Livestock farming practices modulate vulture diet-disease interactions

Key Factors behind the Dynamic Stability of Pairs of Egyptian Vultures in Continental Spain

Conservation science aims to identify the factors influencing the distribution of threatened species, thereby permitting the implementation of effective management strategies. This is key for long-lived species that require long-term monitoring such as the worldwide endangered Egyptian vulture (Neophron percnopterus). We studied temporal and spatial variations in the distribution of breeding pairs and examined the intrinsic and anthropic factors that may be influencing the abundance of breeding territories in continental Spain. Based on the census data of breeding pairs from 2000, 2008, and 2018, we used Rank Occupancy-Abundance Profiles to assess the temporal stability of the population and identified the spatial heterogeneity through a Local Index of Spatial Autocorrelation analysis. The GLMs showed that the abundance distribution was mainly influenced by the abundance of griffon vultures (Gyps fulvus) and cattle at a regional scale. Nonparametric comparisons showed that the presence of wind farms had a significant negative effect on local breeding pairs abundance, but that supplementary feeding stations and food resource-related variables had a positive impact. In light of these findings, we recommend a hierarchical approach in future conservation programs involving actions promoting regional-scale food resource availability and highlight the need to address the negative impact of wind farms at local levels.

Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures

Introduction

Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown.

Methods

In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures.

Results

In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome.

Discussion

Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.

The Importance of the Slaughterhouse in Surveilling Animal and Public Health: A Systematic Review

From the point of public health, the objective of the slaughterhouse is to guarantee the safety of meat in which meat inspection represent an essential tool to control animal diseases and guarantee the public health. The slaughterhouse can be used as surveillance center for livestock diseases. However, other aspects related with animal and human health, such as epidemiology and disease control in primary production, control of animal welfare on the farm, surveillance of zoonotic agents responsible for food poisoning, as well as surveillance and control of antimicrobial resistance, can be monitored. These controls should not be seen as a last defensive barrier but rather as a complement to the controls carried out on the farm. Regarding the control of diseases in livestock, scientific research is scarce and outdated, not taking advantage of the potential for disease control. Animal welfare in primary production and during transport can be monitored throughout ante-mortem and post-mortem inspection at the slaughterhouse, providing valuable individual data on animal welfare. Surveillance and research regarding antimicrobial resistance (AMR) at slaughterhouses is scarce, mainly in cattle, sheep, and goats. However, most of the zoonotic pathogens are sensitive to the antibiotics studied. Moreover, the prevalence at the slaughterhouse of zoonotic and foodborne agents seems to be low, but a lack of harmonization in terms of control and communication may lead to underestimate its real prevalence.

Long-term demographic dynamics of a keystone scavenger disrupted by human-induced shifts in food availability

Scavenging is a key ecological process controlling energy flow in ecosystems and providing valuable ecosystem services worldwide. As long-lived species, the demographic dynamics of vultures can be disrupted by spatiotemporal fluctuations in food availability, with dramatic impacts on their population viability and the ecosystem services provided. In Europe, the outbreak of bovine spongiform encephalopathy (BSE) in 2001 prompted a restrictive sanitary regulation banning the presence of livestock carcasses in the wild on a continental scale. In long-lived vertebrate species, the buffering hypothesis predicts that the demographic traits with the largest contribution to population growth rate should be less temporally variable. The BSE outbreak provides a unique opportunity to test for the impact of demographic buffering in a keystone scavenger suffering abrupt but transient food shortages. We studied the 42-year dynamics (1979-2020) of one of the world's largest breeding colonies of Eurasian griffon vultures (Gyps fulvus). We fitted an inverse Bayesian state-space model with density-dependent demographic rates to the time series of stage-structured abundances to investigate shifts in vital rates and population dynamics before, during, and after the implementation of a restrictive sanitary regulation. Prior to the BSE outbreak the dynamics was mainly driven by adult survival: 83% of temporal variance in abundance was explained by variability in this rate. Moreover, during this period the regulation of population size operated through density-dependent fecundity and subadult survival. However, after the onset of the European ban, a 1-month delay in average laying date, a drop in fecundity, and a reduction in the number of fledglings induced a transient increase in the impact of fledgling and subadult recruitment on dynamics. Although adult survival rate remained constantly high, as predicted by the buffering hypothesis, its relative impact on the temporal variance in abundance dropped to 71% during the sanitary regulation and to 54% after the ban was lifted. A significant increase in the relative impact of environmental stochasticity on dynamics was modeled after the BSE outbreak. These results provide empirical evidence on how abrupt environmental deterioration may induce dramatic demographic and dynamic changes in the populations of keystone scavengers, with far-reaching impacts on ecosystem functioning worldwide.

The value of transhumance for biodiversity conservation: Vulture foraging in relation to livestock movements

In recent decades, intensive techniques of livestock raising have flourished, which has largely replaced traditional farming practices such as transhumance. These changes may have affected scavengers' behaviour and ecology, as extensive livestock is a key source of carrion. This study evaluates the spatial responses of avian scavengers to the seasonal movements of transhumant herds in south-eastern Spain. We surveyed the abundance of avian scavengers and ungulates, and analysed the factors affecting the space use by 30 GPS-tracked griffon vultures (Gyps fulvus). Griffons' foraging activity increased in the pasturelands occupied by transhumant herds, which implied greater vulture abundance at the landscape level during the livestock season. In contrast, facultative scavengers were more abundant without transhumant livestock herds, and the abundance of wild ungulates did not change in relation to livestock presence. We conclude that fostering transhumance and other traditional farming systems, to the detriment of farming intensification, could favour vulture conservation.

Transhumant Sheep Grazing Enhances Ecosystem Multifunctionality in Productive Mountain Grasslands: A Case Study in the Cantabrian Mountains

Understanding the effects of traditional livestock grazing abandonment on the ability of mountain grasslands to sustain multiple ecosystem functions (ecosystem multifunctionality; EMF) is crucial for implementing policies that promote grasslands conservation and the delivery of multiple ecosystem services. In this study, we evaluated the effect of short- and long-term transhumant sheep abandonment on EMF through a grazing exclusion experiment in a grassland of the Cantabrian Mountains range (NW Spain), where transhumant sheep flocks graze in summer. We considered four key ecosystem functions, derived from vegetation and soil functional indicators measured in the field: (A) biodiversity function, evaluated from total plant species evenness, diversity and richness indicators; (B) forage production function, evaluated from cover and richness of perennial and annual herbaceous species indicators; (C) carbon sequestration function, evaluated from woody species cover and soil organic carbon indicators; and (D) soil fertility function, evaluated from NH4+-N, NO3–-N, P and K content in the soil. The EMF index was calculated by integrating the four standardized ecosystem functions through an averaging approach. Based on linear mixed modeling we found that grazing exclusion induced significant shifts in the considered individual ecosystem functions and also on EMF. Long-term livestock exclusion significantly hindered biodiversity and forage production functions, but enhanced the carbon sequestration function. Conversely, the soil fertility function was negatively affected by both short- and long-term grazing exclusion. Altogether, grazing exclusion significantly decreased overall EMF, especially in long-term livestock exclusion areas, while the decline in EMF in short-term exclusions with respect to grazed areas was marginally significant. The results of this study support the sustainability of traditional transhumance livestock grazing for promoting the conservation of grasslands and their ecosystem function in mountain regions.

Oral disease is linked to low nestling condition and brood size in a raptor species living in a highly modified environment

Anthropogenic stressors can favor the occurrence of non-infectious disease that can be worsened by the impact of opportunistic pathogens, making the epizootiology of environmental diseases difficult to unravel. The incidence and impact of oral lesions in nestlings of a facultative scavenger species, the black kite Milvus migrans, were examined over seven breeding seasons in the highly degraded environment close to Madrid, Spain. We found an overall prevalence of 31% of nestlings with oral lesions, with no clear spatial pattern in nests with affected and unaffected individuals. The occurrence and number of oral lesions was negatively associated with nestling body condition and brood size. Broods where all siblings had oral lesions were smaller than those where some or all siblings were apparently healthy, suggesting that oral disease could be causing nestling mortality and, consequently, brood size reduction. In turn, nestling body condition was negatively affected by lesion occurrence, brood size and laying date. Although these relationship were bidirectional, piecewise structural equation modeling analyses showed a greater negative effect of body condition on lesion occurrence than vice versa, indicating that nestlings in poorer body condition were more likely to develop oral lesions (which could contribute to aggravate their state of deterioration) than those in better condition. Nestlings from small broods were also more likely to have oral disease (directly or indirectly through their lower body condition) than nestlings from large broods. Nestlings that hatched last in the broods showed greater development stress than those that hatched first. Anthropogenic stressors could trigger poor body condition, and contribute to microbiota dysbiosis-related diseases. Although further research is needed to determine the consequences for the long-term fitness of individuals, actions should be taken to mitigate adverse conditions that may favor the appearance of environmental diseases associated with peri-urban areas, given their rapid expansion over natural areas.

Genetic signatures of population bottlenecks, relatedness, and inbreeding highlight recent and novel conservation concerns in the Egyptian vulture

The assessment of temporal variation in genetic features can be particularly informative on the factors behind demography and viability of wildlife populations and species. We used molecular methods to evaluate neutral genetic variation, relatedness, bottlenecks, and inbreeding in a declining population of Egyptian vulture (Neophron percnopterus) in central Spain. The results show that the genetic diversity remained relatively stable over a period of twelve years despite the decline in census and effective population sizes in the last decades. A relatively high proportion of nestlings from different and distant territories showed high relatedness in each study year. We also found support for an increasing impact of severe recent (contemporary) rather than distant (historical) past demographic bottlenecks, and the first evidence of inbred mating between full siblings coinciding with lethal malformations in offspring. The inbred nestling with feather malformations was positive to beak and feather disease virus recorded for the first time in this species. These results alert on recent and novel threats potentially affecting health and reducing the adaptive potential of individuals in this threatened species.

Blood Parasites in Sympatric Vultures: Role of Nesting Habits and Effects on Body Condition

Avian haemosporidians are a common and widespread group of vector-borne parasites capable of infecting most bird species around the world. They can negatively affect host condition and fitness. Vultures are assumed to have a very low prevalence of these blood parasites, likely due to their strong immunity; however, factors contributing to variation in host exposure and susceptibility to haemosporidians are complex, and supporting evidence is still very limited. We analyzed blood samples collected from nestlings of three vulture species in Spain over 18 years, and used updated nested-PCR protocols capable of detecting all haesmosporidian cytochrome b lineages typical for diurnal birds of prey (Accipitriformes). Similarly to previous studies, we found low haemosporidian prevalence in cliff-breeding species, with Leucocytozoon as the only represented blood parasite genus: 3.1% in griffon vultures (Gyps fulvus) (n = 128) and 5.3% in Egyptian vultures (Neophron percnopterus) (n = 114). In contrast, the tree-breeding cinereous vulture (Aegypius monachus) had a substantially higher prevalence: 10.3% (n = 146). By far the most common lineage in Spanish scavenging raptors was the Leucocytozoon lineage CIAE02. No effects of nestling age and sex, or temporal trends in prevalence were found, but an effect of nest habitat (tree-nest vs. cliff-nest) was found in the griffon vulture. These patterns may be explained by a preference of vectors to forage in and around trees rather than on cliffs and wide open spaces. We found an apparent detrimental effect of haemosporidians on body mass of nestling cinereous vultures. Further research is needed to evaluate the pathogenicity of each haemosporidian lineage and their interaction with the immune system of nestlings, especially if compromised due to pollution with pharmaceuticals and infection by bacterial and mycotic pathogens.

Seasonal and spatial occurrence of zoonotic Salmonella serotypes in griffon vultures at farmland environments: Implications in pathogen pollution and ecosystem services and disservices

Livestock production is a large source of microbial, pharmaceutical, and antimicrobial pollution worldwide. Vultures are one group of birds with particularly high exposure to food-borne pathogens due to frequent consumption of infected livestock carcasses. The potential origin and spatial-temporal shedding patterns of livestock-adapted Salmonella serotypes of zoonotic importance were evaluated in adult and nestling Griffon vultures (Gyps fulvus). We specifically assessed the exposure source and subsequent elimination of Salmonella-infected carcasses (ecosystem services) or transmission back to livestock (ecosystem disservices) by vultures, thus contributing respectively to disease mitigation or amplification in natural and farmed environments. The results show a seasonal high occurrence and turnover of a high variety of serotypes, especially swine-adapted ones isolated at high frequency. This suggests that vultures can be reservoirs and long-distance carriers of faecal Salmonella shed in supplementary feeding stations and breeding colonies. Contrary to their conservation purposes, feeding stations can act as Salmonella hotspots and reservoirs. However, a role for vultures in the transmission back to food-producing animals seems impossible because they do not come into contact at indoor farms, while transmission to free-ranging ruminants was not supported by the presence of ruminant-adapted serotypes in the vultures. Therefore, vultures do not promote disservices associated with the re-infection of livestock with Salmonella, but can provide quantitatively important ecosystem services by removing carrion contaminated with these and other zoonotic pathogens potentially affecting their health. Sanitary vigilance of the farms authorised to provide food for avian scavengers should avoid the disposal of swine and poultry carcasses with Salmonella and the antibiotics used to treat it. Extensive free-ranging livestock and their carcasses exploited in the countryside should be a priority for the conservation of vultures and their ecological function as cleaners and disease mitigators.

Vultures and Livestock: The Where, When, and Why of Visits to Farms

Recent changes in European legislation have legalized the abandonment of carcasses around livestock farms, but our understanding of how vultures exploit these semi-predictable food sources is still very limited. For filling this gap, we determine the individual and ecological drivers influencing vulture visits to farms. We assessed the effects of individual characteristics of both birds and farms on the frequency of vultures' visits to livestock facilities using data collected from 45 GPS-tagged Egyptian Vultures (Neophron percnopterus) and 318 farms (>94% of livestock) on Fuerteventura Island, Spain. Farms were more visited during the vultures' breeding season. Farms located closer to highly predictable feeding places (i.e., vulture restaurants and garbage dumps) or with more available feeding resources were visited by more vultures, whereas those located close to roads and vultures' breeding territories received fewer visits. Younger territorial birds visited a farm more frequently than older territorial ones, whereas older non-territorial individuals concentrated those visits on farms closer to their activity core areas compared with younger ones. Our findings indicate that visits to farms were determined by their spatial distribution in relation to the age-specific birds' activity centers, the availability of carcasses, seasonality, and individual characteristics of vultures. These interacting factors should be considered in vulture conservation, avoiding very general solutions that ignore population structure.

Winter movement patterns of a globally endangered avian scavenger in south-western Europe

Partial migration, whereby some individuals migrate and some do not, is relatively common and widespread among animals. Switching between migration tactics (from migratory to resident or vice versa) occurs at individual and population levels. Here, we describe for the first time the movement ecology of the largest wintering population of Egyptian Vultures (Neophron percnopterus) in south-west Europe. We combined field surveys and GPS tracking data from December to February during four wintering seasons (2014–2018). The wintering population consisted on average of 85 individuals (range 58–121; 76% adults and 24% subadults). Individuals were counted at five different roosting sites located near farms, unauthorized carcass deposition sites and authorized carcass deposition sites. Our results show that vultures tend to remain close to the roosting site. Moreover, we observed that females exhibited smaller home range sizes than males, which suggests a possible differential use of food sources. Overall, birds relied more on farms than other available food resources, particularly subadult individuals which exploited more intensively these sites. Our results showed that Egyptian Vultures congregate in significant numbers at specific sites throughout the winter period in south-west Spain and that these roosting and feeding sites should be given some level of legal protection and regular monitoring. Furthermore, predictable food sources might be driving the apparent increase in the non-migratory population of Egyptian Vultures, as observed in other avian species which are also changing their migratory behavior.

Molecular diversity of Extended-spectrum β-lactamase-producing Escherichia coli from vultures in Canary Islands

Antimicrobial resistance among isolates from wild animals is increasingly reported. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, and particularly Escherichia coli, have spread worldwide as one of the most common multidrug-resistant organisms. The aim of this study was to determine the carriage rate of ESBL-producing E. coli isolates and their genetic characteristics in wild vultures from the Canary Islands. Faecal samples were collected from 22 apparently healthy free-ranging (wild) vulture chicks from Lanzarote and Fuerteventura (Canary Islands) during July 2019. They were seeded in MacConkey agar supplemented with cefotaxime (2 μg ml^-1 ). Colonies with typical morphology of E. coli were identified by MALDI-TOF-MS. Antimicrobial susceptibility was done by disk diffusion. Phenotypic detection of ESBL was performed by double-disk tests. The presence of bla_CTX-M , bla_SHV , bla_TEM , bla_KPC and bla_OXA-48 genes, as well as mcr-1 (colistin resistance), tetA/tetB and int1 gene, was tested by PCR/sequencing. Phylogenetic groups and multilocus sequence typing (MLST) were determined by PCR/sequencing. ESBL-producing E. coli isolates were detected in 5/22 tested animals (22.7%), and all isolates (one/animal) carried bla_CTX-M genes: bla_CTX-M-15 (n = 3) and bla_CTX-M-55 (n = 2). ESBL-positive isolates were ascribed to phylogenetic group D (two isolates), B₁ (two isolates) and A (one isolate), and five sequence types were detected (ST/phylogenetic-group/ESBL): ST515/B1/CTX-M-15, ST1290/A/CTX-M-15, ST38/D/CTX-M-15, ST457/D/CTX-M-55 and ST6448/B₁ /CTX-M-55; this suggests a genetic diversity among these isolates. Three CTX-M-15-producing isolates contained the bla_TEM gene and one the tetA gene. To our knowledge, this appears to be the first report of ESBL-producing E. coli in vulture chicks from the Canary Islands.

Vultures from different trophic guilds show distinct oral pathogenic yeast signatures and co-occurrence networks

Vultures have evolved adaptive mechanisms to prevent infections associated with their scavenging lifestyle. However, food-borne exposure to antimicrobial pharmaceuticals can promote opportunistic infections with adverse outcomes. Here, we used multivariate and network analyses to increase understanding of the behavior of the yeast communities causing oral mycosis outbreaks recently reported in wild nestling cinereous (Aegypius monachus), griffon (Gyps fulvus) and Egyptian (Neophron percnopterus) vultures (CV, GV and EV, respectively) exposed to antibiotics from livestock farming. Common and unique yeast signatures (of Candida, Debaromyces, Diutina, Meyerozyma, Naganishia, Pichia, Rhodotorula, Trichosporon and Yarrowia species) associated with oral mycoses were identified in the three vulture species. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) highlighted that oral lesions from CV and GV shared similar yeast signatures (of major causative pathogens of opportunistic mycoses, such as Candida albicans, Candida parapsilosis and Candida tropicalis), while EV had a distinct yeast signature (of uncommon pathogenic species, such as Candida dubliniensis, Candida zeylanoides, Pichia fermentans and Rhodotorula spp.). Synergistic interactions between yeast species from distinct fungal phyla were found in lesions from CV and GV, but not in EV. These formed co-occurrence subnetworks with partially or fully connected topology. This study reveals that the composition, assembly and co-occurrence patterns of the yeast communities causing oral mycoses differ between vulture species with distinct feeding habits and scavenging lifestyles. Yeast species widely pathogenic to humans and animals, and yeast co-occurrence relationships, are distinctive hallmarks of oral mycoses in CV and GV. These vulture species are more exposed to antibiotics from intensively medicated livestock carcasses provided in supplementary feeding stations and show higher incidence of thrush-like oral lesions than EV. These findings may be useful for development of new initiatives or changes in the conservation of these avian scavengers affected by anthropogenic activities.

Validation of Multi-Residue Method for Quantification of Antibiotics and NSAIDs in Avian Scavengers by Using Small Amounts of Plasma in HPLC-MS-TOF

Pharmaceuticals are still considered emerging pollutants affecting both aquatic and terrestrial ecosystems. Scavenging bird species may be exposed to veterinary drugs when they feed on livestock carcasses provided at supplementary feeding stations, as these are often stocked with ailing and/or recently medicated animals. Because those animals may be a source of several different pharmaceutical compounds, analytical methods to evaluate residue levels and exposure potential should enable detection and quantification of as many different compounds as possible, preferably from small sample volumes. Four different extraction methods were tested to conduct HPLC-MS-TOF analysis of some of the most common veterinary drugs used in livestock in Spain. The method deemed most viable was a simple extraction, using methanol and 100 µL of plasma, that allowed quantification of seven antibiotics (tetracycline, oxytetracycline, ciprofloxacin, enrofloxacin, nalidixic acid, trimethoprim, sulfadiazine) and five nonsteroidal anti-inflammatory drugs (NSAIDs) (meloxicam, flunixin, carprofen, tolfenamic acid, phenylbutazone). The method was then applied to analysis of 29 Eurasian griffon vulture (Gyps fulvus) nestling samples, wherein enrofloxacin and tolfenamic acid were most commonly detected (69% and 20%, respectively). To our knowledge, this is the first study including NSAIDs in the exposure assessment of different classes of veterinary pharmaceuticals in live avian scavengers.

Avian Scavengers as Bioindicators of Antibiotic Resistance due to Livestock Farming Intensification

Industrial food animal production uses huge amounts of antibiotics worldwide. Livestock, their excreta used for manure and meat subproducts not intended for human consumption can all play important roles in the transmission of bacterial resistance to wildlife. Vultures and other scavengers can be directly exposed to active antibiotics ingested while feeding on livestock carcasses. This study evaluates whether bacterial resistance in the red kite (Milvus milvus) differs between two wintering areas selected based on patent differences in farming practices—particularly in the industrial production of food animals (primarily swine and poultry) vs. scarce and declining sheep herding. The results support the hypothesis that intensification in food animal production is associated with increased bacterial multidrug resistance in wildlife. Resistance was positively correlated with time elapsed since the beginning of the commercial application of each antibiotic in human and veterinary medicine, with clear differences depending on farming intensification between areas. Monitoring programs are encouraged to use red kites and other avian scavengers as valuable sentinels of contamination by antibiotics and clinically relevant resistant pathogens from livestock operations of variable intensities. Farms authorized for supplementary feeding of threatened scavengers should avoid supplying carcasses with active antibiotic residues to avoid bacterial resistance in scavenger wildlife.