More than an anthropogenic phenomenon: Antimicrobial resistance in ungulates from natural and agricultural environments.

Widely considered an anthropogenic phenomenon, antimicrobial resistance (AMR) is a naturally occurring mechanism that microorganisms use to gain competitive advantage. AMR represents a significant threat to public health and has generated criticism towards the overuse of antimicrobial drugs. Livestock have been proposed as important reservoirs for AMR accumulation. Here, we show that assemblages of AMR genes in cattle and ungulates from natural environments (Yellowstone and Rocky Mountain National Parks) are all dominated by genes conferring resistance to tetracyclines. However, cattle feces contained higher proportions of erm(A-X) genes conferring resistance to macrolide antibiotics. Medically important AMR genes differed between cattle and natural ungulates, but cumulatively were more predominant in natural soils. Our findings suggest that the commonly described predominance of tetracycline resistance in cattle feces is a natural phenomenon among multiple ungulate species and not solely a result of antimicrobial drug exposure. Yet, the virtual absence of macrolide resistance genes in natural ungulates suggests that macrolide usage in agriculture may enrich these genes in cattle. Our results show that antimicrobial use in agriculture may be promoting a potential reservoir for specific types of AMR (i.e., macrolide resistance) but that a significant proportion of the ungulate resistome appears to have natural origins.

Migrating bison engineer the green wave.

Newly emerging plants provide the best forage for herbivores. To exploit this fleeting resource, migrating herbivores align their movements to surf the wave of spring green-up. With new technology to track migrating animals, the Green Wave Hypothesis has steadily gained empirical support across a diversity of migratory taxa. This hypothesis assumes the green wave is controlled by variation in climate, weather, and topography, and its progression dictates the timing, pace, and extent of migrations. However, aggregate grazers that are also capable of engineering grassland ecosystems make some of the world's most impressive migrations, and it is unclear how the green wave determines their movements. Here we show that Yellowstone's bison (Bison bison) do not choreograph their migratory movements to the wave of spring green-up. Instead, bison modify the green wave as they migrate and graze. While most bison surfed during early spring, they eventually slowed and let the green wave pass them by. However, small-scale experiments indicated that feedback from grazing sustained forage quality. Most importantly, a 6-fold decadal shift in bison density revealed that intense grazing caused grasslands to green up faster, more intensely, and for a longer duration. Our finding broadens our understanding of the ways in which animal movements underpin the foraging benefit of migration. The widely accepted Green Wave Hypothesis needs to be revised to include large aggregate grazers that not only move to find forage, but also engineer plant phenology through grazing, thereby shaping their own migratory movements.

Evaluation of fecal samples as a valid source of DNA by comparing paired blood and fecal samples from American bison (Bison bison).

BACKGROUND: The collection and analysis of fecal DNA is a common practice, especially when dealing with wildlife species that are difficult to track or capture. While fecal DNA is known to be lower quality than traditional sources of DNA, such as blood or other tissues, few investigations have verified fecal samples as a valid source of DNA by directly comparing the results to high quality DNA samples from the same individuals. Our goal was to compare DNA from fecal and blood samples from the same 50 American plains bison (Bison bison) from Yellowstone National Park, analyze 35 short tandem repeat (STR) loci for genotyping efficiency, and compare heterozygosity estimates. RESULTS: We discovered that some of the fecal-derived genotypes obtained were significantly different from the blood-derived genotypes from the same bison. We also found that fecal-derived DNA samples often underestimated heterozygosity values, in some cases by over 20%. CONCLUSIONS: These findings highlight a potential shortcoming inherent in previous wildlife studies that relied solely on a multi-tube approach, using exclusively low quality fecal DNA samples with no quality control to account for false alleles and allelic dropout. Herein, we present a rigorous marker selection protocol that is applicable for a wide range of species and report a set of 15 STR markers for use in future bison studies that yielded consistent results from both fecal and blood-derived DNA.

Risk-enhancing behaviors associated with human injuries from bison encounters at Yellowstone National Park, 2000-2015.

Yellowstone National Park is home to the largest bison population on public land in the United States. Although Yellowstone regulations require visitors to remain at least 23 m from bison, since 1980, bison have injured more visitors to Yellowstone than any other animal. We examined a series of bison-related injuries at Yellowstone to evaluate the circumstances of these injuries and to identify common risk-enhancing behaviors that lead to injury. To do this, we analyzed narrative case incident records from law enforcement regarding bison-human encounters in Yellowstone during 2000-2015. Data regarding demographics, preencounter activities, number of persons involved, type of injury, and acknowledgement of appropriate viewing distance were extracted from the records. Bison encounters resulted in injury to 25 persons (21 visitors and 4 employees). Age range for injured persons was 7-68 years (median: 49 years), and 13 were female. All injuries occurred in areas of high visitor concentration. Mean visitor distance from bison before injury was 3.4 m (range: 0.3-6.1 m). Twenty persons (80%) actively approached bison before their injuries; 5 (20%) failed to retreat when bison approached. Fifteen persons (60%) were injured when in a group of ≥3 persons approaching bison. Twelve persons (48%) sustained injuries while photographing bison. Six persons (24%) acknowledged they were too close to bison. Education alone might not be sufficient to reduce bison-related injuries. Effective injury prevention campaigns for national parks require an understanding of the behaviors and motivations of persons who approach bison. Including behavioral science and behavior change techniques in bison injury prevention campaigns might reduce injuries at Yellowstone.

Brucellosis Transmission between Wildlife and Livestock in the Greater Yellowstone Ecosystem: Inferences from DNA Genotyping.

The wildlife of the Greater Yellowstone Ecosystem carries brucellosis, which was first introduced to the area by cattle in the 19th century. Brucellosis transmission between wildlife and livestock has been difficult to study due to challenges in culturing the causative agent, Brucella abortus . We examined B. abortus transmission between American bison ( Bison bison ), Rocky Mountain elk ( Cervus elaphus nelsoni), and cattle ( Bos taurus ) using variable number tandem repeat (VNTR) markers on DNA from 98 B. abortus isolates recovered from populations in Idaho, Montana, and Wyoming, US. Our analyses reveal interspecies transmission. Two outbreaks (2007, 2008) in Montana cattle had B. abortus genotypes similar to isolates from both bison and elk. Nevertheless, similarity in elk and cattle isolates from the 2008 outbreak suggest that elk are the likely source of brucellosis transmission to cattle in Montana and Wyoming. Brucella abortus isolates from sampling in Montana appear to be divided in two clusters: one found in local Montana elk, cattle, and bison; and another found mainly in elk and a bison from Wyoming, which is consistent with brucellosis having entered Montana via migration of infected elk from Wyoming. Our findings illustrate complex patterns of brucellosis transmission among elk, bison, and cattle as well as the utility of VNTRs to infer the wildlife species of origin for disease outbreaks in livestock.

Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison.

Yellowstone National Park is home to one of the only plains bison populations that have continuously existed on their present landscape since prehistoric times without evidence of domestic cattle introgression. Previous studies characterized the relatively high levels of nuclear genetic diversity in these bison, but little is known about their mitochondrial haplotype diversity. This study assessed mitochondrial genomes from 25 randomly selected Yellowstone bison and found 10 different mitochondrial haplotypes with a haplotype diversity of 0.78 (± 0.06). Spatial analysis of these mitochondrial DNA (mtDNA) haplotypes did not detect geographic population subdivision (FST = -0.06, p = 0.76). However, we identified two independent and historically important lineages in Yellowstone bison by combining data from 65 bison (defined by 120 polymorphic sites) from across North America representing a total of 30 different mitochondrial DNA haplotypes. Mitochondrial DNA haplotypes from one of the Yellowstone lineages represent descendants of the 22 indigenous bison remaining in central Yellowstone in 1902. The other mitochondrial DNA lineage represents descendants of the 18 females introduced from northern Montana in 1902 to supplement the indigenous bison population and develop a new breeding herd in the northern region of the park. Comparing modern and historical mitochondrial DNA diversity in Yellowstone bison helps uncover a historical context of park restoration efforts during the early 1900s, provides evidence against a hypothesized mitochondrial disease in bison, and reveals the signature of recent hybridization between American plains bison (Bison bison bison) and Canadian wood bison (B. b. athabascae). Our study demonstrates how mitochondrial DNA can be applied to delineate the history of wildlife species and inform future conservation actions.

Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock.

Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (∼3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.

Notes from the Field: Injuries Associated with Bison Encounters - Yellowstone National Park, 2015.

Since 1980, bison have injured more pedestrian visitors to Yellowstone National Park (Yellowstone) than any other animal (1). After the occurrence of 33 bison-related injuries during 1983-1985 (range = 10-13/year), the park implemented successful outreach campaigns (1) to reduce the average number of injuries to 0.8/year (range = 0-2/year) during 2010-2014 (unpublished data, National Park Service, September 2015). During May-July 2015, five injuries associated with bison encounters occurred (Table). Case reports were reviewed to evaluate circumstances surrounding these injuries to inform prevention.

Yersinia enterocolitica: an unlikely cause of positive brucellosis tests in greater yellowstone ecosystem bison (Bison bison).

Yersinia enterocolitica serotype O:9 has identical O-antigens to those of Brucella abortus and has apparently caused false-positive reactions in numerous brucellosis serologic tests in elk (Cervus canadensis) from southwest Montana. We investigated whether a similar phenomenon was occurring in brucellosis antibody-positive bison (Bison bison) using Y. enterocolitica culturing techniques and multiplex PCR of four diagnostic loci. Feces from 53 Yellowstone bison culled from the population and 113 free-roaming bison from throughout the Greater Yellowstone Ecosystem (GYE) were tested. Yersinia enterocolitica O:9 was not detected in any of 53 the bison samples collected at slaughter facilities or in any of the 113 fecal samples from free-ranging bison. One other Y. enterocolitica serotype was isolated; however, it is not known to cause cross-reaction on B. abortus serologic assays because it lacks the perosamine synthetase gene and thus the O-antigens. These findings suggest that Y. enterocolitica O:9 cross-reactivity with B. abortus antigens is unlikely to have been a cause of false-positive serology tests in GYE bison and that Y. enterocolitica prevalence was low in bison in the GYE during this study.

Predicting bison migration out of Yellowstone National Park using bayesian models.

Long distance migrations by ungulate species often surpass the boundaries of preservation areas where conflicts with various publics lead to management actions that can threaten populations. We chose the partially migratory bison (Bison bison) population in Yellowstone National Park as an example of integrating science into management policies to better conserve migratory ungulates. Approximately 60% of these bison have been exposed to bovine brucellosis and thousands of migrants exiting the park boundary have been culled during the past two decades to reduce the risk of disease transmission to cattle. Data were assimilated using models representing competing hypotheses of bison migration during 1990-2009 in a hierarchal bayesian framework. Migration differed at the scale of herds, but a single unifying logistic model was useful for predicting migrations by both herds. Migration beyond the northern park boundary was affected by herd size, accumulated snow water equivalent, and aboveground dried biomass. Migration beyond the western park boundary was less influenced by these predictors and process model performance suggested an important control on recent migrations was excluded. Simulations of migrations over the next decade suggest that allowing increased numbers of bison beyond park boundaries during severe climate conditions may be the only means of avoiding episodic, large-scale reductions to the Yellowstone bison population in the foreseeable future. This research is an example of how long distance migration dynamics can be incorporated into improved management policies.

Vaccination strategies for managing brucellosis in Yellowstone bison.

Concerns over migratory bison (Bison bison) at Yellowstone National Park transmitting brucellosis (Brucella abortus) to cattle herds on adjacent lands led to proposals for bison vaccination. We developed an individual-based model to evaluate how brucellosis infection might respond under alternate vaccination strategies, including: (1) vaccination of female calves and yearlings captured at the park boundary when bison move outside the primary conservation area; (2) combining boundary vaccination with the remote delivery of vaccine to female calves and yearlings distributed throughout the park; and (3) vaccinating all female bison (including adults) during boundary capture and throughout the park using remote delivery of vaccine. Simulations suggested Alternative 3 would be most effective, with brucellosis seroprevalence decreasing by 66% (from 0.47 to 0.16) over a 30-year period resulting from 29% of the population receiving protection through vaccination. Under this alternative, bison would receive multiple vaccinations that extend the duration of vaccine protection and defend against recurring infection in latently infected animals. The initial decrease in population seroprevalence will likely be slow due to high initial seroprevalence (40-60%), long-lived antibodies, and the culling of some vaccinated bison that were subsequently exposed to field strain Brucella and reacted positively on serologic tests. Vaccination is unlikely to eradicate B. abortus from Yellowstone bison, but could be an effective tool for reducing the level of infection. Our approach and findings have applicability world-wide for managers dealing with intractable wildlife diseases that cross wildlife-livestock and wildlife-human interfaces and affect public health or economic well-being.

Covariates affecting spatial variability in bison travel behavior in Yellowstone National Park.

Understanding mechanisms influencing the movement paths of animals is essential for comprehending behavior and accurately predicting use of travel corridors. In Yellowstone National Park (USA), the effects of roads and winter road grooming on bison (Bison bison) travel routes and spatial dynamics have been debated for more than a decade. However, no rigorous studies have been conducted on bison spatial movement patterns. We collected 121 380 locations from 14 female bison with GPS collars in central Yellowstone to examine how topography, habitat type, roads, and elevation affected the probability of bison travel year-round. We also conducted daily winter bison road use surveys (2003-2005) to quantify how topography and habitat type influenced spatial variability in the amount of bison road travel. Using model comparison techniques, we found the probability of bison travel and spatial distribution of travel locations were affected by multiple topographic and habitat type attributes including slope, landscape roughness, habitat type, elevation, and distances to streams, foraging areas, forested habitats, and roads. Streams were the most influential natural landscape feature affecting bison travel, and results suggest the bison travel network throughout central Yellowstone is spatially defined largely by the presence of streams that connect foraging areas. Also, the probability of bison travel was higher in regions of variable topography that constrain movements, such as in canyons. Pronounced travel corridors existed both in close association with roads and distant from any roads, and results indicate that roads may facilitate bison travel in certain areas. However, our findings suggest that many road segments used as travel corridors are overlaid upon natural travel pathways because road segments receiving high amounts of bison travel had similar landscape features as natural travel corridors. We suggest that most spatial patterns in bison road travel are a manifestation of general spatial travel trends. Our research offers novel insights into bison spatial dynamics and provides conceptual and analytical frameworks for examining movement patterns of other species.