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Background Gastrointestinal parasites are neglected infections, yet they cause significant burden to animal and human health globally. To date, most studies of gastrointestinal parasites focus on host-parasite systems that involve either a single parasite or a host species. However, when hosts share habitat and resources, they may also cross-transmit generalist gastrointestinal parasites. Here we explore multi-host-parasite interactions in a single ecosystem to understand the infection patterns, especially those linked to livestock-wildlife interfaces and zoonotic risk. Methods We used both coprological methods (flotation and sedimentation; N = 1,138 fecal samples) and molecular identification techniques (rDNA and mtDNA; N = 18 larvae) to identify gastrointestinal parasites in nine sympatric host species (cattle, sheep, goats, wildebeest, Grant's gazelles, Thomson's gazelles, impala, vervet monkeys and baboons) in the Amboseli ecosystem, Kenya. Results We found that the host community harbored a diverse community of gastrointestinal helminths, including 22 species and/or morphotypes that were heterogeneously distributed across the hosts. Six zoonotic gastrointestinal helminths were identified: Trichuris spp., Trichostrongylus colubriformis, Enterobius spp. Oesophagostomum bifurcum, Strongyloides stercoralis and Strongyloides fuelleborni. The dominant parasite was Trichuris spp, whose ova occurred in two morphological types. Baboons were co-infected with Strongyloides fuelleborni and S. stercoralis. Conclusions We found that the interface zone shared by wild ungulates, livestock and non-human primates is rich in diversity of gastrointestinal helminths, of which some are extensively shared across the host species. Closely related host species were most likely to be infected by the same parasite species. Several parasites showed genetic sub-structuring according to either geography or host species. Of significance and contrary to expectation, we found that livestock ha

The development of non-manipulative molecular tools to determine the origin of parasite infections in the animal trade (if infected before their export or import) is of great interest worldwide for both the animal trade industry and for animal welfare. Molecular tools have a wide range of applications, including forensic identification, wildlife preservation and conservation, veterinary public health protection, and food safety. Nonetheless, genetic markers were not reported to detect the source of infection in the animal trade. In this study we tested the applicability of molecular tools to detect the origin of Sarcoptes mite infection of wildebeest imported by the United Arab Emirate (UAE) from Tanzania. Using one multiplex of seven microsatellite markers and control samples from UAE, Kenya and Italy, we demonstrated the usefulness of the multiplex STR-typing as a molecular tool of pivotal interest to help commercialist, authorities, and conservationists, to identify the geographical origin of parasitic infections

Background Defining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is that isolated (and eventually small) wild animal populations hide unexpected genetic diversity due to their maintenance of ancient polymorphisms or introgressions. Results We tested this hypothesis using the Iberian ibex (Capra pyrenaica) as an example. Previous studies based on large sample sizes taken from its principal populations have revealed that the Iberian ibex has a remarkably small MHC DRB1 diversity (only six remnant alleles) as a result of recent population bottlenecks and a marked demographic decline that has led to the extinction of two recognized subspecies. Extending on the geographic range to include non-studied isolated Iberian ibex populations, we sequenced a new MHC DRB1 in what seemed three small isolated populations in Southern Spain (n = 132). The findings indicate a higher genetic diversity than previously reported in this important gene. The newly discovered allele, MHC DRB1*7, is identical to one reported in the domestic goat C. aegagrus hircus. Whether or not this is the result of ancient polymorphisms maintained by balancing selection or, alternatively, introgressions from domestic goats through hybridization needs to be clarified in future studies. However, hybridization between Iberian ibex and domestic goats has been reported in Spain and the fact that the newly discovered allele is only present in one of the small isolated populations and not in the others suggests introgression. The new discovered allele is not expected to increase fitness in C. pyrenaica since it generates the same protein as the existing MHC DRB1*6. Analysis of a microsatellite locus (OLADRB1) near the new MHC DRB1*7 gene reveals a linkage disequilibrium between these two loci. The allele OLADRB1, 187 bp in length, was unambiguously linked to

Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long-term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.

Pilobolus are abundant in herbivore dung. Although they are non-pathogenic to herbivores, they are vectors to lungworms present in the dung that cause bronchitis if ingested. Thus, determining the presence of Pilobolus in the field might prove useful to assess a link between Pilobolus and lungworm infections, as well as the areas where they occur. Species identification within the genus has mostly relied on morphological data, which lacks accuracy due to the overlap of morphological characters. In this study, we applied genetic identification to assess the presence of Pilobolus species in Nairobi National Park, Kenya. This method is more reliable than the more commonly used morphometric analyses, and the generated sequences are useful for future reference. In this study, we collected dung samples from different herbivores in Nairobi National Park, and sporangium isolates were obtained for pure cultures. DNA was extracted from the pure cultures and fungal barcode primers were employed for PCR amplification and sequencing. Two species of Pilobolus were identified, Pilobolus pullus, with a high genetic affinity, and a second cryptic species, morphologically identified as Pilobolus crystallinus, but did not have a close genetic match to any species in Genbank. Lack of identification of other Pilobolus species, known as key species in lungworm transmission, may suggest the absence of such in the sampled area.

The sanitary control of threatened wild animals is of pivotal interest for their conservation. This task, however, is highly complex in wildlife/livestock systems. In this paper we report findings from a 2-year cross-sectional study of the epidemiology and attempted control of a Sarcoptes mite infestation in the threatened cheetah population in Masai Mara (Kenya), and discuss its interaction with sympatric wild (lion, wildebeest and Thomson's gazelle) and domestic (dog, cattle and sheep) animals. Sarcoptes scabiei was isolated from cheetahs, Thomson's gazelles, wildebeests, lions, cattle, goats and dogs; Psoroptes ovis, on the other hand, was only isolated from sheep. The prevalence study revealed 12·77% infection rates in cheetahs, 4·7% in dogs, 0·8% in Thomson's gazelles, 0·8% in sheep, 0·09% in cattle, and 0·09% in goats, while it opportunistically affected lions and wildebeest. Our study revealed that prevalence of Sarcoptes mite in cheetah population was not associated with the studied geographical blocks, animal sex or the presence of affected domestic animals. Cheetah infection with S. scabiei was associated with the climatic conditions (dry more than wet season) and the balancing between the total number of Thomson's gazelles and the prevalence of infected individuals. Apparently the high prevalence of mangy gazelles has a negative effect on cheetah; this negative effect was reduced when the number of healthy gazelles was increased. Treatment with injectable ivermectin of the clinically affected wild and domestic animals during the first year of this study was associated with much lower incidence of sarcoptic mange during the second year

Background Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. Methodology/Principal Findings We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Conclusions Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies.

Following mass deaths of Laughing Doves (Streptopelia senegalensis) in different localities throughout Kenya, internal organs obtained during necropsy of two moribund birds were sampled and analyzed by next generation sequencing. We isolated the virulent strain of pigeon paramyxovirus type-1 (PPMV-1), PPMV1/Laughing Dove/Kenya/Isiolo/B2/2012, which had a characteristic fusion gene motif (110)GGRRQKRF(117). We obtained a partial full genome of 15,114 nucleotides. The phylogenetic relationship based on the fusion gene and genomic sequence grouped our isolate as class II genotype VI, a group of viruses commonly isolated from wild birds but potentially lethal to Chickens (Gallus gallus domesticus). The fusion gene isolate clustered with PPMV-I strains from pigeons (Columbidae) in Nigeria. The complete genome showed a basal and highly divergent lineage to American, European, and Asian strains, indicating a divergent evolutionary pathway. The isolated strain is highly virulent and apparently species-specific to Laughing Doves in Kenya. Risk of transmission of such a strain to poultry is potentially high whereas the cyclic epizootic in doves is a threat to conservation of wild Columbidae in Kenya.

In this study, we analysed the Sarcoptes scabiei infrapopulations of 315 Iberian ibex (Capra pyrenaica) by means of skin digestion and differential mite counts. Mean density reached 178.2 mites/cm (range: 0.71-4514.29). Although the most frequently affected zones were hosts extremities and withers, higher mite densities were obtained from lips and extremities, suggesting that indirect infection through the substrate could also play a role in the disease epidemiology, together with direct transmission. The sex ratio of mites was female-biased (mean: 5.18 ♀♀/♂, range: 0.5-17). Larvae were more frequently found (nearly 50% of specimens) than nymphs, adult females or adult males. Mite density varied significantly between years and decreased with host age. Most of the variance was explained by the year, host sex, weight and kidney fat index (KFI). Taking into account the catabolic nature of the disease, our results suggest that hosts in good body condition could evidence a certain degree of resistance to the disease, which presumably has a genetic basis.

Very little is known about the influence of massive and long distance migration on parasite epidemiology. Migration can simultaneously minimize exposure to common parasites in their habitats and increase exposure to novel pathogens from new environments and habitats encountered during migration, while physiological stress during long distance movement can lead to immune suppression, which makes migrants vulnerable to parasites. In this paper, we investigated the diversity, prevalence, parasite load, co-infection patterns and predilection sites of adult gastrointestinal helminths in 130 migrating wildebeests and tested for their relation with animal age, sex and migration time (which also could indicate different migration routes), and compared them with the non-migratory wildebeest. Surprisingly, only four parasite species were found, Oesophagostomum columbianum, Haemonchus placei, Calicophoron raja and Moniezia expansa, which were lower than in non-migratory wildebeest reported in the literature. These parasites were generalists, infecting livestock, and suggests that wildebeest and livestock, because of their interaction during migration, have a cross-infection risk. There was a negative relation between parasites diversity, prevalence and intensity of infection, and host age, which suggests that wildebeests acquire protective immunity against these parasites as they get older. Prevalence and intensity of infection were higher among wildebeest crossing the Mara Bridge (early migrants) compared to those crossing the Serena (late migrants), which suggests that early migrants (or migrants originating from different areas) have varying infection intensities. The prevalence and intensity of infection were higher in males compared to females and may be due to ecological, behavioural, or physiological differences between males and females. Our findings compared to those of previous studies suggest that migration may provide a mechanism to minimize exposure of hosts to co

[Background] Filarioid nematode parasites are major health hazards with important medical, veterinary and economic implications. Recently, they have been considered as indicators of climate change., [Findings] In this paper, we report the first record of Setaria tundra in roe deer from the Iberian Peninsula. Adult S. tundra were collected from the peritoneal cavity during the post-mortem examination of a 2 year-old male roe deer, which belonged to a private fenced estate in La Alcarria (Guadalajara, Spain). Since 2012, the area has suffered a high roe deer decline rate (75 %), for unknown reasons. Aiming to support the morphological identification and to determine the phylogenetic position of S. tundra recovered from the roe deer, a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from the two morphologically identified parasites was amplified, sequenced and compared with corresponding sequences of other filarioid nematode species. Phylogenetic analyses revealed that the isolate of S. tundra recovered was basal to all other formely reported Setaria tundra sequences. The presence of all other haplotypes in Northern Europe may be indicative of a South to North outbreak in Europe., [Conclusions] This is the first report of S. tundra in roe deer from the Iberian Peninsula, with interesting phylogenetic results, which may have further implications in the epidemiological and genetic studies of these filarioid parasites. More studies are needed to explore the reasons and dynamics behind the rapid host/geographic expansion of the filarioid parasites in Europe.

[Background] The mite Sarcoptes scabiei has a known host-range of over 100 mammal species including humans. One of the prime objectives of the Sarcoptes-World Molecular Network (WMN) is to design and develop universal Sarcoptes PCR-based diagnosis methods., [Methods] We describe here for the first time two universal mitochondrial-based diagnosis methods: (i) conventional end-point PCR and (ii) TaqMan real-time PCR. The design of both of these universal diagnosis methods was based on Sarcoptes samples collected from 23 host species in 14 countries., [Results] These methods, based on skin scrapings, were successfully used to etiologically confirm the diagnosis of different clinical degrees of sarcoptic mange in 48 animals belonging to six species. These universal PCR-based diagnosis methods are highly specific, technically sensitive and simple, and are based on the amplification of 135 bp from the Mitochondrial 16S rDNA. The method based on TaqMan real-time qPCR was more sensitive than the conventional end-point PCR., [Conclusions] Two universal PCR-based diagnosis methods for S. scabiei were successfully designed and applied; one based on conventional end-point PCR and the other on TaqMan real-time PCR. We recommend further testing and the application of these new universal methods worldwide.

[Background] A huge effort in rhinoceros conservation has focused on poaching and habitat loss as factors leading to the dramatic declines in the endangered eastern black rhinoceros (Diceros bicornis michaeli) and the southern white rhinoceros (Ceratotherium simum simum). Nevertheless, the role disease and parasite infections play in the mortality of protected populations has largely received limited attention. Infections with piroplasmosis caused by Babesia bicornis and Theileria bicornis has been shown to be fatal especially in small and isolated populations in Tanzania and South Africa. However, the occurrence and epidemiology of these parasites in Kenyan rhinoceros is not known., [Results] Utilizing 18S rRNA gene as genetic marker to detect rhinoceros infection with Babesia and Theileria, we examined blood samples collected from seven rhinoceros populations consisting of 114 individuals of black and white rhinoceros. The goal was to determine the prevalence in Kenyan populations, and to assess the association of Babesia and Theileria infection with host species, age, sex, location, season and population mix (only black rhinoceros comparing to black and white rhinoceros populations). We did not detect any infection with Babesia in the sequenced samples, while the prevalence of T. bicornis in the Kenyan rhinoceros population was 49.12% (56/114). White rhinoceros had significantly higher prevalence of infection (66%) compared to black rhinoceros (43%). The infection of rhinoceros with Theileria was not associated with animal age, sex or location. The risk of infection with Theileria was not higher in mixed species populations compared to populations of pure black rhinoceros., [Conclusion] In the rhinoceros studied, we did not detect the presence of Babesia bicornis, while Theileria bicornis was found to have a 49.12% prevalence with white rhinoceros showing a higher prevalence (66%) comparing with black rhinoceros (43%). Other factors such as age, sex, location, and population mix were not found to play a significant role.