Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.

Infection-nutrition feedbacks: fat supports pathogen clearance but pathogens reduce fat in a wild mammal

Though far less obvious than direct effects (clinical disease or mortality), the indirect influences of pathogens are difficult to estimate but may hold fitness consequences. Here, we disentangle the directional relationships between infection and energetic reserves, evaluating the hypotheses that energetic reserves influence infection status of the host and that infection elicits costs to energetic reserves. Using repeated measures of fat reserves and infection status in individual bighorn sheep (Ovis canadensis) in the Greater Yellowstone Ecosystem, we documented that fat influenced ability to clear pathogens (Mycoplasma ovipneumoniae) and infection with respiratory pathogens was costly to fat reserves. Costs of infection approached, and in some instances exceeded, costs of rearing offspring to independence in terms of reductions to fat reserves. Fat influenced probability of clearing pathogens, pregnancy and over-winter survival; from an energetic perspective, an animal could survive for up to 23 days on the amount of fat that was lost to high levels of infection. Cost of pathogens may amplify trade-offs between reproduction and survival. In the absence of an active outbreak, the influence of resident pathogens often is overlooked. Nevertheless, the energetic burden of pathogens likely has consequences for fitness and population dynamics, especially when food resources are insufficient.

Evaluating the transmission dynamics and host competency of aoudad (Ammotragus lervia) experimentally infected with Mycoplasma ovipneumoniae and leukotoxigenic Pasteurellaceae

Feral populations of aoudad (Ammotragus lervia) occur in Texas bighorn sheep (Ovis canadensis) habitat and pose several conceptual ecological threats to bighorn sheep re-establishment efforts. The potential threat of disease transmission from aoudad to bighorn sheep may exacerbate these issues, but the host competency of aoudad and subsequent pathophysiology and transmissibility of pneumonic pathogens involved in the bighorn sheep respiratory disease complex is largely unknown. Because the largest population-limiting diseases of bighorn sheep involve pathogens causing bronchopneumonia, we evaluated the host competency of aoudad for Mycoplasma ovipneumoniae and leukotoxigenic Pasteurellaceae. Specifically, we described the shedding dynamics, pathogen carriage, seroconversion, clinical patterns, and pathological effects of experimental infection among wild aoudad held in captivity. We found that aoudad are competent hosts capable of maintaining and intraspecifically transmitting Mycoplasma ovipneumoniae and Pasteurellaceae and can shed the bacteria for 53 days after exposure. Aoudad developed limited clinical signs and pathological findings ranged from mild chronic lymphohistiocytic bronchointerstitial pneumonia to severe and acute suppurative pneumonia, similarly, observed in bighorn sheep infected with Mycoplasma spp. and Pasteurellaceae bacteria, respectively. Furthermore, as expected, clinical signs and lesions were often more severe in aoudad inoculated with a combination of Mycoplasma ovipneumoniae and Pasteurellaceae as compared to aoudad inoculated with only Mycoplasma ovipneumoniae. There may be evidence of interindividual susceptibility, pathogenicity, and/or transmissibility, indicated by individual aoudad maintaining varying severities of chronic infection who may be carriers continuously shedding pathogens. This is the first study to date to demonstrate that aoudad are a conceptual disease transmission threat to sympatric bighorn sheep populations due to their host competency and intraspecific transmission capabilities.

Pathology of Chronic Mycoplasma ovipneumoniae Carriers in a Declining Bighorn Sheep (Ovis canadensis) Population

Bighorn sheep (Ovis canadensis) across North America commonly experience population-limiting epizootics of respiratory disease. Although many cases of bighorn sheep pneumonia are polymicrobial, Mycoplasma ovipneumoniae is most frequently associated with all-age mortality events followed by years of low recruitment. Chronic carriage of M. ovipneumoniae by adult females serves as a source of exposure of naïve juveniles; relatively few ewes may be responsible for maintenance of infection within a herd. Test-and-remove strategies focused on removal of adult females with evidence of persistent or intermittent shedding (hereafter chronic carriers) may reduce prevalence and mitigate mortality. Postmortem confirmation of pneumonia in chronic carriers has been inadequately reported and the pathology has not been thoroughly characterized, limiting our understanding of important processes shaping the epidemiology of pneumonia in bighorn sheep. Here we document postmortem findings and characterize the lesions of seven ewes removed from a declining bighorn sheep population in Wyoming, USA, following at least two antemortem detections of M. ovipneumoniae within a 14-mo period. We confirmed that 6/7 (85.7%) had variable degrees of chronic pneumonia. Mycoplasma ovipneumoniae was detected in the lung of 4/7 (57.1%) animals postmortem. Four (57.1%) had paranasal sinus masses, all of which were classified as inflammatory, hyperplastic lesions. Pasteurella multocida was detected in all seven (100%) animals, while Trueperella pyogenes was detected in 5/7 (71.4%). Our findings indicate that not all chronic carriers have pneumonia, nor do all have detectable M. ovipneumoniae in the lung. Further, paranasal sinus masses are a common but inconsistent finding, and whether sinus lesions predispose to persistence or result from chronic carriage remains unclear. Our findings indicate that disease is variable in chronic M. ovipneumoniae carriers, underscoring the need for further efforts to characterize pathologic processes and underlying mechanisms in this system to inform management.

Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)

With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer (Odocoileus virginianus) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (Mycoplasma ovipneumoniae, Trueperella pyogenes, Pasteurella multocida, Anaplasma phagocytophilum, Fusobacterium necrophorum); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.

Bighorn sheep associations: understanding tradeoffs of sociality and implications for disease transmission

Sociality directly influences mating success, survival rates, and disease, but ultimately likely evolved for its fitness benefits in a challenging environment. The tradeoffs between the costs and benefits of sociality can operate at multiple scales, resulting in different interpretations of animal behavior. We investigated the influence of intrinsic (e.g., relatedness, age) and extrinsic factors (e.g., land cover type, season) on direct contact (simultaneous GPS locations ≤ 25 m) rates of bighorn sheep (Ovis canadensis) at multiple scales near the Waterton-Glacier International Peace Park. During 2002-2012, male and female bighorn were equipped with GPS collars. Indirect contact (GPS locations ≤ 25 m regardless of time) networks identified two major breaks whereas direct contact networks identified an additional barrier in the population, all of which corresponded with prior disease exposure metrics. More direct contacts occurred between same-sex dyads than female-male dyads and between bighorn groups with overlapping summer home ranges. Direct contacts occurred most often during the winter-spring season when bighorn traveled at low speeds and when an adequate number of bighorn were collared in the area. Direct contact probabilities for all dyad types were inversely related to habitat quality, and differences in contact probability were driven by variables related to survival such as terrain ruggedness, distance to escape terrain, and canopy cover. We provide evidence that probabilities of association are higher when there is greater predation risk and that contact analysis provides valuable information for understanding fitness tradeoffs of sociality and disease transmission potential.

Restoration of bighorn sheep: History, successes, and remaining conservation issues

Mammals are imperiled worldwide, primarily from habitat loss or modification, and exhibit downward trends in their populations and distributions. Likewise, large-bodied herbivores have undergone a collapse in numbers and are at the highest extinction risk of all mammals. Bighorn sheep (Ovis canadensis) are among those large-bodied herbivores that possess a slow-paced life history, suffer from debilitating diseases, and have experienced range contractions across their historical distribution since the late 1800s. Translocations and reintroductions of these mountain ungulates are key aspects of restoration and often are used to re-establish populations in historical habitat or to supplement declining herds. Millions of US dollars and much effort by state and federal natural resource agencies, as well as public and private organizations, have been expended to restore bighorn sheep. Despite those efforts, translocated populations of bighorn sheep have not always been successful. We assessed restoration of bighorn sheep to provide insights in the context of conservation of populations of bighorn sheep, because this management tool is a frequently used to re-establish populations. We focused briefly on past efforts to restore bighorn sheep populations and followed with updates on the value of habitat enhancements, genetic issues, the importance of ecotypic or phenotypic adaptations when restoring populations, predation, and disease transmission. We also raised issues and posed questions that have potential to affect future decisions regarding the restoration of bighorn sheep. This information will help conservationists improve the success of conserving these iconic large mammals.

Animal movement and associated infectious disease risk in a metapopulation

Animal movements among habitat patches or populations are important for maintaining long-term genetic and demographic viability, but connectivity may also facilitate disease spread and persistence. Understanding factors that influence animal movements is critical to understanding potential transmission risk and persistence of communicable disease in spatially structured systems. We evaluated effects of sex, age and Mycoplasma ovipneumoniae infection status at capture on intermountain movements and seasonal movement rates observed in desert bighorn sheep (Ovis canadensis nelsoni) using global positioning system collar data from 135 individuals (27 males, 108 females) in 14 populations between 2013 and 2018, following a pneumonia outbreak linked to the pathogen M. ovipneumoniae in the Mojave Desert, California, USA. Based on logistic regression analysis, intermountain movements were influenced by sex, age and most notably, infection status at capture: males, older animals and uninfected individuals were most likely to make such movements. Based on multiple linear regression analysis, females that tested positive for M. ovipneumoniae at capture also had lower mean daily movement rates that were further influenced by season. Our study provides empirical evidence of a pathogenic infection decreasing an individual's future mobility, presumably limiting that pathogen's ability to spread, and ultimately influencing transmission risk within a spatially structured system.

Population connectivity patterns of genetic diversity, immune responses and exposure to infectious pneumonia in a metapopulation of desert bighorn sheep

Habitat fragmentation is an important driver of biodiversity loss and can be remediated through management actions aimed at maintenance of natural connectivity in metapopulations. Connectivity may protect populations from infectious diseases by preserving immunogenetic diversity and disease resistance. However, connectivity could exacerbate the risk of infectious disease spread across vulnerable populations. We tracked the spread of a novel strain of Mycoplasma ovipneumoniae in a metapopulation of desert bighorn sheep Ovis canadensis nelsoni in the Mojave Desert to investigate how variation in connectivity among populations influenced disease outcomes. M. ovipneumoniae was detected throughout the metapopulation, indicating that the relative isolation of many of these populations did not protect them from pathogen invasion. However, we show that connectivity among bighorn sheep populations was correlated with higher immunogenetic diversity, a protective immune response and lower disease prevalence. Variation in protective immunity predicted infection risk in individual bighorn sheep and was associated with heterozygosity at genetic loci linked to adaptive and innate immune signalling. Together, these findings may indicate that population connectivity maintains immunogenetic diversity in bighorn sheep populations in this system and has direct effects on immune responses in individual bighorn sheep and their susceptibility to infection by a deadly pathogen. Our study suggests that the genetic benefits of population connectivity could outweigh the risk of infectious disease spread and supports conservation management that maintains natural connectivity in metapopulations.

Mycoplasma ovipneumoniae: A Most Variable Pathogen

Mycoplasma ovipneumoniae, a well-established respiratory pathogen of sheep and goats, has gained increased importance recently because of its detection in wild ruminants including members of the Cervidae family. Despite its frequent isolation from apparently healthy animals, it is responsible for outbreaks of severe respiratory disease which are often linked to infections with multiple heterologous strains. Furthermore, M. ovipneumoniae is characterized by an unusually wide host range, a high degree of phenotypic, biochemical, and genomic heterogeneity, and variable and limited growth in mycoplasma media. A number of mechanisms have been proposed for its pathogenicity, including the production of hydrogen peroxide, reactive oxygen species production, and toxins. It shows wide metabolic activity in vitro, being able to utilize substrates such as glucose, pyruvate, and isopropanol; these patterns can be used to differentiate strains. Treatment of infections in the field is complicated by large variations in the susceptibility of strains to antimicrobials, with many showing high minimum inhibitory concentrations. The lack of commercially available vaccines is probably due to the high cost of developing vaccines for diseases in small ruminants not presently seen as high priority. Multiple strains found in affected sheep and goats may also hamper the development of effective vaccines. This review summarizes the current knowledge and identifies gaps in research on M. ovipneumoniae, including its epidemiology in sheep and goats, pathology and clinical presentation, infection in wild ruminants, virulence factors, metabolism, comparative genomics, genotypic variability, phenotypic variability, evolutionary mechanisms, isolation and culture, detection and identification, antimicrobial susceptibility, variations in antimicrobial susceptibility profiles, vaccines, and control.

Pathogen surveillance and epidemiology in endangered Peninsular bighorn sheep (Ovis canadensis nelsoni)

Peninsular bighorn sheep (Ovis canadensis nelsoni) are found exclusively in Southern California and Baja Mexico. They are federally endangered due to multiple threats, including introduced infectious disease. From 1981 - 2017, we conducted surveillance for 16 pathogens and estimated population sizes, adult survival, and lamb survival. We used mixed effects regression models to assess disease patterns at the individual and population levels. Pathogen infection/exposure prevalence varied both spatially and temporally. Our findings indicate that the primary predictor of individual pathogen infection/exposure was the region in which an animal was captured, implying that transmission is driven by local ecological or behavioral factors. Higher Mycoplasma ovipneumoniae seropositivity was associated with lower lamb survival, consistent with lambs having high rates of pneumonia-associated mortality, which may be slowing population recovery. There was no association between M. ovipneumoniae and adult survival. Adult survival was positively associated with population size and parainfluenza-3 virus seroprevalence in the same year, and orf virus seroprevalence in the previous year. Peninsular bighorn sheep are recovering from small population sizes in a habitat of environmental extremes, compounded by infectious disease. Our research can help inform future pathogen surveillance and population monitoring for the long-term conservation of this population.

The first Mycoplasma ovipneumoniae recovered from a sheep with respiratory disease in Brazil - draft genome and genomic analysis

Mycoplasma ovipneumoniae is an important etiological agent of sheep respiratory disease worldwide. Here, we describe the first isolation and draft genome sequence of M. ovipneumoniae strain USP-BR2017 retrieved from tracheobronchial lavage of a sheep showing clinical signs of respiratory disease in the Rio de Janeiro State, Brazil. The culture of tracheobronchial lavage resulted in glucose-fermenting fried egg colonies, which were identified as M. ovipneumoniae by polymerase chain reaction. The genome was sequenced using the Illumina NextSeq 2000 and de novo assembled using SPAdes. The genome of the sequenced organism presented an approximate size of 1,122,253 bp. The annotation revealed 773 coding DNA sequences (CDSs), 806 genes, three rRNAs, and 30 tRNAs. Data analysis revealed M. ovipneumoniae strain USP-BR2017 contains a few virulence genes, including the hemolysing C gene (hlyC). In addition, strain USP-BR2017 showed high identity over the 16S rRNA gene with other sheep isolates from China and United States. This first description of M. ovipneumoniae in diseased Brazilian sheep demonstrates the importance of continuous surveillance and diagnostics of pathogens causing respiratory disease in sheep in Brazil.

Using transcriptomics to predict and visualize disease status in bighorn sheep (Ovis canadensis)

Increasing risk of pathogen spillover coupled with overall declines in wildlife population abundance in the Anthropocene make infectious disease a relevant concern for species conservation worldwide. While emerging molecular tools could improve our diagnostic capabilities and give insight into mechanisms underlying wildlife disease risk, they have rarely been applied in practice. Here, employing a previously reported gene transcription panel of common immune markers to track physiological changes, we present a detailed analysis over the course of both acute and chronic infection in one wildlife species where disease plays a critical role in conservation, bighorn sheep (Ovis canadensis). Differential gene transcription patterns distinguished between infection statuses over the course of acute infection and differential correlation (DC) analyses identified clear changes in gene co-transcription patterns over the early stages of infection, with transcription of four genes-TGFb, AHR, IL1b and MX1-continuing to increase even as transcription of other immune-associated genes waned. In a separate analysis, we considered the capacity of the same gene transcription panel to aid in differentiating between chronically infected animals and animals in other disease states outside of acute disease events (an immediate priority for wildlife management in this system). We found that this transcription panel was capable of accurately identifying chronically infected animals in the test dataset, though additional data will be required to determine how far this ability extends. Taken together, our results showcase the successful proof of concept and breadth of potential utilities that gene transcription might provide to wildlife disease management, from direct insight into mechanisms associated with differential disease response to improved diagnostic capacity in the field.

Multilocus Sequence Typing of Mycoplasma ovipneumoniae Detected in Dall's Sheep (Ovis dalli dalli) and Caribou (Rangifer tarandus grantii) in Alaska, USA

In 2018, Mycoplasma ovipneumoniae was detected in free-ranging caribou (Rangifer tarandus grantii) and Dall's sheep (Ovis dalli dalli) in Alaska, US. Evaluation of additional nasal swabs and archived tissues for M. ovipneumoniae suggested that this bacterium was widespread geographically and temporally in populations of both species. Multilocus sequence typing of four loci identified a single, novel, apparently stable strain type of M. ovipneumoniae in 11 Dall's sheep and 15 caribou in multiple populations across Alaska sampled over a period of 15 yr (2004-19). This strain type differs from those detected to date from wild or domestic sheep (Ovis aries) or goats (Capra aegagrus hircus) tested in Alaska or the lower 48 states. Although the population health implications of this strain are unknown, it has not been associated with population-wide mortality events. The presence of this strain does not decrease the potential risk from the introduction of a pathogenic M. ovipneumoniae strain associated with severe disease in other wildlife populations; therefore, continued monitoring for signs of disease and additional strains is important.

PATHOGEN SURVEY AND PREDICTORS OF LYMPHOPROLIFERATIVE DISEASE VIRUS INFECTION IN WILD TURKEYS (MELEAGRIS GALLOPAVO)

Growing populations of Wild Turkeys (Meleagris gallopavo) may result in increased disease transmission among wildlife and spillover to poultry. Lymphoproliferative disease virus (LPDV) is an avian retrovirus that is widespread in Wild Turkeys of eastern North America, and infections may influence mortality and parasite co-infections. We aimed to identify individual and spatial risk factors of LPDV in Maine's Wild Turkeys. We also surveyed for co-infections between LPDV and reticuloendotheliosis virus (REV), Mycoplasma gallisepticum, and Salmonella pullorum to estimate trends in prevalence and examine covariance with LPDV. From 2017 to 2020, we sampled tissues from hunter-harvested (n=72) and live-captured (n=627) Wild Turkeys, in spring and winter, respectively, for molecular detection of LPDV and REV. In a subset of captured individuals (n=235), we estimated seroprevalence of the bacteria M. gallisepticum and S. pullorum using a plate agglutination test. Infection rates for LPDV and REV were 59% and 16% respectively, with a co-infection rate of 10%. Seroprevalence for M. gallisepticum and S. pullorum were 74% and 3.4%, with LPDV co-infection rates of 51% and 2.6%, respectively. Infection with LPDV and seroprevalence of M. gallisepticum and S. pullorum decreased, whereas REV infection increased, between 2018 and 2020. Females (64%), adults (72%), and individuals sampled in spring (76%) had higher risks of LPDV infection than males (47%), juveniles (39%), and individuals sampled in winter (57%). Furthermore, LPDV infection increased with percent forested cover (β=0.014±0.007) and decreased with percent agriculture cover for juveniles (β=-0.061±0.018) sampled in winter. These data enhance our understanding of individual and spatial predictors of LPDV infection in Wild Turkeys and aid in assessing the associated risk to Wild Turkey populations and poultry operations.

SOURCE AND SEASONALITY OF EPIZOOTIC MYCOPLASMOSIS IN FREE-RANGING PRONGHORN (ANTILOCAPRA AMERICANA)

Mycoplasma bovis is an economically important bacterial pathogen of cattle (Bos taurus) and bison (Bison bison) that most commonly causes pneumonia, polyarthritis, and mastitis. It is prevalent in cattle and ranched bison; however, infections in other species are rare. In early 2019, we identified M. bovis in free-ranging pronghorn (Antilocapra americana) in northeastern Wyoming. Here, we report on additional pronghorn mortalities caused by M. bovis, in the same approximately 120-km2 geographic region 1 yr later. Genetic analysis by multilocus sequence typing revealed that the mortalities were caused by the same M. bovis sequence type, which is unique among all sequence types documented thus far in North America. To explore whether pronghorn maintain chronic infections and begin assessing M. bovis status in other sympatric species, we used PCR testing of nasal swabs to opportunistically survey select free-ranging ungulates. We found no evidence of subclinical infections in 13 pronghorn sampled from the outbreak area (upper 95% binomial confidence limit [bCL], ∼24.7%) or among 217 additional pronghorn (upper 95% bCL, ∼1.7%) sampled from eight additional counties in Wyoming and 10 in Montana. All mule deer (Odocoileus hemionus; n=231; upper 95% bCL, ∼1.6%) sampled from 11 counties in Wyoming also were PCR negative. To assess the potential for environmental transmission, we examined persistence of M. bovis in various substrates and conditions. Controlled experiments revealed that M. bovis can remain viable for 6 h in shaded water and 2 h in direct sunlight. Our results indicate that environmental transmission of M. bovis from livestock to pronghorn is possible and that seasonality of infection could be due to shared resources during late winter. Further investigations to better understand transmission dynamics, to assess population level impacts to pronghorn, and to determine disease risks among pronghorn and other ungulate taxa appear warranted.

Bighorn sheep show similar in-host responses to the same pathogen strain in two contrasting environments

Ecological context-the biotic and abiotic environment, along with its influence on population mixing dynamics and individual susceptibility-is thought to have major bearing on epidemic outcomes. However, direct comparisons of wildlife disease events in contrasting ecological contexts are often confounded by concurrent differences in host genetics, exposure histories, or pathogen strains. Here, we compare disease dynamics of a Mycoplasma ovipneumoniae spillover event that affected bighorn sheep populations in two contrasting ecological contexts. One event occurred on the herd's home range near the Rio Grande Gorge in New Mexico, while the other occurred in a captive facility at Hardware Ranch in Utah. While data collection regimens varied, general patterns of antibody signal strength and symptom emergence were conserved between the two sites. Symptoms appeared in the captive setting an average of 12.9 days postexposure, average time to seroconversion was 24.9 days, and clinical signs peaked at approximately 36 days postinfection. These patterns were consistent with serological testing and subsequent declines in symptom intensity in the free-ranging herd. At the captive site, older animals exhibited more severe declines in body condition and loin thickness, higher symptom burdens, and slower antibody response to the pathogen than younger animals. Younger animals were more likely than older animals to clear infection by the time of sampling at both sites. The patterns presented here suggest that environment may not be a major determinant of epidemiological outcomes in the bighorn sheep-M. ovipneumoniae system, elevating the possibility that host- or pathogen-factors may be responsible for observed variation.

Disease Ecology of a Low-Virulence Mycoplasma ovipneumoniae Strain in a Free-Ranging Desert Bighorn Sheep Population

Simple Summary

Like many wildlife diseases, bighorn sheep pneumonia can vary in burden. Here, we report on a bighorn sheep pneumonia event that showed much lower symptom and mortality burdens than have been documented previously. We provide detailed descriptions of symptoms, diagnostic testing results, and mixing patterns throughout the population, and end by discussing mechanisms that could have generated the distinct disease ecology associated with this event.

Abstract

Infectious pneumonia associated with the bacterial pathogen Mycoplasma ovipneumoniae is an impediment to bighorn sheep (Ovis canadensis) population recovery throughout western North America, yet the full range of M. ovipneumoniae virulence in bighorn sheep is not well-understood. Here, we present data from an M. ovipneumoniae introduction event in the Zion desert bighorn sheep (Ovis canadensis nelsoni) population in southern Utah. The ensuing disease event exhibited epidemiology distinct from what has been reported elsewhere, with virtually no mortality (0 adult mortalities among 70 animals tracked over 118 animal-years; 1 lamb mortality among 40 lambs tracked through weaning in the two summers following introduction; and lamb:ewe ratios of 34.9:100 in the year immediately after introduction and 49.4:100 in the second year after introduction). Individual-level immune responses were lower than expected, and M. ovipneumoniae appeared to fade out approximately 1.5 to 2 years after introduction. Several mechanisms could explain the limited burden of this M. ovipneumoniae event. First, most work on M. ovipneumoniae has centered on Rocky Mountain bighorn sheep (O. c. candensis), but the Zion bighorns are members of the desert subspecies (O. c. nelsoni). Second, the particular M. ovipneumoniae strain involved comes from a clade of strains associated with weaker demographic responses in other settings. Third, the substructuring of the Zion population may have made this population more resilient to disease invasion and persistence. The limited burden of the disease event on the Zion bighorn population underscores a broader point in wildlife disease ecology: that one size may not fit all events.

Experimental cross species transmission of a major viral pathogen in bees is predominantly from honeybees to bumblebees

Cross-species transmission of a pathogen from a reservoir to a recipient host species, spillover, can have major impacts on biodiversity, domestic species and human health. Deformed wing virus (DWV) is a panzootic RNA virus in honeybees that is causal in their elevated colony losses, and several correlative field studies have suggested spillover of DWV from managed honeybees to wild bee species such as bumblebees. Yet unequivocal demonstration of DWV spillover is lacking, while spillback, the transmission of DWV from a recipient back to the reservoir host, is rarely considered. Here, we show in fully crossed laboratory experiments that the transmission of DWV (genotype A) from honeybees to bumblebees occurs readily, yet we neither detected viral transmission from bumblebees to honeybees nor onward transmission from experimentally infected to uninoculated bumblebees. Our results support the potential for viral spillover from honeybees to other bee species in the field when robbing resources from heterospecific nests or when visiting the same flowers. They also underscore the importance of studies on the virulence of DWV in wild bee species so as to evaluate viral impact on individual and population fitness as well as viral adaption to new host species.

Natural history of a bighorn sheep pneumonia epizootic: Source of infection, course of disease, and pathogen clearance

A respiratory disease epizootic at the National Bison Range (NBR) in Montana in 2016-2017 caused an 85% decline in the bighorn sheep population, documented by observations of its unmarked but individually identifiable members, the subjects of an ongoing long-term study. The index case was likely one of a small group of young bighorn sheep on a short-term exploratory foray in early summer of 2016. Disease subsequently spread through the population, with peak mortality in September and October and continuing signs of respiratory disease and sporadic mortality of all age classes through early July 2017. Body condition scores and clinical signs suggested that the disease affected ewe groups before rams, although by the end of the epizootic, ram mortality (90% of 71) exceeded ewe mortality (79% of 84). Microbiological sampling 10 years to 3 months prior to the epizootic had documented no evidence of infection or exposure to Mycoplasma ovipneumoniae at NBR, but during the epizootic, a single genetic strain of M. ovipneumoniae was detected in affected animals. Retrospective screening of domestic sheep flocks near the NBR identified the same genetic strain in one flock, presumptively the source of the epizootic infection. Evidence of fatal lamb pneumonia was observed during the first two lambing seasons following the epizootic but was absent during the third season following the death of the last identified M. ovipneumoniae carrier ewe. Monitoring of life-history traits prior to the epizootic provided no evidence that environmentally and/or demographically induced nutritional or other stress contributed to the epizootic. Furthermore, the epizootic occurred despite proactive management actions undertaken to reduce risk of disease and increase resilience in this population. This closely observed bighorn sheep epizootic uniquely illustrates the natural history of the disease including the (presumptive) source of spillover, course, severity, and eventual pathogen clearance.

Previously Unrecognized Exposure of Desert Bighorn Sheep (Ovis canadensis nelsoni) to Mycoplasma ovipneumoniae in the California Mojave Desert

A 2013 outbreak of respiratory disease in bighorn sheep from California's Mojave Desert metapopulation caused high mortality in at least one population. Subsequent PCR and strain-typing indicate widespread infection of a single strain of Mycoplasma ovipneumoniae throughout this region. Serosurvey of archived samples showed that some populations have had antibodies to M. ovipneumoniae since at least 1986, although pre-2013 strain-type data are unavailable.

1H NMR based metabolic profiling distinguishes the differential impact of capture techniques on wild bighorn sheep

Environmental metabolomics has the potential to facilitate the establishment of a new suite of tools for assessing the physiological status of important wildlife species. A first step in developing such tools is to evaluate the impacts of various capture techniques on metabolic profiles as capture is necessary to obtain the biological samples required for assays. This study employed ¹H nuclear magnetic resonance (NMR)-based metabolite profiling of 562 blood serum samples from wild bighorn sheep to identify characteristic molecular serum makers of three capture techniques (dart, dropnet, and helicopter-based captures) to inform future sampling protocols for metabolomics studies, and to provide insights into the physiological impacts of capture. We found that different capture techniques induce distinct changes in amino acid serum profiles, the urea cycle, and glycolysis, and attribute the differences in metabolic patterns to differences in physical activity and stress caused by the different capture methods. These results suggest that when designing experiments involving the capture of wild animals, it may be prudent to employ a single capture technique to reduce confounding factors. Our results also supports administration of tranquilizers as soon as animals are restrained to mitigate short-term physiological and metabolic responses when using pursuit and physical restraint capture techniques.

The Emotional Dimensions of Animal Disease Management: A Political Ecology Perspective for a Time of Heightened Biosecurity

The ongoing devastation of the Covid-19 pandemic has brought new urgency to questions surrounding the origins, management, and complex dynamics of infectious diseases. In this mini review, we use growing international concern over the pandemic potential of emerging infectious diseases as motivation for outlining a research approach to study the emotional dimensions of animal disease management. We sketch out this important analytical terrain by first locating opportunities for literature on the biosecurization of nature to intersect with the emerging field of emotional political ecology. Second, we describe three biosecurity contexts and environmental conflicts at the wildlife-livestock interface: African swine fever in wild boar, brucellosis in elk, and pneumonia in bighorn and domestic sheep. We argue that in these “contact zones,” a focus on emotions can add a new layer of explanation for analyzing the manifestations, implications, and varied experiences of biosecurity.

Genomic association with pathogen carriage in bighorn sheep (Ovis canadensis)

Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population-level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well-studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family-based genome-wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome-wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP-based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.

Impact of Mycoplasma ovipneumoniae on juvenile bighorn sheep (Ovis canadensis) survival in the northern Basin and Range ecosystem

Determining the demographic impacts of wildlife disease is complex because extrinsic and intrinsic drivers of survival, reproduction, body condition, and other factors that may interact with disease vary widely. Mycoplasma ovipneumoniae infection has been linked to persistent mortality in juvenile bighorn sheep (Ovis canadensis), although mortality appears to vary widely across subspecies, populations, and outbreaks. Hypotheses for that variation range from interactions with nutrition, population density, genetic variation in the pathogen, genetic variation in the host, and other factors. We investigated factors related to survival of juvenile bighorn sheep in reestablished populations in the northern Basin and Range ecosystem, managed as the formerly-recognized California subspecies (hereafter, "California lineage"). We investigated whether survival probability of 4-month juveniles would vary by (1) presence of M. ovipneumoniae-infected or exposed individuals in populations, (2) population genetic diversity, and (3) an index of forage suitability. We monitored 121 juveniles across a 3-year period in 13 populations in southeastern Oregon and northern Nevada. We observed each juvenile and GPS-collared mother semi-monthly and established 4-month capture histories for the juvenile to estimate survival. All collared adult females were PCR-tested at least once for M. ovipneumoniae infection. The presence of M. ovipneumoniae-infected juveniles was determined by observing juvenile behavior and PCR-testing dead juveniles. We used a known-fate model with different time effects to determine if the probability of survival to 4 months varied temporally or was influenced by disease or other factors. We detected dead juveniles infected with M. ovipneumoniae in only two populations. Derived juvenile survival probability at four months in populations where infected juveniles were not detected was more than 20 times higher. Detection of infected adults or adults with antibody levels suggesting prior exposure was less predictive of juvenile survival. Survival varied temporally but was not strongly influenced by population genetic diversity or nutrition, although genetic diversity within most study area populations was very low. We conclude that the presence of M. ovipneumoniae can cause extremely low juvenile survival probability in translocated bighorn populations of the California lineage, but found little influence that genetic diversity or nutrition affect juvenile survival. Yet, after the PCR+ adult female in one population died, subsequent observations found 11 of 14 ( 79%) collared adult females had surviving juveniles at 4-months, suggesting that targeted removals of infected adults should be evaluated as a management strategy.

Evaluating wildlife translocations using genomics: A bighorn sheep case study

Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.

How sure are you? A web-based application to confront imperfect detection of respiratory pathogens in bighorn sheep

The relationships between host-pathogen population dynamics in wildlife are poorly understood. An impediment to progress in understanding these relationships is imperfect detection of diagnostic tests used to detect pathogens. If ignored, imperfect detection precludes accurate assessment of pathogen presence and prevalence, foundational parameters for deciphering host-pathogen dynamics and disease etiology. Respiratory disease in bighorn sheep (Ovis canadensis) is a significant impediment to their conservation and restoration, and effective management requires a better understanding of the structure of the pathogen communities. Our primary objective was to develop an easy-to-use and accessible web-based Shiny application that estimates the probability (with associated uncertainty) that a respiratory pathogen is present in a herd and its prevalence given imperfect detection. Our application combines the best-available information on the probabilities of detection for various respiratory pathogen diagnostic protocols with a hierarchical Bayesian model of pathogen prevalence. We demonstrated this application using four examples of diagnostic tests from three herds of bighorn sheep in Montana. For instance, one population with no detections of Mycoplasma ovipneumoniae (PCR assay) still had an 6% probability of the pathogen being present in the herd. Similarly, the apparent prevalence (0.32) of M. ovipneumoniae in another herd was a substantial underestimate of estimated true prevalence (0.46: 95% CI = [0.25, 0.71]). The negative bias of naïve prevalence increased as the probability of detection of testing protocols worsened such that the apparent prevalence of Mannheimia haemolytica (culture assay) in a herd (0.24) was less than one third that of estimated true prevalence (0.78: 95% CI = [0.43, 0.99]). We found a small difference in the estimates of the probability that Mannheimia spp. (culture assay) was present in one herd between the binomial sampling approach (0.24) and the hypergeometric approach (0.22). Ignoring the implications of imperfect detection and sampling variation for assessing pathogen communities in bighorn sheep can result in spurious inference on pathogen presence and prevalence, and potentially poorly informed management decisions. Our Shiny application makes the rigorous assessment of pathogen presence, prevalence and uncertainty straightforward, and we suggest it should be incorporated into a new paradigm of disease monitoring.

The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method

Inference of genetic clusters is a key aim of population genetics, sparking development of numerous analytical methods. Within these, there is a conceptual divide between finding de novo structure versus assessment of a priori groups. Recently developed, Discriminant Analysis of Principal Components (DAPC), combines discriminant analysis (DA) with principal component (PC) analysis. When applying DAPC, the groups used in the DA (specified a priori or described de novo) need to be carefully assessed. While DAPC has rapidly become a core technique, the sensitivity of the method to misspecification of groups and how it is being empirically applied, are unknown. To address this, we conducted a simulation study examining the influence of a priori versus de novo group designations, and a literature review of how DAPC is being applied. We found that with a priori groupings, distance between genetic clusters reflected underlying F_ST. However, when migration rates were high and groups were described de novo there was considerable inaccuracy, both in terms of the number of genetic clusters suggested and placement of individuals into those clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de novo clusters, and for the majority (62.5%) the stated goal matched the results. However, most studies (52.3%) omit key run parameters, preventing repeatability and transparency. Therefore, we present recommendations for standard reporting of parameters used in DAPC analyses. The influence of groupings in genetic clustering is not unique to DAPC, and researchers need to consider their goal and which methods will be most appropriate.

Individual variation creates diverse migratory portfolios in native populations of a mountain ungulate

Ecological theory and empirical studies have demonstrated population-level demographic benefits resulting from a diversity of migratory behaviors with important implications for ecology, conservation, and evolution of migratory organisms. Nevertheless, evaluation of migratory portfolios (i.e., the variation in migratory behaviors across space and time among individuals within populations) has received relatively little attention in migratory ungulates, where research has focused largely on the dichotomous behaviors (e.g., resident and migrant) of partially migratory populations. Using GPS data from 361 female bighorn sheep (Ovis canadensis) across 17 (4 restored, 6 augmented, 7 native) populations in Montana and Wyoming, USA, we (1) characterized migratory portfolios based on behavioral and spatial migratory characteristics and (2) evaluated the relative influence of landscape attributes and management histories on migratory diversity. Native populations, which had been extant on the landscape for many generations, had more diverse migratory portfolios, higher behavioral switching rates, reduced seasonal range fidelity, and broad dispersion of individuals across summer and winter ranges. In contrast, restored populations with an abbreviated history on the landscape were largely non-migratory with a narrow portfolio of migratory behaviors, less behavioral switching, higher fidelity to seasonal ranges, and less dispersion on summer and winter ranges. Augmented populations were more variable and contained characteristics of both native and restored populations. Differences in migratory diversity among populations were associated with management histories (e.g., restored, augmented, or native). Landscape characteristics such as the duration and regularity of green-up, human landscape alterations, topography, and snow gradients were not strongly associated with migratory diversity. We suggest a two-pronged approach to restoring migratory portfolios in ungulates that first develops behavior-specific habitat models and then places individuals with known migratory behaviors into unoccupied areas in an effort to bolster migratory portfolios in restored populations, potentially with synergistic benefits associated with variation among individuals and resulting portfolio effects. Management efforts to restore diverse migratory portfolios may increase the abundance, resilience, and long-term viability of ungulate populations.

Anthropogenic factors affecting wildlife species status outcomes: why the fixation on pesticides?

Most Americans are at least three generations removed from the farm, thereby at least three generations removed from the reality of where their food comes from. Not surprisingly, there are many misconceptions about modern food production, including the potential collateral environmental damage attributed to agriculture, particularly the application of pesticides. However, the implication of conventional agriculture in the broader narrative of wildlife species status outcomes (SSOs) lacks context and relativity. Since the dawn of civilization, humans have had a profound impact on their environment. Originating as hunter-gatherer societies, our ancient ancestors initially exploited anything that could be consumed or brought to bear. With the advent of the "first proto-farmers," humans began manipulating their environments to maximize available resources. Urban centers propagated and flourished proximal to agricultural origins, where modern societies have been built primarily on an abundance of food. As societies "developed," and continue to develop, an inevitable economic transition occurs from agriculture to industry/service predominance, culminating in a corresponding shift in land use. Developed countries have typically experienced maximal expansion of the agricultural frontier, where farmland is now steadily eroding by a proverbial flood of urban development. In contrast, in developing countries, this shift in economic development has not yet fully manifested and the agricultural footprint continues to expand at the expense of native habitats. Thus, the relative influence of "agriculture" on SSOs, in terms of land use, is primarily dependent on economic developmental status, which can be, at least in part, ameliorated via technology by increasing yield from existing land. Moreover, in addition to the land use challenge, there are multiple other factors affecting wildlife SSOs, including a figurative plague of invasive species, a literal plague of disease, a barrage of buildings, bumpers, grilles, and windshields to collide with, light pollution to confuse cues with, poachers to contend with, and even more complicated factors such as climate change. Being an easy target does not mean pesticides are the right target, and this fixation can potentially detract from public awareness regarding the primary drivers affecting SSOs as well as the opportunity to proactively address them. So, relatively speaking, how do these other factors compare to "pesticides" in terms of driving SSOs? Moreover, why is the popular media so fixated on the pesticide narrative? Based on the available evidence, this manuscript attempts to address these questions from a holistic and relative perspective within the context of land use change, economic development, population growth, and associated implications of global connectivity and commerce.

Removal of chronic Mycoplasma ovipneumoniae carrier ewes eliminates pneumonia in a bighorn sheep population

Chronic pathogen carriage is one mechanism that allows diseases to persist in populations. We hypothesized that persistent or recurrent pneumonia in bighorn sheep (Ovis canadensis) populations may be caused by chronic carriers of Mycoplasma ovipneumoniae (Mo). Our experimental approach allowed us to address a conservation need while investigating the role of chronic carriage in disease persistence.We tested our hypothesis in two bighorn sheep populations in South Dakota, USA. We identified and removed Mo chronic carriers from the Custer State Park (treatment) population. Simultaneously, we identified carriers but did not remove them from the Rapid City population (control). We predicted removal would result in decreased pneumonia, mortality, and Mo prevalence. Both population ranges had similar habitat and predator communities but were sufficiently isolated to preclude intermixing.We classified chronic carriers as adults that consistently tested positive for Mo carriage over a 20-month sampling period (n = 2 in the treatment population; n = 2 in control population).We failed to detect Mo or pneumonia in the treatment population after chronic carrier removal, while both remained in the control. Mortality hazard for lambs was reduced by 72% in the treatment population relative to the control (CI = 36%, 91%). There was also a 41% reduction in adult mortality hazard attributable to the treatment, although this was not statistically significant (CI = 82% reduction, 34% increase). Synthesis and Applications: These results support the hypothesis that Mo is a primary causative agent of persistent or recurrent respiratory disease in bighorn sheep populations and can be maintained by a few chronic carriers. Our findings provide direction for future research and management actions aimed at controlling pneumonia in wild sheep and may apply to other diseases.

Does host socio-spatial behavior lead to a fine-scale spatial genetic structure in its associated parasites?

Gastro-intestinal nematodes, especially Haemonchus contortus, are widespread pathogenic parasites of small ruminants. Studying their spatial genetic structure is as important as studying host genetic structure to fully understand host-parasite interactions and transmission patterns. For parasites having a simple life cycle (e.g., monoxenous parasites), gene flow and spatial genetic structure are expected to strongly rely on the socio-spatial behavior of their hosts. Based on five microsatellite loci, we tested this hypothesis for H. contortus sampled in a wild Mediterranean mouflon population (Ovis gmelini musimon × Ovis sp.) in which species- and environment-related characteristics have been found to generate socio-spatial units. We nevertheless found that their parasites had no spatial genetic structure, suggesting that mouflon behavior was not enough to limit parasite dispersal in this study area and/or that other ecological and biological factors were involved in this process, for example other hosts, the parasite life cycle, or the study area history.

Genetic structure of Mycoplasma ovipneumoniae informs pathogen spillover dynamics between domestic and wild Caprinae in the western United States

Spillover diseases have significant consequences for human and animal health, as well as wildlife conservation. We examined spillover and transmission of the pneumonia-associated bacterium Mycoplasma ovipneumoniae in domestic sheep, domestic goats, bighorn sheep, and mountain goats across the western United States using 594 isolates, collected from 1984 to 2017. Our results indicate high genetic diversity of M. ovipneumoniae strains within domestic sheep, whereas only one or a few strains tend to circulate in most populations of bighorn sheep or mountain goats. These data suggest domestic sheep are a reservoir, while the few spillovers to bighorn sheep and mountain goats can persist for extended periods. Domestic goat strains form a distinct clade from those in domestic sheep, and strains from both clades are found in bighorn sheep. The genetic structure of domestic sheep strains could not be explained by geography, whereas some strains are spatially clustered and shared among proximate bighorn sheep populations, supporting pathogen establishment and spread following spillover. These data suggest that the ability to predict M. ovipneumoniae spillover into wildlife populations may remain a challenge given the high strain diversity in domestic sheep and need for more comprehensive pathogen surveillance.