Hidden diversity of cestodes in wild African carnivores: I. Non-taeniid cyclophyllideans

Our knowledge of parasites in wildlife remains limited, primarily due to restricted access to samples, especially of parasites from protected species. This present study contributes to the comprehension of the enigmatic world of helminths of African wild mammals and cestode biodiversity by combining both molecular and morphological analysis. Cestode samples were opportunistically collected from 77 individual definitive hosts in South Africa, Namibia and Ethiopia, encompassing 15 different species of wild African carnivores and additionally domestic cats. The analysis revealed 32 different cyclophyllidean species of which 21 (65.6 %) represent previously unknown genetic entities. They belong to the families Mesocestoididae, Hymenolepididae, Dipylidiidae and Taeniidae. Here we cover the non-taeniid cestodes, while the taeniids will be addressed in a separate publication. Three of the non-taeniid species uncovered in this study could be assigned to the genus Mesocestoides and were isolated from servals and domestic cats. The white-tailed mongoose was found to be a suitable host for a species belonging to the Hymenolepididae, which was identified as Pseudandrya cf. mkuzii. Both feline and canine genotypes of Dipylidium caninum were detected in domestic cats, the canine genotype also in an African wolf. In addition to these, a novel species of Dipylidium was discovered in an aardwolf. Lastly, four distinct species of Joyeuxiella were found in this study, revealing a cryptic species complex and emphasizing the need for a taxonomic reassessment of this genus. Despite the limited scope of our study in terms of geography and sample size, the results highlight that biodiversity of cestodes in African wild mammals is grossly under-researched and follow-up studies are urgently required, in particular linking morphology to gene sequences.

High species diversity of Echinococcus spp. in wild mammals of Namibia

An opportunistic survey for Echinococcus spp. in wild mammals was conducted in seven distinct study areas throughout Namibia, representing all major ecosystems, between 2012 and 2021. In total, 184 individually attributable faeces and 40 intestines were collected from eight species of carnivores, and 300 carcasses or organs of thirteen species of ungulates were examined for Echinococcus cysts. Nested PCR and sequencing of the mitochondrial nad1 gene led to the identification of five species of the Echinococcus granulosus sensu lato complex. Echinococcus canadensis G6/7 was found throughout Namibia at low frequency in lions, cheetahs, African wild dogs, black-backed jackals and oryx antelopes. Echinococcus equinus was present only in northern Namibia, locally at high frequency in lions, black-backed jackals and plains zebras. Echinococcus felidis was found only in one small area in the north-east of Namibia, but with high frequency in lions and warthogs. Echinococcus granulosus sensu stricto was identified only in two African wild dogs in the north-east of Namibia, and Echinococcus ortleppi occurred in central and southern Namibia in black-backed jackals and oryx antelopes. The development of fertile cysts indicated active intermediate host roles of oryx antelopes for E. canadensis and E. ortleppi, of warthogs for E. felidis, and of plains zebras for E. equinus. Our data support earlier hypotheses of exclusive or predominant wildlife life-cycles for E. felidis involving lions and warthogs, and - in Namibia - for E. equinus involving lions and/or black-backed jackals and plains zebras. Our data further support an interlink of wild and domestic transmission for E. ortleppi. A possible involvement of livestock and domestic dogs in transmission of E. canadensis G6/7 and E. granulosus s.s., the two parasite species with highest zoonotic potential, is uncertain for Namibia and needs further investigation.

When wildlife comes to town: interaction of sylvatic and domestic host animals in transmission of Echinococcus spp. in Namibia

The present study was conducted in the isolated desert town of Oranjemund in the far south of Namibia. It is an extremely arid region where no livestock husbandry is practiced and only animals adapted to the desert can be found. However, in and around the city, artificial irrigation maintains lush green patches of grass that attract wild animals, in particular oryx antelopes (Oryx gazella). In 2015 four oryx antelopes were euthanised due to poor conditions and a post-mortem examination was conducted. Two were found positive for cystic echinococcosis and 16 cysts were collected for molecular analyses. In addition, faecal samples from black-backed jackals (n=5) and domestic dogs (n=9), which were regularly observed to feed on oryx carcasses, were collected and taeniid eggs isolated. Parasite species identification of the cysts and eggs was done by amplifying and sequencing the mitochondrial nad1 gene. Both oryx antelopes were found infected with E. ortleppi and one co-infected with E. canadensis G6/7. Both Echinococcus species were able to develop fertile cysts in oryx, making oryx antelopes competent hosts for these parasites. Therefore, the analysis of faecal samples was of high interest and although the numbers were quite small, taeniid eggs were found in three out of five faecal samples of jackals and in all nine dog samples. However, species determination was only successful with two jackal and one dog sample. All three were positive for E. canadensis G6/7. The absence of E. ortleppi may be due to the low number of faecal samples examined. In our small study, we discovered a rather unique lifecycle of Echinococcus spp. between jackals and domestic dogs as definitive hosts and oryx antelopes as intermediate hosts. Here, the presence of E. canadensis G6/7 is of particular concern, as it is the second most important causative agent of CE in humans.

A community approach for pathogens and their arthropod vectors (ticks and fleas) in cats of sub-Saharan Africa

Background

Arthropod-borne pathogens and their vectors are present throughout Africa. They have been well studied in livestock of sub-Saharan Africa, but poorly studied in companion animals. Given their socioeconomic importance, the African Small Companion Animal Network (AFSCAN), as part of the WSAVA Foundation, initiated a standardized multi-country surveillance study.

Methods

In six countries (Ghana, Kenya, Nigeria, Tanzania, Uganda, and Namibia) in both rural and urban settings, 160 infested cats were sampled to assess their ectoparasite community (ticks and fleas), as well as the micro-parasite prevalence within those ectoparasites (60 and 118 pools of ticks and fleas, respectively) and blood (276 cats, including 116 non-infested).

Results

Almost two thirds of all infested cats originated from Tanzania and Kenya. Despite the large macro-geographical variation, no consistent difference was found in ectoparasite diversity and numbers between East and West Africa. Far more flea-infested than tick-infested cats were found. The most dominant ectoparasite was Ctenocephalides felis. Among the ticks, the exophilic Haemaphysalis spp. were the commonest, including species that are not typically linked with companion animals (Haemaphysalis spinulosa and Haemaphysalis elliptica). The most prevalent pathogens found in the blood and fleas were Bartonella henselae and Mycoplasma haemofelis. In the ticks, the dog-associated Hepatozoon canis was most commonly found. A high degree of co-parasitism was found in all countries and habitats.

Conclusions

Our continent-wide standardized field study highlights the cat’s potential to serve as a reservoir of pathogens that can be transmitted to humans or livestock, especially when cats are expected to become more commonly kept in African villages and towns.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05436-y.

Cystic echinococcosis of ruminant livestock in Namibia

Cystic echinococcosis (CE) is widespread and locally frequent in southern Africa where it affects humans, livestock, and wild mammals. However, most data from the region are old and do not provide information on the causative Echinococcus species. For Namibian livestock only anecdotal records were available prior to this preliminary survey. Our retrospective analysis of slaughterhouse records of CE in cattle from the commercial farming area in central and southern Namibia resulted in 1.65% CE prevalence among 35,143 slaughtered cattle in the period 2015-2016. For comparison, carcasses of ruminant livestock were prospectively examined in the communal farming areas of northern Namibia, resulting in three CE cases among only 12 cattle, and no cases among nine goats. To determine the Echinococcus species affecting Namibian livestock, a total of 53 cysts were collected from all parts of the country and analysed for species and genotype by amplification and sequencing of the nad1 gene. All 50 cattle cysts (isolated from 40 cattle), both from the commercial and communal farming areas, were Echinococcus ortleppi (all fertile, and 42/50 from the lungs), while three opportunistically collected cysts from three sheep in southern Namibia were E. canadensis G7. Our data suggest that E. ortleppi is the only CE agent that is relevant for cattle infection in Namibia, and that low prevalence in the commercial farming areas contrasts with high CE burden in the northern traditional husbandry systems. The present data provide baseline information to stimulate epidemiological studies on the transmission pathways of various CE agents in livestock, wildlife, and humans in Namibia and neighbouring countries.

Population structure, inbreeding and stripe pattern abnormalities in plains zebras

One of the most iconic wild equids, the plains zebra occupies a broad region of sub-Saharan Africa and exhibits a wide range of phenotypic diversity in stripe patterns that have been used to classify multiple subspecies. After decades of relative stability, albeit with a loss of at least one recognized subspecies, the total population of plains zebras has undergone an approximate 25% decline since 2002. Individuals with abnormal stripe patterns have been recognized in recent years but the extent to which their appearance is related to demography and/or genetics is unclear. Investigating population genetic health and genetic structure are essential for developing effective strategies for plains zebra conservation. We collected DNA from 140 plains zebra, including seven with abnormal stripe patterns, from nine locations across the range of plains zebra, and analyzed data from restriction site-associated and whole genome sequencing (RAD-seq, WGS) libraries to better understand the relationships between population structure, genetic diversity, inbreeding, and abnormal phenotypes. We found that genetic structure did not coincide with described subspecific variation, but did distinguish geographic regions in which anthropogenic habitat fragmentation is associated with reduced gene flow and increased evidence of inbreeding, especially in certain parts of East Africa. Further, zebras with abnormal striping exhibited increased levels of inbreeding relative to normally striped individuals from the same populations. Our results point to a genetic cause of stripe pattern abnormalities, and dramatic evidence of the consequences of habitat fragmentation.

Mapping and assessing the impact of small-scale ephemeral water sources on wildlife in an African seasonal savannah

In many savannah regions of Africa, pronounced seasonal variability in rainfall results in wildlife being restricted to floodplains and other habitats adjacent to permanent surface water in the dry season. During the wet season, rainfall fills small-scale, ephemeral water sources that allow wildlife to exploit forage and other resources far from permanent surface water. These water sources remain difficult to quantify, however, due to their small and ephemeral nature, and as a result are rarely included in quantitative studies of wildlife distribution, abundance, and movement. Our goal was to map ephemeral water in Bwabwata National Park in Namibia using two different approaches and to relate measures of ephemeral water to the abundance, distribution, and movement of two large wildlife species. We used high-resolution Google Earth and Esri World imagery to visually identify waterholes. Additionally, we used Sentinel-2 satellite imagery to map ephemeral water across the study area using the Normalized Difference Water Index. With these mapped waterhole layers and data from GPS-collared individuals of African elephant (Loxodonta africana) and African buffalo (Syncerus caffer), we evaluated the importance of ephemeral water in conditioning abundance and movement of these two species. The two approaches to mapping ephemeral water resulted in the visual identification of nearly 10,000 waterholes, and a predicted ephemeral water layer of ~76% accuracy. The inclusion of ephemeral water into models of abundance and movement resulted in improved goodness of fit relative to those without water, and water impacts on abundance and movement were among the strongest of all variables considered. The potential importance of ephemeral water in conditioning the movements and distributions of large herbivores in African savannahs has been difficult to quantify relative to vegetation drivers. Our results suggest research into ephemeral water impacts deserves more attention.

Genetic differentiation of the G6/7 cluster of Echinococcus canadensis based on mitochondrial marker genes

Among the genotype/species causing cystic echinococcosis, the taxonomic status of Echinococcus canadensis is only partially resolved. Within E. canadensis, four genotypes (G6, G7, G8 and G10) have been described based on short mitochondrial sequences, of which G6 and G7 (the 'camel' and the 'pig' strain, respectively) are closely related and variously regarded as microvariants of a single strain G6/7. Globally, this G6/7 cluster is the second most important agent of human cystic echinococcosis and is the predominant Echinococcus taxon in large parts of sub-Saharan Africa. To add data on the internal structure and the geographical distribution of this cluster, we analysed diversity and population structure of 296 isolates of E. canadensis from sub-Saharan Africa, the Middle East and Europe using the complete mitochondrial cytochrome c oxidase subunit 1 (cox1) (1,608bp) and NADH dehydrogenase subunit 1 (nad1) (894bp) gene sequences. Polymorphism of the mtDNA loci gave 51 (cox1), 33 (nad1) and 73 (cox1-nad1 concatenated) haplotypes. African and Middle Eastern isolates mainly grouped in a star-like structure around a predominant haplotype, while the European isolates produced more diversified networks. Although the cox1 diagnostic sequence for G6 is frequent in the African/Middle Eastern sub-cluster, and that for G7 is common in the European isolates, numerous intermediate variants prevent a clear distinction into 'G6' or 'G7', and the entire taxon is best treated as a common haplotype cluster G6/7. Meanwhile, the G6/7 cluster is clearly distinct from sequences of wildlife isolates of G8 and G10 from the northern hemisphere, and sequences of the latter genotypes were remarkably distant from each other. It is clear from the present study that, based on mitochondrial data, G6/7 is a coherent genotypic entity within E. canadensis that retains substantial intraspecific variance, and sub-populations share common ancestral polymorphisms and haplotypes. This study provides the basis for wider biogeographic comparison and population genetics studies of this taxon.

The global decline of cheetah Acinonyx jubatus and what it means for conservation

Establishing and maintaining protected areas (PAs) are key tools for biodiversity conservation. However, this approach is insufficient for many species, particularly those that are wide-ranging and sparse. The cheetah Acinonyx jubatus exemplifies such a species and faces extreme challenges to its survival. Here, we show that the global population is estimated at ∼7,100 individuals and confined to 9% of its historical distributional range. However, the majority of current range (77%) occurs outside of PAs, where the species faces multiple threats. Scenario modeling shows that, where growth rates are suppressed outside PAs, extinction rates increase rapidly as the proportion of population protected declines. Sensitivity analysis shows that growth rates within PAs have to be high if they are to compensate for declines outside. Susceptibility of cheetah to rapid decline is evidenced by recent rapid contraction in range, supporting an uplisting of the International Union for the Conservation of Nature (IUCN) Red List threat assessment to endangered. Our results are applicable to other protection-reliant species, which may be subject to systematic underestimation of threat when there is insufficient information outside PAs. Ultimately, conserving many of these species necessitates a paradigm shift in conservation toward a holistic approach that incentivizes protection and promotes sustainable human-wildlife coexistence across large multiple-use landscapes.

Rift Valley Fever Virus among Wild Ruminants, Etosha National Park, Namibia, 2011

After a May 2011 outbreak of Rift Valley fever among livestock northeast of Etosha National Park, Namibia, wild ruminants in the park were tested for the virus. Antibodies were detected in springbok, wildebeest, and black-faced impala, and viral RNA was detected in springbok. Seroprevalence was high, and immune response was long lasting.

Comprehensive Serology Based on a Peptide ELISA to Assess the Prevalence of Closely Related Equine Herpesviruses in Zoo and Wild Animals

Equine herpesvirus type 1 (EHV-1) causes respiratory disorders and abortion in equids while EHV-1 regularly causes equine herpesvirus myeloencephalopathy (EHM), a stroke-like syndrome following endothelial cell infection in horses. Both EHV-1 and EHV-9 infections of non-definitive hosts often result in neuronal infection and high case fatality rates. Hence, EHV-1 and EHV-9 are somewhat unusual herpesviruses and lack strict host specificity, and the true extent of their host ranges have remained unclear. In order to determine the seroprevalence of EHV-1 and EHV-9, a sensitive and specific peptide-based ELISA was developed and applied to 428 sera from captive and wild animals representing 30 species in 12 families and five orders. Members of the Equidae, Rhinocerotidae and Bovidae were serologically positive for EHV-1 and EHV-9. The prevalence of EHV-1 in the sampled wild zebra populations was significantly higher than in zoos suggesting captivity may reduce exposure to EHV-1. Furthermore, the seroprevalence for EHV-1 was significantly higher than for EHV-9 in zebras. In contrast, EHV-9 antibody prevalence was high in captive and wild African rhinoceros species suggesting that they may serve as a reservoir or natural host for EHV-9. Thus, EHV-1 and EHV-9 have a broad host range favoring African herbivores and may have acquired novel natural hosts in ecosystems where wild equids are common and are in close contact with other perissodactyls.

A sylvatic lifecycle of Echinococcus equinus in the Etosha National Park, Namibia

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A wildlife cycle of Echinococcus equinus exists in the Etosha National Park.

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Lions, jackals and plain zebras are host of E. equinus.

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Haplotype identity and diversity was similar to samples from Europe.

Various species of Echinococcus have been described in the past from wild mammals of sub-Saharan Africa. However, it is only recently, that a few isolates have become available for molecular identification; therefore, the involvement of wildlife in the lifecycles of the various cryptic species within Echinococcus granulosus sensu lato is still only partially known. A preliminary survey was undertaken in Etosha National Park, Namibia, from August to October 2012. Faecal samples were obtained from 34 individual wild carnivores, and metacestodes were collected from carcasses of 18 culled herbivores. Single eggs and metacestode tissue were lysed and identified from sequences of the mitochondrial nad1 gene. In case of metacestodes, the cox1 gene was additionally sequenced and haplotype networks were constructed.

Echinococcus equinus was found in lions (4 of 6), black-backed jackals (2 of 7) and Burchell's zebras (11 of 12). The frequency of this parasite in the absence of domestic dogs, horses and donkeys strongly indicates its transmission in a wildlife cycle. Further, a variety of sequences were obtained from eggs and cysticerci from lions, cheetahs, caracals, spotted hyenas and oryx, which most closely clustered with species of Taenia. Only 3 of them, 2 of lion and 1 of hyena origin, could be allocated to Hydatigera (=Taenia) taeniaeformis (lion), Taenia regis (lions and oryx) and Taenia cf. crocutae (spotted hyena and oryx).