Wild griffon vultures (Gyps fulvus) as a source of Salmonella and Campylobacter in Eastern Spain

High-risk lineages of extended spectrum cephalosporinase producing Escherichia coli from Eurasian griffon vultures (Gyps fulvus) foraging in landfills in north-eastern Spain

Extended-spectrum cephalosporinase producing (ESC) E. coli are regarded as key indicator microorganisms of antimicrobial resistance (AMR), calling for a One Health integrated global surveillance strategy. Wildlife is exposed to antibiotic contaminants and/or resistant bacteria that have been released into the environment, potentially acting as reservoirs and spreaders of resistance genes as well as sentinels of anthropogenic pressure. Monitoring AMR in wildlife has become crucial in determining anthropogenic environmental impacts as well as transmission routes. In this study, we determined the occurrence and potential sources of ESC E. coli in 218 Eurasian griffon vultures (Gyps fulvus) foraging regularly on human waste disposed at a dumpsite in north-eastern Spain. Minimal inhibitory concentration for 14 different antimicrobials was performed to evaluate the phenotype of the isolates, and whole genome sequencing was carried out to investigate lineages and plasmids harbouring ESC genes. Our sequences were compared to previously published Spanish sequences of human, animal, and wildlife origin. We report a high prevalence of CTX-M-15, as well as the presence of other resistance genes such as OXA-10, CTX-M-27, and CTX-M-65 which are rarely described in European livestock, suggesting a human origin. The isolates also carried a diverse range of additional AMR genes for a broad spectrum of drug families, with the majority being multi-drug resistant. The phylogenomic analyses suggests the transmission of high-risk lineages from humans to vultures, with 49 % of our isolates matching the most common extraintestinal pathogenic E. coli (ExPEC) lineages described in humans worldwide, including ST131, ST10 and ST58. We conclude that anthropogenically altered habitats, such as landfills, are hotspots for the acquisition and spread of high-risk ESC E. coli lineages associated with hospital infections. Measures must be implemented to limit their spread into natural environments.

HEALTH ASSESSMENT OF CAPTIVE BEARDED VULTURES (GYPAETUS BARBATUS) IN CATALONIA (SPAIN)

Bearded vulture (Gypaetus barbatus) populations are declining worldwide primarily due to anthropogenic factors. A captive breeding program has been established in Spain, a country with one of the largest free-living populations in Europe, to further enhance the conservation efforts of this emblematic species. However, captive vulture populations can be exposed to different risks through food, such as drug residues and antimicrobial-resistant (AMR) bacteria. Health surveillance of species involved in captive breeding programs is important to face introduction of healthy animals in situ and to obtain baseline clinical data. The objective of this study was to assess the general health status of bearded vultures held in captivity in Catalonia (northeastern Spain) by carrying out hematologic, biochemical, toxicologic, and bacteriologic analyses. A total of 16 bearded vultures were sampled; the data obtained from one vulture, with a chronic tibiotarsal fracture, were excluded from the statistical analysis. Hematologic and biochemical parameters of the bearded vultures were mostly within the range of standard values as stated in previous studies. Basal feather and serum corticosterone levels were analyzed and described for the first time in this species. A total of 15 Escherichia coli isolates were obtained that were resistant to fluoroquinolones (80%), tetracycline (60%), trimethoprim and ampicillin (40%), sulfamethoxazole (33%), and colistin (20%), with 40% of them being multidrug resistant. Three of 15 isolates were carriers of the mcr-1 gene. Only the injured bird previously treated with enrofloxacin was positive for fluoroquinolone residues. Periodic monitoring for the presence of AMR bacteria would be recommended in captive breeding programs as a preventive action to establish future therapies.

First reported Porrocaecum angusticolle infection in Griffon vulture (Gyps fulvus) in China

This present study is the first case of a Porrocaecum angusticolle (P. angusticolle) infection reported in Griffon vulture (Gyps fulvus) in China. This study aimed to identify the nematode species and explore the genetic evolution of worms infecting Gyps fulvus (G.fulvus). Clinical examination revealed several milky white parasites in the stomach and intestinal tract. Polymerase chain reaction and partial 18S gene sequencing analyses identified these worms to be P. angusticolle (SD isolates). Further phylogenetic analyses revealed that they shared the highest genetic identity (99.9%) with a P. angusticolle isolate (EU004820.1) from Germany. Our study is the first report on the identification and characterization of P. angusticolle infecting G.fulvus in China, based on clinical findings and molecular diagnosis. Therefore, our study provides novel insights for the diagnosis of P. angusticolle infections and the prevention of nematode transmission in wild and domestic animals.

A Systematic Review on the Role of Wildlife as Carriers and Spreaders of Campylobacter spp

Campylobacter spp. are important zoonotic pathogens and can cause one of the main bacterial diarrheal diseases worldwide. Research in the context of infection arising from transmission from other humans and other vertebrates has been extensive. A large fraction of these investigations has focused on domestic animals; however, there are also a number of publications which either totally, or at least in part, consider the role of wild or feral animals as carriers or spreaders of Campylobacter spp. Here, we carry out a systematic review to explore the role played by wild vertebrates as sources of Campylobacter spp. with a compilation of prevalence data for more than 150 species including reptiles, mammals and birds. We found that numerous vertebrate species can act as carriers of Campylobacter species, but we also found that some host specificity may exist, reducing the risk of spread from wildlife to domestic animals or humans.

Ecology and epidemiology of Salmonella spp. isolated from the environment and the roles played by wild animals in their maintenance

Salmonella is a ubiquitous organism of public health importance that causes diarrhea and other systemic disease syndromes. The ecology and epidemiology of the organism in addition to the roles played by wild animals are important in understanding its disease. Relevant published peer-reviewed literature was obtained after imputing the study's keywords into the Google search engine. The publications were thereafter saved for the study. The study revealed the ecology of Salmonella is directly related to its epidemiology. These were found to be either positively or negatively influenced by the living and non-living parts of the environment. Free-ranging and captive wild animals can serve as asymptomatic carriers of Salmonella, therefore, help to maintain the cycle of the disease since wildlife serves as reservoir hosts to over 70% of emerging zoonotic diseases. Cockroaches transmit Salmonella through their feces, and body parts and when ingested by birds and animals. The statistically significant over 83% of Salmonella isolation in lizards suggests the reptile could be a source of Salmonella distribution. Snakes, foxes, badgers, rodents, and raccoons have been reported to have Salmonella as a natural component of their gut with the ability to shed the organism often. The high occurrence (>45%) of diverse Salmonella serovars coupled with the fact that some of these animals were handled, kept as pets and consumed by man portends these animals as potential sources of transmission of the organism and the disease. The etiology and epidemiology of Salmonella are overtly affected by several environmental factors which also determine their survival and maintenance. The roles played by wild animals in the relationship, transmission, growth or interaction within and between Salmonella spp., the occurrence, prevalence, and distribution of the organism help maintain the organism in the environment. An understanding of the roles played by the different parts of the environment and wild animals in the ecology and epidemiology of Salmonella can help make informed decisions on the prevention and control of the diseases it causes. This review aimed to investigate the relationship between ecology, epidemiology, and environment, including the roles played by wild animals in the maintenance of the organism and its disease.

Genotypic and Phenotypic Characterization of Pathogenic Escherichia coli, Salmonella spp., and Campylobacter spp., in Free-Living Birds in Mainland Portugal

Birds are potential carriers of pathogens affecting humans and agriculture. Aiming to evaluate the occurrence of the top three most important foodborne pathogens in free-living birds in Portugal, we investigated 108 individual fecal samples from free-living birds and one pooled sample of gull feces (n = 50) for the presence of Escherichia coli (pathogenic and non-pathogenic), Salmonella spp. and Campylobacter spp. Virulence- and antimicrobial resistance- (AMR) associated genes were detected by PCR and Whole-Genome Sequencing (WGS), and phenotypic (serotyping and AMR profiles) characterization was performed. Overall, 8.9% of samples tested positive for pathogenic E. coli, 2.8% for Salmonella spp., and 9.9% for Campylobacter spp. AMR was performed on all pathogenic isolates and in a fraction of non-pathogenic E. coli, being detected in 25.9% of them. Ten of the tested E. coli isolates were multidrug-resistant (MDR), and seven of them were Extended-spectrum β-lactamase (ESBL) producers. Among Salmonella (n = 3) and Campylobacter (n = 9), only one strain of C. jejuni was identified as MDR. Most of the identified serotypes/sequence types had already been found to be associated with human disease. These results show that free-living birds in Portugal may act as carriers of foodborne pathogens linked to human disease, some of them resistant to critically important antimicrobials.

Eurasian griffon vultures carry widespread antimicrobial resistant Salmonella and Campylobacter of public health concern

The global emergence of antimicrobial-resistant (AMR) strains of Salmonella and Campylobacter is a serious public health concern. Both bacteria are leading causes of human gastrointestinal foodborne infections and the two most reported zoonoses in the European Union. By feeding on livestock carcasses, especially from intensive farming, as well as on landfill sites, obligate avian scavengers can become infected with zoonotic pathogens and AMR strains, and can be considered large-scale sentinels of the environmental burden. In this study, we assessed the occurrence and AMR of Salmonella spp. and Campylobacter spp. in 218 Eurasian griffon vultures (Gyps fulvus) captured in north-eastern Spain. We isolated Salmonella from 8.1 % of individuals and Campylobacter lari from 4.7 %. Among the 10 different Salmonella serovars found, monophasic S. Typhimurium was the most frequent. Genotyping analysis revealed same strains of monophasic S. Typhimurium shared by gulls, livestock and humans. Isolates from both bacterial species presented AMR to important antimicrobials (tetracyclines, fluoroquinolones and β-lactams). In conclusion, this study shows that Eurasian griffon vultures in north-eastern Spain are carriers of widespread AMR zoonotic Salmonella and Campylobacter. More comprehensive analyses are still needed to understand the potential risk of spill-over from those wild birds to humans.

Campylobacter in Wild Birds: Is It an Animal and Public Health Concern?

Campylobacteriosis continues to be one of the leading causes of foodborne bacterial zoonotic infections worldwide. Despite its public health importance, the status of this disease in wild birds and the possibility of transmission from wild birds to domestic animals and humans have not been clearly elucidated yet. This article reviews the available literature with the aim of making a comprehensive manuscript on this disease status in wild birds and the possibility of interspecies transmission. Campylobacter has been isolated from various species of wild birds worldwide, with C. jejuni being the most commonly isolated species. The prevalence of Campylobacter in wild birds may vary depending on several factors like geographical location, season, the bird’s health status, bird species, sample type, the method used, and ecological factors. Molecular studies over the past two to three decades have characterized Campylobacter strains isolated from wild birds and have come up with results that fall into two categories. The first are those that report overlapping strains among human, domestic animal, and wild bird isolates. The results of the studies under this category emphasize that wild birds carry strains of Campylobacter, which are indistinguishable from domestic animals and humans and are therefore an important public and animal health concern. In contrast, the studies under the second category highlight significant differences in Campylobacter population structure among these hosts. Despite the controversiality and the inadequacy of current research to draw a full conclusion, the role of wild birds in the epidemiology of Campylobacter should not be undermined as drug-resistant strains, especially resistance to tetracycline and fluoroquinolones, are increasingly documented. In addition, source attribution studies have linked human cases of Campylobacter infections to wild birds. Therefore, the role of wild birds in the epidemiology of Campylobacter infection should not be neglected. However, in order to determine disease status in wild birds and the precise role of wild birds in domestic animals and human health, detail-oriented epidemiological investigations characterizing the genetic relatedness of isolates from the respective species and environment through one health approach are warranted.

Prevalence and antimicrobial resistance of Campylobacter from wild birds of prey in Spain

Wild birds have been identified as a relevant reservoir of Campylobacter spp., therefore, a potential source of infection in humans and domestic animals. The objective of this study was to determine the occurrence of Campylobacter spp. on birds of prey in Spain. In addition, antibiotic resistance profiles of the isolates were evaluated. A total of 689 specimens of 28 raptor species were analyzed, with a resulting individual prevalence of 7.5%. C. jejuni was the most frequently isolated species (88.5%), followed by C. coli and C. lari (3.8% each). The occurrence of Campylobacter was significantly higher (p < 0.05) in nocturnal birds of prey (15.3%), in spring season (12.2%) and in carnivorous species (9.4%). Isolates displayed a remarkable resistance to nalidixic acid (69.9%), ciprofloxacin (69.9%), and tetracycline (55.6%), and a low resistance to streptomycin (6.7%). Our findings highlight the importance of birds of prey as reservoirs of Campylobacter strains and their significant role as carriers of antimicrobial resistance.

Help from the sky: Can vultures contribute to Cystic Echinococcosis control in endemic areas?

Cystic echinococcosis (CE) is endemic in Sardinia and constitutes a serious public health concern due to high prevalence in livestock and humans. Despite sustained efforts, control of the disease had been unsuccessful in the region. Problematic carcass disposal due to soaring incineration costs and free access of dogs to infected carrion are dominant factors, fueling endemicity among other. As sole obligate scavenger, griffon vultures (Gyps fulvus) are uniquely specialized to eliminate carcasses swiftly and efficiently, saving on unnecessary environmental and economic costs for carrion disposal. However, following drastic population declines across Europe, griffon vultures practically went extinct in Italy. A conservation expansion program in Sardinia successfully reinforced the last remaining Italian vulture population by mitigating the main threats to its survival; food shortage. Through the establishment of supplementary feeding stations, permanent supply of livestock cadavers was provided. In this research, the management and conservation implications on the controlled disposal of carcass disposal through vulture feeding stations on the control of CE in Sardinia were assessed. During the course of the project, vultures scavenged a total of 81,361 kg of biomass, saving €90,041 in incineration costs and € 1,054 in CO₂ emission. Through extrapolation of these results, a total of 5,304 kg of suspected CE infected sheep carcasses (65.3%) was calculated to have been disposed by griffons, considerably reducing the CE risk and burden in Sardinia. A quantification of the amount of biomass that could be eliminated by griffon in a succeeding conservation project was also made. These calculations implied that 162,722 kg of biomass, including 10,608 kg of infected biomass from sheep, would be consumed over a period of 5 years, further lowering the CE burden in Sardinia. Our results, driven under one health approach, emphasize the crucial and direct role of griffons in breaking the lifecycle of CE as well as their indirect role in rendering multiple ecosystem and economic services through the elimination of carcasses. Please view a video Abstract here: https://youtu.be/Tm820nPq5KE.

Cystic echinococcosis (CE), is a major parasitic disease of animal and public health significance due to high morbidity and mortality. The infection is caused by the larval stage of the dog tapeworm Echinococcus granulosus, frequently reported in rural pastoral regions. In Sardinia, CE is very abundant in livestock, especially in sheep (65.3%). Several control strategies were attempted to limit the spread of CE, however, it turns out that the elimination of disease requires long lasting efforts. High prevalence of CE in Sardinia is due to multiple factors, but the cost of carcass incineration and free access of dogs to unattended carcasses are major points in the persistency of the infection. Griffon vultures as sole obligate scavengers, are highly specialized in removing the animal carcasses swiftly and efficiently, but have suffered severe population declines in the last decade. A wildlife conservation project in Sardinia envisioned to expand the griffon population by utilizing animal carcasses of animals as feed for vultures. We aimed to investigate these natural scavenging habits of vultures and the use of such “vulture restaurants” in relation to the control of CE. Our results show that the vultures remove a significant quantity of infected biomass, simultaneously saving high cost for incineration and carbon emission. The study is one of the pioneer investigations in the biological control of CE along with its estimation of ecosystem and economic services provided by the griffons.

Exposure to Anthropogenic Areas May Influence Colonization by Zoonotic Microorganisms in Scavenging Birds

Wild bird species have commonly been implicated as potential vectors of pathogens to other species, humans included. However, the habitat where birds live could influence the probability to acquire these pathogens. Here, we evaluated if the characteristics of the environment used by obligate scavenging birds (vultures) influence their colonization by zoonotic pathogens. For this, we particularly focused on Salmonella spp., a zoonotic pathogen commonly present in bird species. The occurrence of this bacteria was evaluated in free ranging Andean condors (Vultur gryphus) using natural environments from Argentina and compared with those obtained from condors under human care. In addition, we compared our results with those reported for other wild vultures using natural and anthropized environments at a global scale. We did not find Salmonella spp. in samples of wild condors. Captive condor samples presented Salmonella spp. with an occurrence of 2.8%, and one isolate of Meticilin Resistant Staphylococcus aureus, among other potential pathogenic microorganisms. Moreover, some species of free ranging vultures from diverse geographical areas using anthropized environments tend to present higher occurrences of Salmonella spp. These results highlight the importance of pristine ecosystems to protect vultures' health toward pathogenic microorganisms that can produce disease in these birds, but also in other species. We call for more studies evaluating differences in occurrence of zoonotic pathogens in vultures according to the quality of the environment they use. Even when vultures have not been implicated in zoonotic pathogen spread, our results add information to evaluate potential events of pathogen spillover between vultures and from these birds to other species.

Prevalence and potential risk of Salmonella enterica in migratory birds from South Korea

Salmonella is a type of zoonotic bacteria that represents an economic and public health concern worldwide. Difficulties in sample collection from migratory birds mean little is known about their importance as a reservoir of Salmonella. The present study evaluated the prevalence and potential risk of Salmonella enterica in migratory birds. From 2012-2017, 3661 cloacal swabs from migratory birds were collected in South Korea and tested to isolate S. enterica. Strains were tested for antimicrobial resistance and the presence of virulence genes. Thirty-six S. enterica strains, including S. enterica serovar Typhimurium (n = 19), S. Berta (n = 16), and S. Virchow (n = 1), were isolated from 34 birds. Two migratory birds were simultaneously co-infected with two serotypes. S. enterica was isolated from the Mallard duck, Northern pintail, Eurasian wigeon, Spot-billed duck, Eastern great egret, and Intermediate egret. S. Virchow was resistant to ciprofloxacin, with a point mutation (Ser-83-Phe) in the gyrA gene. Ten virulence genes were detected; sixteen strains were positive for all ten virulence genes. Salmonella was isolated from different migratory bird species and geographic locations with up to 100 % similarity of PFGE type. Eight S. Virchow strains taken from migratory birds, poultry farms, and chicken meat showed the same PFGE type. Salmonella was transmitted across species, space, and time in migratory birds. These birds may play a role in the dispersal of pathogenic and antimicrobial-resistant Salmonella and sporadic Salmonella infections in poultry; therefore, they may represent a direct or indirect public health threat.

Urban birds: An important source of antimicrobial resistant Salmonella strains in Central Spain

Antimicrobial resistance (AMR) is one of the most important threats of the 21 st century. Wild birds have been described as reservoirs of AMR in different bacterial species, such as Salmonella spp. Privation of food, climate change and overpopulation have forced many wild species to modify their feeding habits, attending urban areas. In this context, the aim of this study was to study Salmonella presence, as well as related AMR in urban birds that inhabit the city and its surroundings. A total of 300 urban birds were sampled for Salmonella detection according to the ISO 6579-1:2017 (Annex D) recommendations, and serotyping was carried out according to the White-Kauffman-Le Minor scheme. Antimicrobial susceptibility was tested following 2013/652/EU Decision guides. Wild birds analysed were positive for Salmonella in 12.3 % of cases, with white storks fed in landfills as the most Salmonella prevalent species (p < 0.05). The most common serovars isolated were zoonotic (S. Enteritidis, S. Typhimurium and S. Typhimurium monophasic variant). From Salmonella isolated strains, 40.5 % were resistant to the most prevalent AMRs found in urban birds were ciprofloxacin (36.4 %), nalidixic acid (36.4 %) and colistin (27.3 %). The scientific community, public administration and population in general should work together to control antimicrobial administration and drug waste management in order to decrease the development and spread of AMR.

Microorganisms Resistant to Antimicrobials in Wild Canarian Egyptian Vultures (Neophron percnopterus majorensis)

Simple Summary

Antibiotics are used to prevent and treat bacterial infections in both animals and humans. If bacteria become resistant to them, in particular as the result of the misuse and overuse of antibiotics, the infections that they cause are harder to treat. Therefore, the detection of microorganisms resistant to antimicrobial drugs is an important issue, considering the interaction among domestic animals, human, the ecosystem and wild animals. Wild birds, and particularly birds-of-prey, are sentinels, reservoirs, spreaders and a source of infection for human beings and other animals. Wildlife can also act as an asymptomatic reservoir for zoonotic bacteria (e.g., Salmonella). The presence of antimicrobial-resistant microorganisms was investigated for a period of three years and the differences between chicks in the nest (n = 81) and adult and immature birds (n = 61) were analyzed. Gram negative bacteria were isolated in all the samples. Escherichia coli was obtained in 80.28% of the samples, where the prevalence of Salmonella in our study was 6.3%. The results of our study support the idea that raptors could act as reservoirs of Salmonella and antimicrobial-resistant bacteria, posing a risk not only to wildlife but also to livestock and the human population.

Abstract

Due to their predatory habits, raptors may serve as indicators of the presence of antimicrobial-resistant bacteria in the environment, but they also represent a public health risk for livestock and humans because they can act as reservoirs, sources and spreaders of these bacteria. Our objective was to determine the presence of antimicrobial-resistant bacteria in cloacal samples of Canarian Egyptian vultures (Neophron percnopterus majorensis), an endemic bird of prey. One hundred and forty-two cloacal swabs were obtained; Escherichia coli was isolated from 80.28% and Salmonella from 6.3% of these samples. Low levels of susceptibility to ampicillin, tetracycline and trimethoprim/sulfamethoxazole were found. About 20% of the isolates were resistant or presented intermediate susceptibility to fluoroquinolones. Surprisingly, we found isolates resistant to imipenem (6.96%). Isolates from chicks were more susceptible to antimicrobial drugs than adult and immature birds. About 50% of E. coli isolates were resistant to ampicillin, tetracycline and trimethoprim/sulfamethoxazole, and about 20% to piperacillin, enrofloxacin and marbofloxacin. High percentages of isolates of Salmonella were found to be resistant to cephalexin (88%) and aminoglycosides (greater than 77%). Our results support the idea that raptors could act as reservoirs of Salmonella and antimicrobial-resistant bacteria, posing a risk not only to wildlife but also to livestock and the human population, thus reinforcing the need to minimize the exposure of wildlife to antimicrobial agent through human and livestock waste.

Wild griffon vultures (Gyps fulvus) fed at supplementary feeding stations: Potential carriers of pig pathogens and pig-derived antimicrobial resistance?

The carriage of two important pathogens of pigs, that is enterotoxigenic Escherichia coli (ETEC) and Clostridioides difficile, was investigated in 104 cloacal samples from wild griffon vultures (Gyps fulvus) fed on pig carcasses at supplementary feeding stations (SFS), along with their level of antimicrobial resistance (AMR). E. coli was isolated from 90 (86.5%) samples, but no ETEC was detected, likely because ETEC fimbriae confer the species specificity of the pathogen. Resistance to at least one antimicrobial agent was detected in 89.9% of E. coli isolates, with AMR levels being extremely high (>70%) for tetracycline and streptomycin and very high (>50%) for ampicillin and sulfamethoxazole-trimethoprim. Resistance to other critically important antimicrobials such as colistin and extended-spectrum cephalosporins was 2.2% and 1.1%, respectively, and was encoded by the mcr-1 and bla_SHV-12 genes. Multidrug resistance was displayed by 80% of the resistant E. coli, and bla_SHV-12 gene shared plasmid with other AMR genes. In general, resistance patterns in E. coli from vultures mirrored those found in pigs. Clostridioides difficile was detected in three samples (2.9%); two of them belonged to PCR ribotype 078 and one to PCR ribotype 126, both commonly found in pigs. All C. difficile isolates were characterized by a moderate-to-high level of resistance to fluoroquinolones and macrolides but susceptible to metronidazole or vancomycin, similar to what is usually found in C. difficile isolates from pigs. Thus, vultures may contribute somewhat to the environmental dissemination of some pig pathogens through their acquisition from pig carcasses and, more importantly, of AMR for antibiotics of critical importance for humans. However, the role of vultures would likely be much lesser than that of disposing pig carcasses at the SFS. The monitoring of AMR, and particularly of colistin-resistant and ESBL-producing E. coli, should be considered in pig farms used as sources of carcasses for SFS.

California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals

Around the world, scavenging birds such as vultures and condors have been experiencing drastic population declines. Scavenging birds have a distinct digestive process to deal with higher amounts of bacteria in their primary diet of carcasses in varying levels of decay. These observations motivate us to present an analysis of captive and healthy California condor (Gymnogyps californianus) microbiomes to characterize a population raised together under similar conditions. Shotgun metagenomic DNA sequences were analyzed from fecal and cloacal samples of captive birds. Classification of shotgun DNA sequence data with peptide signatures using the Sequedex package provided both phylogenetic and functional profiles, as well as individually annotated reads for targeted confirmatory analysis. We observed bacterial species previously associated with birds and gut microbiomes, including both virulent and opportunistic pathogens such as Clostridium perfringens, Propionibacterium acnes, Shigella flexneri, and Fusobacterium mortiferum, common flora such as Lactobacillus johnsonii, Lactobacillus ruminus, and Bacteroides vulgatus, and mucosal microbes such as Delftia acidovorans, Stenotrophomonas maltophilia, and Corynebacterium falsnii. Classification using shotgun metagenomic reads from phylogenetic marker genes was consistent with, and more specific than, analysis based on 16S rDNA data. Classification of samples based on either phylogenetic or functional profiles of genomic fragments differentiated three types of samples: fecal, mature cloacal and immature cloacal, with immature birds having approximately 40% higher diversity of microbes.

Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5],12:i:- Strains Isolated from Wild Griffon Vultures in Eastern Spain

Monophasic Salmonella enterica subsp. enterica serovar Typhimurium is one of the most common zoonotic pathogens. Salmonella species reside in a wide variety of hosts, including wild animals. Thus, we report here the genome sequences of 12 monophasic S. Typhimurium strains isolated from healthy wild vultures to gain better insight into their epidemiology and host-pathogen interactions.

Wild Bonelli's eagles (Aquila fasciata) as carrier of antimicrobial resistant Salmonella and Campylobacter in Eastern Spain

Wild birds have repeatedly been found to be involved in the dissemination of enteric bacterial pathogens in the environment. The aim of this study was to determine the occurrence of Salmonella and Campylobacter as well as the antimicrobial resistance in wild Bonelli's eagles nestlings in Eastern Spain. In addition, we compared the efficiency of two sampling methods (fresh faecal samples from nest and cloacal swabs from nestlings) for detection of both bacteria. A total of 28 nests with 45 nestlings were analysed. In the nest, Salmonella occurrence was 61 ± 9.2%, while Campylobacter occurrence was 11 ± 5.8% (p < 0.05). In the nestlings, Salmonella occurrence was 36 ± 7.1%, while Campylobacter occurrence was 11 ± 4.7% (p < 0.05). Eight Salmonella serovars were identified, and the most frequently isolated were S. Enteritidis, S. Typhimurium, S. Houston, and S. Cerro. Only one Campylobacter species was identified (C. jejuni). Regarding antimicrobial resistance, the Salmonella strains isolated were found to be most frequently resistant to ampicillin and to tigecycline; however, the sole Campylobacter strain recovered was multidrug resistant. In conclusion, this study demonstrated that wild Bonelli's eagles nestlings are greater carriers of Salmonella than of Campylobacter. Both Salmonella and Campylobacter isolates exhibited antimicrobial resistance. In addition, faecal samples from nests were most reliable for Salmonella detection, while cloacal swab from nestlings were most reliable for Campylobacter detection.

Scavenger birds exploiting rubbish dumps: Pathogens at the gates

Different bacteria are present in rubbish dumps used as food resources by various bird species. Birds may be good indicators of the presence of zoonotic diseases in these sites since they can be infected with zoonotic pathogens by foraging on organic waste, and can also act as carriers. We studied if foraging in rubbish dumps increases the occurrence of Salmonella spp. and Chlamydia psittaci in American black vultures (Coragyps atratus, hereafter black vultures) from northwest Patagonia. We compared these pathogens isolated from or detected in cloacae and oropharynx swabs in two different groups of black vultures: individuals trapped in (a) the Patagonian wild steppe and (b) in a rubbish dump. We found that black vultures are colonized by Salmonella spp. (particularly Salmonella enterica serotypes Typhi, Paratyphi A, Salmonella enterica subsp. arizonae) and Chlamydia psittaci. Interestingly, there were differences in the prevalence of Salmonella spp., especially Salmonella Typhi, between individuals foraging in the rubbish dump and the steppe, but not in the prevalence of Chlamydia psittaci. The pathogens isolated from black vultures may impact their health status but could also have health impacts in other bird species and even humans. In fact, Salmonella Typhi can cause severe disease in humans leading to death. Our results are globally relevant given that bacterial infections from rubbish dumps may affect different species exploiting these sites around the world. There is a need to better control pathogens in rubbish dumps to avoid the risk of infecting wildlife, which could act as potential dispersers and reservoirs of these pathogens.

Supplementary feeding stations for conservation of vultures could be an important source of monophasic Salmonella typhimurium 1,4,[5],12:i:

Vultures are nature's most successful scavengers, feeding on the carcasses of dead animals present in the field. Availability of domestic carrion has been unstable due to rapidly changing agro-grazing economies and increasing sanitary regulations that may require burial or burning of livestock carcasses. Thus, several griffon vulture (Gyps fulvus) recoveries are based on European legislation that guarantees the animals' welfare, avoids intense persecution of the vultures and allows the feeding of threatened wildlife in supplementary feeding stations (SFS). However, in recent years, many studies have speculated on the likelihood that avian scavengers may be infected by feeding on pig carcasses at SFS from intensive livestock. In this context, the present study evaluated whether free-living griffon vultures and pig farms share zoonotic Salmonella strains to test the hypothesis that vulture are infected during consumption of carcasses provided at SFS. Here, the occurrence, serotypes and genomic DNA fingerprinting (phage typing and pulsed-field gel electrophoresis) of isolated strains were carried out in griffon vultures and pig farms authorised to provided carcasses at SFS in Castellón province (eastern Spain). The bacteriological analyses revealed that 21.1% of vultures and 14.5% for pig farms samples tested were Salmonella-positive. Monophasic S. typhimurium 1,4,[5],12:i:- was the most frequently isolated serovar. Comparison of Salmonella strains isolated from vultures and pig farms revealed that monophasic S. typhimurium 1,4,[5],12:i:-, S. Derby and S. Rissen strains were highly genetically homogeneous (similar DNA fingerprint). In conclusion, the current study indicates that free-living griffon vultures and pig farms that provide the carcasses at SFS share several zoonotic Salmonella strains. On this basis, and although transmission could be bidirectional, our result seems to corroborate the pig carcasses-to-vulture transmission and cross-infection at SFS. As an immediate Salmonella control strategy in wild avian scavengers, we suggest the implementation of a programme to guarantee that solely pig carcasses from Salmonella-free farms arrive at SFS.

Culture- and molecular-based detection of swine-adapted Salmonella shed by avian scavengers

Salmonella can play an important role as a disease agent in wildlife, which can then act as carriers and reservoirs of sanitary importance at the livestock-human interface. Transmission from livestock to avian scavengers can occur when these species consume contaminated carcasses and meat remains in supplementary feeding stations and rubbish dumps. We compared the performance of PCR-based detection with conventional culture-based methods to detect Salmonella in the faeces of red kites (Milvus milvus) and griffon vultures (Gyps fulvus) in central Spain. The occurrence of culturable Salmonella was intermediate in red kites (1.9%, n=52) and high in griffon vultures (26.3%, n=99). These proportions were clearly higher with PCR-based detection (13.5% and 40.4%, respectively). Confirmation cultures failed to grow Salmonella in all faecal samples positive by the molecular assay but negative by the initial conventional culture in both scavenger species, indicating the occurrence of false (non-culturable) positives by PCR-based detection. This suggests that the molecular assay is highly sensitive to detecting viable Salmonella in cultures, but also partial genomes and dead or unviable bacteria from past infections or contamination. Thus, the actual occurrence of Salmonella in a particular sampling time period can be underestimated when using only culture detection. The serovars found in the scavenger faeces were among the most frequently isolated in pigs from Spain and other EU countries, especially those generally recognized as swine-adapted monophasic variants of S. Typhimurium. Because the studied species obtain much of their food from pig carcasses, this livestock may be the primary source of Salmonella via direct ingestion of infected carcasses and indirectly via contamination due to the unsanitary conditions found in supplementary feeding stations established for scavenger conservation. Combining culture- and molecular-based detection is encouraged to understand the epidemiology and impact of Salmonella in wildlife populations.

Occurrence of enteropathogenic bacteria in birds of prey in Italy

The importance of wild birds as potential vectors of disease has received recent renewed empirical interest, especially regarding human health although information regarding the enteropathogenic bacteria in birds of prey continue to be scant. This study was performed with the aim to evaluate the occurrence of enteropathogenic bacteria (i.e. Campylobacter spp. Escherichia coli, Salmonella spp.) in birds of prey carcasses in Southern Italy. The results of the present study showed a prevalence of 33·1% (49/148) for Campylobacter spp. where all positive isolates (49/49) were identified as Campylobacter jejuni, and among these positive 12/49 were also identified as Campylobacter coli. Thus, 12/49 birds of prey showed mixed infections for both Campylobacter species. Differences in Campylobacter spp. prevalence between diurnal and nocturnal birds were statistically significant (P = 0·016). Escherichia coli showed a prevalence of 6·8% (10/148) and were serogrouped as O26 (n = 3), O55 (n = 2), O145 (n = 5). Salmonella spp. showed a prevalence of 6·8% (10/148) and were serotyped as S. Napoli (n = 4), Salmonella salamae (n = 3) and S. Typhimurium (n = 3). Although wildlife disease outbreaks have often been underreported in the broader context of global epidemiology, results of the present study suggest that birds of prey may serve as a reservoir of pathogens for livestock and human health, acting at the animal-human-ecosystem interface.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study confirms the role of birds of prey as a reservoir of enteropathogenic bacteria (i.e. Campylobacter spp., Escherichia coli, Salmonella spp.). Wild birds can contaminate environment with their faeces and play a crucial role in the transmission of pathogens to poultry and livestock farms and aquifers supplying water to humans. Furthermore, wild birds could disseminate pathogens within rescue and rehabilitation centres where they are admitted.

Supplementary feeding as a source of multiresistant Salmonella in endangered Egyptian vultures

Wild birds have repeatedly been highlighted as vectors in the dissemination of livestock and human pathogens. Here, the occurrence, serotypes and antimicrobial resistance of Salmonella were assessed in adult Egyptian vultures (Neophron percnopterus), to test the hypothesis that infection is associated with the consumption of swine carcasses provided at supplementary feeding stations (SFSs). Faeces of year-round resident griffon vultures (Gyps fulvus) were also tested to assess whether infection was acquired in the breeding grounds of both species or in the African wintering quarters of Egyptian vultures. Depending on the shedding rate criteria considered, the occurrence of infection in Egyptian vultures varied between the three consecutive sampling days in a range with a minimum of 23%-41% and a maximum of 64%-92% of individuals (n = 11-14 individuals, 27-39 faeces). The occurrence in the single sampling of griffon vultures was 61% of faeces (n = 18). Vultures mostly fed on pig carcasses, which together with their predominant infection with multiresistant serotypes (mostly the monophasic 4,12:i:- variant resistant to aminopenicillins, aminoglycosides and tetracyclines) typically found in pigs from Spain, strongly supports a carcass-to-vulture transmission and cross-infection routes at SFSs. Efforts are encouraged to avoid discarding carcasses of pigs with Salmonella at SFSs established for the conservation of threatened scavengers. This could contribute to reducing the long-distance transmission of resistant pathogens with an impact on livestock and human health while avoiding infection risk and its effects on wildlife.

Occurrence of veterinary pharmaceuticals in golden eagle nestlings: Unnoticed scavenging on livestock carcasses and other potential exposure routes

Wildlife exposure to pharmaceuticals can occur through contaminated water, and through the excreta and carcasses of medicated livestock, with potential for bioaccumulation and transfer through food webs. We evaluated whether nestling exposure to pharmaceuticals can occur from food delivered to nests in the golden eagle (Aquila chrysaetos), a top predator and facultative scavenger. Despite the fact that diet analysis suggests an apparently low dependence on livestock carcasses reduced to two piglets remains (1.5% of food remains, n=134), a high proportion of nestlings (71%, n=7) showed fluoroquinolone residues in plasma, mostly enrofloxacin, which is exclusively used in veterinary treatments. The occurrence and concentration (54.5±6.6μg·L^-1) of fluoroquinolones in plasma was similar to those found in the nestlings of three vulture species largely dependent on livestock carcasses obtained at supplementary feeding stations, which are managed for the conservation of their populations. Although the number of analysed eaglets is comparatively small, the fact that enrofloxacin was found in all nests sampled in three breeding seasons suggest an exposure to the drugs similar to that of vultures. An underestimation of the role of carrion, especially from small piglets whose consumption may have gone unnoticed, and the predation of semi-domestic prey and generalist prey exploiting carcasses of medicated livestock, can contribute to explaining the unexpectedly high occurrence of these drugs in eaglets.

Supplementary feeding and endoparasites in threatened avian scavengers: Coprologic evidence from red kites in their wintering stronghold

Many obligate and facultative avian scavengers are increasingly dependent on food provided in supplementary feeding stations (SFS), which are managed for the conservation of these species. Deliberate feeding can influence disease-related host demography and population dynamics through physiological changes and density-dependent parasite acquisition and transmission, but information on this threat to avian scavengers is scarce. Due to their effects on host aggregation and density, we hypothesised that the predictability and concentration of food in SFS can exacerbate parasite infection. This hypothesis was tested by comparing the prevalence, richness, abundance and mixed infection of endoparasites (coccidia and helminths) in red kites Milvus milvus foraging on livestock carcasses (mostly of pigs and poultry) in overcrowded and confined conditions at SFS, relative to those foraging alone or in small groups on wild prey unevenly randomly distributed within large areas during winter, mostly wild rabbits (Oryctolagus cuniculus). No clear differences were found between areas with and without SFS in the prevalence and abundance of oocyst of Eimeria. This coccidian genus appears to include parasites of the prey rather than the raptors, thus representing parasite transport or pseudo-parasitism rather than actual parasitism in the kites. A higher prevalence and richness of helminths, as well as mixed infections with several phyla, was found in kites exploiting SFS than in those feeding on wild prey in the area without SFS. The unsanitary conditions derived from the stack of livestock carcasses and the contamination of carrion with the faeces of multiple scavenger hosts can increase the accumulation and persistence of helminths eggs and intermediate hosts. The regular use and frequent confinement of large numbers of red kites at SFS can promote the spread of parasites to a large proportion of the European breeding population distributed across Spain during the winter. We encourage that carcasses of free roaming livestock can be left in the countryside, as well as the conservation management of wildlife exploited as food by red kites (especially wild rabbits), to attempt avoiding overcrowded and confined conditions at SFS. Further research is required to assess the impact of deliberate feeding on the spread of parasites and other disease agents in the threatened species SFS are intended to favour.

Food safety in scavenger conservation: Diet-associated exposure to livestock pharmaceuticals and opportunist mycoses in threatened Cinereous and Egyptian vultures

Pharmaceuticals from veterinary treatments may enter terrestrial food webs when medicated livestock are available to wildlife in supplementary feeding stations aimed at the conservation of endangered scavengers. Here, we hypothesized that the exposure risk to livestock fluoroquinolones, as indicators of pharmaceutical burden in food, is related to the variable reliance of scavengers on domestic versus wild animal carcasses. Since the misuse of broad-spectrum antibiotics is a major predisposing factor for opportunistic mycoses, we evaluated disease signs potentially associated with diet-dependent drug exposure in nestlings of two threatened vultures. A greater occurrence (100%, n=14) and concentration of fluoroquinolones (mean±SD=73.0±27.5µgL^-1, range=33.2-132.7), mostly enrofloxacin, were found in Cinereous vultures, Aegypius monachus, due to their greater dependence on livestock carcasses than Egyptian vultures, Neophron percnopterus (fluoroquinolones occurrence: 44%, n=16, concentration: 37.9±16.6µgL^-1, range=11.5-55.9), which rely much more on carcasses of wild animals (42% of remains vs. 23% in the cinereous vulture). The chaotic, chronic and pulsed ingestion of these drugs throughout nestling development is proposed as one of the most plausible explanations for the high occurrence and intensity of oral Candida-like lesions in nestling vultures. The high occurrence of fluoroquinolone residues and disease hindered the probing of a cause-effect relationship between both factors in individual vultures. This relationship could be evaluated through a population-based approach by sampling vultures not exposed to these drugs. The high dependence of vultures on domestic animals today compared to past decades and the growing intensification of livestock farming, imply an expected increase in the impact of pharmaceuticals on scavenger populations. This requires further evaluation due to potential consequences in biodiversity conservation and environmental health. We encourage the prioritization of efforts to promote the use of less medicated free-ranging livestock carcasses left in the countryside, rather than stabled stocks made available in vulture restaurants. Additionally, attention should be paid to the population recovery of wild species that dominated scavenger diets in the past.

Evaluation of bacteriocinogenic activity, safety traits and biotechnological potential of fecal lactic acid bacteria (LAB), isolated from Griffon Vultures (Gyps fulvus subsp. fulvus)

Background

Lactic acid bacteria (LAB) are part of the gut microbiota and produce ribosomally synthesized antimicrobial peptides or bacteriocins with interest as natural food preservatives and therapeutic agents. Bacteriocin-producing LAB are also attractive as probiotics. Griffon vultures (Gyps fulvus subspecies fulvus) are scavenger birds that feed almost exclusively on carrion without suffering apparent ill effects. Therefore, griffon vultures might be considered a reservoir of bacteriocin-producing lactic acid bacteria (LAB) with potential biotechnological applications.

Results

Griffon vulture feces were screened for LAB with antimicrobial activity, genes encoding bacteriocins, potential virulence determinants, susceptibility to antibiotics, genotyping and characterization of bacteriocins. In this study, from 924 LAB evaluated 332 isolates (36 %) showed direct antimicrobial activity against Gram-positive bacteria only. The molecular identification of the most antagonistic 95 isolates showed that enterococci was the largest LAB group with antimicrobial activity (91 %) and E. faecium (40 %) the most identified antagonistic species. The evaluation of the presence of bacteriocin structural genes in 28 LAB isolates with the highest bacteriocinogenic activity in their supernatants determined that most enterococcal isolates (75 %) encoded multiple bacteriocins, being enterocin A (EntA) the largest identified (46 %) bacteriocin. Most enterococci (88 %) were resistant to multiple antibiotics. ERIC-PCR and MLST techniques permitted genotyping and recognition of the potential safety of the bacteriocinogenic enterococci. A multiple-step chromatographic procedure, determination of the N-terminal amino acid sequence of purified bacteriocins by Edman degradation and a MALDI TOF/TOF tandem MS procedure permitted characterization of bacteriocins present in supernatants of producer cells.

Conclusions

Enterococci was the largest LAB group with bacteriocinogenic activity isolated from griffon vulture feces. Among the isolates, E. faecium M3K31 has been identified as producer of enterocin HF (EntHF), a bacteriocin with remarkable antimicrobial activity against most evaluated Listeria spp. and of elevated interest as a natural food preservative. E. faecium M3K31 would be also considered a safe probiotic strain for use in animal nutrition.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0840-2) contains supplementary material, which is available to authorized users.

Determination of fluoroquinolone antibiotic residues in the plasma of Eurasian griffon vultures (Gyps fulvus) in Spain

Due to the possible toxicological impact, the accumulation of pharmaceuticals in wildlife as a consequence of human practices is of growing concern. The consumption of carrion at feeding stations - the so-called 'vulture restaurants' - with no management of the veterinary drugs it contains may expose scavengers to pharmaceuticals. To demonstrate this, we analyzed plasma from Eurasian griffon vultures (Gyps fulvus) originating from two different areas of Spain for antibiotics such as enrofloxacin and ciprofloxacin, its primary metabolite. Quinolone residues were detected in about 65% (n=106) of birds, of which 15.1% (16/106) had quantifiable amounts of enrofloxacin (0.049±0.102μg/mL) and 5.7% (6/106) of ciprofloxacin (0.009±0.007μg/mL). The differences in exposure between the two sampled areas are attributable to different types of carrion management: the vultures that fed in areas with a high density of dead livestock (supplied directly to feeding stations) were more prone to exposure than those that sought food in areas where carcass availability is more unpredictable. Our findings are evidence that vultures have access to medicated livestock and that there are quantifiable levels of livestock antibiotics in vulture plasma. However, the vultures analyzed in this study had maximum antibiotic concentrations of only 0.4μg/mL, much less than the concentrations used in the clinical treatment of scavengers and a level that is probably too small to cause intoxication.

Wildlife contamination with fluoroquinolones from livestock: Widespread occurrence of enrofloxacin and marbofloxacin in vultures

There is much recent interest in the presence and impact of veterinary pharmaceuticals in wildlife. Livestock carcasses are often disposed of in supplementary feeding stations for avian scavengers, as a management and conservation tool for these species worldwide. In feeding stations, vultures and other scavengers can consume carcasses almost immediately after disposal, which implies the potential ingestion of veterinary pharmaceuticals as a non-target consequence of supplementary feeding. Using UPLC-MS/MS and HPLC-TOF, we evaluated the presence and concentration of fluoroquinolone residues in plasma of nestling vultures feeding on domestic livestock carrion. Three different fluoroquinolones (marbofloxacin, enrofloxacin and its metabolite ciprofloxacin) and a non-targeted β-lactam (nafcillin) were detected in vulture plasma. The high proportion of individuals (92%) with fluoroquinolone residues at variable concentrations (up to ∼20 μg L(-1) of enrofloxacin and ∼150 μg L(-1) of marbofloxacin) sampled in several geographically distant colonies and on different dates suggests that these and other drugs were potentially ingested throughout nestling development. Contamination with veterinary fluoroquinolones and other pharmaceuticals should be considered as an unintended but alarming consequence of food management in threatened wildlife.

Exploring the avian gut microbiota: current trends and future directions

Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill crucial roles in providing the host with nutrition and protection from pathogens. Across the field of avian microbiology knowledge is extremely uneven, with several species accounting for an overwhelming majority of all microbiological investigations. These include agriculturally important birds, such as chickens and turkeys, as well as birds of evolutionary or conservation interest. In our previous study we attempted the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available data sets. We have now extended our analysis to explore the microbiology of several key species in detail, to consider the avian microbiota within the context of what is known about other vertebrates, and to identify key areas of interest in avian microbiology for future study.

Global Epidemiology of Campylobacter Infection

Campylobacter jejuni infection is one of the most widespread infectious diseases of the last century. The incidence and prevalence of campylobacteriosis have increased in both developed and developing countries over the last 10 years. The dramatic increase in North America, Europe, and Australia is alarming, and data from parts of Africa, Asia, and the Middle East indicate that campylobacteriosis is endemic in these areas, especially in children. In addition to C. jejuni, there is increasing recognition of the clinical importance of emerging Campylobacter species, including Campylobacter concisus and Campylobacter ureolyticus. Poultry is a major reservoir and source of transmission of campylobacteriosis to humans. Other risk factors include consumption of animal products and water, contact with animals, and international travel. Strategic implementation of multifaceted biocontrol measures to reduce the transmission of this group of pathogens is paramount for public health. Overall, campylobacteriosis is still one of the most important infectious diseases that is likely to challenge global health in the years to come. This review provides a comprehensive overview of the global epidemiology, transmission, and clinical relevance of Campylobacter infection.