highly pathogenic for poultry.
In 2015, the mcr-1 gene was discovered in Escherichia coli in domestic swine in China that conferred resistance to colistin, an antibiotic of last resort used in treating multi-drug resistant bacterial infections in humans. Since then, mcr-1 was found in other human and animal populations, including wild gulls. Because gulls could disseminate the mcr-1 gene, we conducted an experiment to assess whether gulls are readily colonized with mcr-1 positive E. coli, their shedding patterns, transmission among conspecifics, and environmental deposition. Shedding of mcr-1 E. coli by small gull flocks followed a lognormal curve and gulls shed one strain >101 log10 CFU/g in their feces for 16.4 days, which persisted in the environment for 29.3 days. Because gulls are mobile and can shed antimicrobial-resistant bacteria for extended periods, gulls may facilitate transmission of mcr-1 positive E. coli to humans and livestock through fecal contamination of water, public areas and agricultural operations.
Understanding influenza A virus (IAV) persistence in wetlands is limited by a paucity of field studies relating to the maintenance of infectivity over time. The duration of IAV infectivity in water has been assessed under variable laboratory conditions, but results are difficult to translate to more complex field conditions. We tested a field-based method to assess the viability of IAVs in an Alaska wetland during fall and winter which incorporated physical and chemical properties of the waterbody in which samples were held. Filtered pond water was inoculated with avian fecal samples collected from the environment, aliquoted into a series of duplicate sealed vials and submerged back in the wetland for up to 132 days (October 2018–March 2019). Sample aliquots were sequentially recovered and tested for IAVs by rRT-PCR and virus isolation. One sample remained rRT-PCR positive for the duration of the study and virus isolation positive for 118 days. The surrounding water temperature was 1°–6 °C with near neutral pH (6.6–7.3) for the duration of the study. This proof of concept study demonstrates a protocol for testing the persistence of infectious IAV naturally shed from waterfowl under ambient environmental conditions.
Alaska represents a globally important region for the ecology of avian-origin influenza A viruses (IAVs) given expansive wetlands in this region which serve as habitat for numerous hosts of IAVs that disperse among four continents during the annual cycle. Extensive sampling of wild birds for IAVs in Alaska since 1991 has greatly extended inference regarding intercontinental viral exchange between North America and East Asia and the importance of Beringian endemic species to IAV ecology within this region. Data on IAVs in aquatic birds inhabiting Alaska has also been useful for helping to establish global patterns of prevalence in wild birds and viral dispersal across the landscape. In this review, we summarize main findings from investigations of IAVs in wild birds and wetlands of Alaska with the aim of providing readers with an understanding of viral ecology within this region. More specifically, we review viral detections, evidence of IAV exposure, and genetic characterization of isolates derived from wild bird samples collected in Alaska by host taxonomy. Additionally, we provide a short overview of wetland complexes within Alaska that may be important to IAV ecology at the continental scale.
The proliferation of antibiotic resistant bacteria in the environment has potential negative economic and health consequences. Thus, previous investigations have targeted wild animals to understand the occurrence of antibiotic resistance in diverse environmental sources. In this critical review and synthesis, we summarize important concepts learned through the sampling of wildlife for antibiotic resistant indicator bacteria. These concepts are helpful for understanding dissemination of resistance through environmental pathways and helping to guide future research efforts. Our review is comprised of six sections. The first section briefly introduces antibiotic resistance as it pertains to bacteria harbored in environmental sources such as wild animals. Next, we differentiate wildlife from other animals in the context of how diverse taxa provide different information on antibiotic resistance in the environment. In the third section, we identify representative research and seminal works that illustrate important associations between the occurrence of antibiotic resistant bacteria in wildlife and anthropogenic inputs into the environment. For example, we highlight numerous investigations that support the premise that anthropogenic inputs into the environment drive the occurrence of antibiotic resistance in bacteria harbored by free-ranging wildlife. Additionally, we summarize previous research demonstrating foraging as a mechanism by which wildlife may be exposed to anthropogenic antibiotic resistance contamination in the environment. In the fourth section of our review, we summarize molecular evidence for the acquisition and dissemination of resistance among bacteria harbored by wildlife. In the fifth section, we identify what we believe to be important data gaps and potential future directions that other researchers may find useful towards the development of efficient, informative, and impactful investigations of antibiotic resistant bacteria in wildlife. Finally, we conclude our review by highlighting the need to move from surveys that simply identify antibiotic resistant bacteria in wildlife towards hypothesis-driven investigations that: (1) identify point sources of antibiotic resistance; (2) provide information on risk to human and animal health; (3) identify interventions that may interrupt environmentally mediated pathways of antibiotic resistance acquisition/transmission; and (4) evaluate whether management practices are leading to desirable outcomes.
For pathogens known to transmit across host species, strategic investment in disease control requires knowledge about where and when spillover transmission is likely. One approach to estimating spillover is to directly correlate observed spillover events with covariates. An alternative is to mechanistically combine information on host density, distribution, and pathogen prevalence to predict where and when spillover events are expected to occur. We use several case studies at the wildlife-livestock disease interface to highlight the challenges, and potential solutions, to estimating spatio-temporal variation in spillover risk. Datasets on multiple host species often do not align in space, time or resolution, and may have no estimates of observation error. Linking these datasets requires they be related to a common spatial and temporal resolution and appropriately propagating errors in predictions can be difficult. Hierarchical models are one potential solution, but for fine-resolution predictions at broad spatial scales many models become computationally challenging. Despite these limitations, the confrontation of mechanistic predictions with observed events is an important avenue for developing a better understanding of pathogen spillover. Systems where data have been collected at all levels in the spillover process are rare, or non-existent, and require investment and sustained effort across disciplines.
We tested extended‐spectrum β‐lactamase producing bacteria from wild gulls ( Larus spp.) sampled in 2009 for the presence of mcr ‐1. We report the detection of mcr ‐1 and describe genome characteristics of four Escherichia coli and one Klebsiella pneumoniae isolate from Spain and Portugal that also exhibited colistin resistance. Results represent the earliest evidence for colistin‐resistant bacteria in European wildlife.
Emperor geese ( Anser canagicus ) are endemic to coastal areas within Beringia and have previously been found to have antibodies to or to be infected with influenza A viruses (IAVs) in Alaska. In this study, we use virological, serological and tracking data to further elucidate the role of emperor geese in the ecology of IAVs in Beringia during the non‐breeding period. Specifically, we assess evidence for: (a) active IAV infection during spring staging, autumn staging and wintering periods; (b) infection with novel Eurasian‐origin or interhemispheric reassortant viruses; (c) contemporary movement of geese between East Asia and North America; (d) previous exposure to viruses of 14 haemagglutinin subtypes, including Eurasian lineage highly pathogenic (HP) H5 IAVs; and (e) subtype‐specific antibody seroconversion and seroreversion. Emperor geese were found to shed IAVs, including interhemispheric reassortant viruses, throughout the non‐breeding period; migrate between Alaska and the Russian Far East prior to and following remigial moult; have antibodies reactive to a diversity of IAVs including, in a few instances, Eurasian lineage HP H5 IAVs; and exhibit relatively broad and stable patterns of population immunity among breeding females. Results of this study suggest that emperor geese may play an important role in the maintenance and dispersal of IAVs within Beringia during the non‐breeding period and provide information that may be used to further optimize surveillance activities focused on the early detection of Eurasian‐origin IAVs in North America.