Systematics and Emerging Infectious Diseases: From Management to Solution

Navigating the Landscape of Tick Diversity: Integrating Molecular Approaches for Enhanced Control Measures

The emergence and spread of infectious diseases, particularly zoonotic diseases originating from wildlife, pose significant threats to global health and economy. This review examines the pivotal role of ticks as vectors in transmitting pathogens to humans, livestock, and wildlife and the use of molecular techniques in their identification. Tick infestations result in economic losses through reduced animal productivity, anemia, and quality deterioration of hides. Furthermore, ticks serve as reservoirs for a wide range of pathogens including viruses, bacteria, fungi, protozoa, and nematodes, contributing to the transmission of diseases such as Crimean-Congo hemorrhagic fever, tick-borne encephalitis, and African swine fever among others. The interface between wildlife, livestock, and humans facilitates the transmission of zoonotic pathogens, exacerbated by nomadic and pastoralist lifestyles that promote interactions between wildlife and domestic animals. This movement of animals across landscapes enhances the dispersion of tick vectors, increasing the risk of pathogen exposure for diverse populations. Historically, tick identification in sub-Saharan Africa has relied on morphological characteristics despite limitations such as species overlap and variability. Molecular techniques offer a more precise means of species identification, providing critical data for effective tick and pathogen management strategies. Integrating molecular approaches into tick research enhances our understanding of tick diversity, distribution patterns, and pathogen dynamics. This knowledge is essential for developing targeted interventions to mitigate the impact of tick-borne diseases on public and veterinary health worldwide.

Epidemiology and diversity of gastrointestinal tract helminths of wild ruminants in sub-Saharan Africa: a review

This review summarises studies on distribution, diversity, and prevalence of gastrointestinal helminth infections in wild ruminants in sub-Saharan Africa. The results showed that 109 gastrointestinal tract (GIT) helminth species or species complexes were recorded in 10 sub-Saharan African countries. South Africa reported the highest number of species because most studies were carried out in this country. Eighty-eight nematode species or species complexes were recorded from 30 wild ruminant species across eight countries. The genus Trichostrongylus recorded the highest number of species and utilised the highest number of wild ruminant species, and along with Haemonchus spp., was the most widely distributed geographically. Fifteen trematode species or species complexes were reported from seven countries. The genus Paramphistomum recorded the highest number of species, and Calicophoron calicophoron was the most commonly occurring species in sub-Saharan African countries and infected the highest number of hosts. Six cestode species or species complexes from one family were documented from 14 wild hosts in seven countries. Moniezia spp. were the most commonly distributed in terms of host range and geographically. Impala were infected by the highest number of nematodes, whilst Nyala were infected by the highest number of trematode species. Greater kudu and Impala harbored the largest number of cestodes. The prevalence amongst the three GIT helminths taxa ranged between 1.4% and 100% for nematodes, 0.8% and 100% for trematodes, and 1.4% and 50% for cestodes. There is still limited information on the distribution and diversity of GIT helminths in wild ruminants in most sub-Saharan African countries.

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO’s virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

Application of Viral Metagenomics for Study of Emerging and Reemerging Tick-Borne Viruses

Ticks are important vectors for different tick-borne viruses, some of which cause diseases and death in humans, livestock, and wild animals. Tick-borne encephalitis virus, Crimean-Congo hemorrhagic fever virus, Kyasanur forest disease virus, severe fever with thrombocytopenia syndrome virus, Heartland virus, African swine fever virus, Nairobi sheep disease virus, and Louping ill virus are just a few examples of important tick-borne viruses. The majority of tick-borne viruses have RNA genomes that routinely undergo rapid genetic modifications such as point mutations during their replication. These genomic changes can influence the spread of viruses to new habitats and hosts and lead to the emergence of novel viruses that can pose a threat to public health. Therefore, investigation of the viruses circulating in ticks is important to understand their diversity, host and vector range, and evolutionary history, as well as to predict new emerging pathogens. The choice of detection method is important, as most methods detect only those viruses that have been previously well described. On the other hand, viral metagenomics is a useful tool to simultaneously identify all the viruses present in a sample, including novel variants of already known viruses or completely new viruses. This review describes tick-borne viruses, their historical background of emergence, and their reemergence in nature, and the use of viral metagenomics for viral discovery and studies of viral evolution.

Diagnosing bovine parafilariosis: utility of the cytochrome c oxidase subunit 1 gene and internal transcribed spacer region for PCR detection of Parafilaria bovicola in skin biopsies and serohemorrhagic exudates of cattle

Background

Parafilaria bovicola (Nematoda: Filariidae) causes cutaneous bleedings in bovine species. Flies serve as intermediate hosts. In recent years, reports on bovine parafilariosis have become more frequent, corroborating the necessity of reliable diagnostic interventions especially since no molecular or serological test has been available. We aimed to establish a polymerase chain reaction assay to detect DNA of P. bovicola in flies, skin biopsies and serohemorraghic exudates of bleeding spots.

Methods

PCRs targeting the cytochrome c oxidase subunit 1 (cox1) gene and the internal transcribed spacer region (ITS) of the ribosomal RNA gene cluster were evaluated for their diagnostic sensitivity as well as performance and specificity on biopsy and serohemorrhagic exudate samples from P. bovicola-infected cattle.

Results

Using serohemorrhagic exudates (n = 6), biopsies (n = 2) and flies (n = 1), the PCR targeting the cox1 gene resulted in a gel band of almost 700 bp. Cloning, sequencing, and removal of primer sequences yielded a 649-bp fragment of the P. bovicola cox1 gene. The PCR targeting the ITS region showed a band of about 1100 bp. Cloning, sequencing, and removal of primer sequences resulted in a 1083 bp stretch of the P. bovicola ITS region. Testing samples from presumably affected animals, the cox1-PCR resulted in bands with the expected size and they were all confirmed as P. bovicola by sequencing. In contrast, the ITS-PCR proved to be less sensitive and less specific and additionally amplified the ITS region of Musca domestica or buttercup DNA. When analysing for sensitivity, the cox1-PCR yielded visible bands up to 2 ng of genomic DNA, whereas the ITS-PCR produced bands up to 3 ng. In a plasmid dilution series, the minimum number of target DNA copies was 10² for the cox1-PCR and 10¹ in the ITS-PCR.

Conclusions

The evaluated cox1-PCR enables reliable detection of P. bovicola DNA in skin biopsies and serohemorrhagic exudates. This PCR and, to a limited extent, the ITS-PCR, may help evaluate different therapeutic approaches. Furthermore, the cox1-PCR may be useful for epidemiological studies on the geographical distribution of P. bovicola. Further understanding of the epidemiology of this parasite will help develop and implement effective control strategies.

Hypothesis: Multiple sclerosis is caused by three-hits, strictly in order, in genetically susceptible persons

Multiple Sclerosis is a chronic, progressive and debilitating neurological disease which, despite extensive study for over 100 years, remains of enigmatic aetiology. Drawn from the epidemiological evidence, there exists a consensus that there are environmental (possibly infectious) factors that contribute to disease pathogenesis that have not yet been fully elucidated. Here we propose a three-tiered hypothesis: 1) a clinic-epidemiological model of multiple sclerosis as a rare late complication of two sequential infections (with the temporal sequence of infections being important); 2) a proposal that the first event is helminthic infection with Enterobius Vermicularis, and the second is Epstein Barr Virus infection; and 3) a proposal for a testable biological mechanism, involving T-Cell exhaustion for Epstein-Barr Virus protein LMP2A. We believe that this model satisfies some of the as-yet unexplained features of multiple sclerosis epidemiology, is consistent with the clinical and neuropathological features of the disease and is potentially testable by experiment. This model may be generalizable to other autoimmune diseases.

The importance of recognising parasite cryptic diversity for research programmes on foodborne trematodiases

The development of molecular tools in the last two decades enhanced our capacity to accurately describe biodiversity on Earth. Analysis of molecular data may lead to the discovery of cryptic species (morphologically indistinguishable, genetically distinct species lineages). As cryptic species are discovered with increasing frequency among parasites, we must consider their potential implications, especially for the epidemiology, diagnostics and control of parasitic diseases that affect humans. Investigators that conduct research on different aspects of infectious diseases, for example, on foodborne trematodiases, must remain aware of the possibility for undiscovered cryptic species and how this could impact their conclusions.

Evolution in action: climate change, biodiversity dynamics and emerging infectious disease

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host-parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)--phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference--provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization.

Landscape characteristics influence helminth infestations in a peri-domestic rodent--implications for possible zoonotic disease

BACKGROUND

Anthropogenic habitat change often results in altered landscapes that can provide new environments where hosts, parasites and pathogens can interact. The latter can have implications for human and animal health when in close proximity to developed areas. We recorded the helminth species richness and level of infestation in the peri-domestic rodent, Rhabdomys pumilio, in three different human linked landscapes. The aim was, to investigate the potential of R. pumilio to act as a reservoir host for zoonotic helminths and to compare the effect of anthropogenic habitat change on its parasite infestation patterns.

METHODS

Rodents (n = 518) were trapped in natural areas (nature reserves) and in three human linked landscapes (crop, livestock and urban fragments). Gastrointestinal parasite burdens were recovered and helminths identified from each animal. Generalized linear models were applied to investigate the effect of different landscape types on helminth infestation.

RESULTS

Rhabdomys pumilio was the most abundant rodent species within each landscape type. Eight helminths species were recovered and overall helminth prevalence was 86.68%. Mean helminth species richness, prevalence and abundance were significantly higher in crop fragments compared to natural landscapes and overall lower for nematodes in livestock and urban areas. Cestode prevalence showed a tendency to be elevated at anthropogenic linked landscape types.

CONCLUSIONS

Host parameters and parasite infestations were strongly influenced by landscape characteristics. Resource-rich landscapes (crop fragments) provide favorable conditions for helminth infestations, while landscapes that are more closely associated with humans (livestock and urban landscapes) pose a larger risk by zoonotic species.

Applying evolutionary concepts to wildlife disease ecology and management

Existing and emerging infectious diseases are among the most pressing global threats to biodiversity, food safety and human health. The complex interplay between host, pathogen and environment creates a challenge for conserving species, communities and ecosystem functions, while mediating the many known ecological and socio-economic negative effects of disease. Despite the clear ecological and evolutionary contexts of host-pathogen dynamics, approaches to managing wildlife disease remain predominantly reactionary, focusing on surveillance and some attempts at eradication. A few exceptional studies have heeded recent calls for better integration of ecological concepts in the study and management of wildlife disease; however, evolutionary concepts remain underused. Applied evolution consists of four principles: evolutionary history, genetic and phenotypic variation, selection and eco-evolutionary dynamics. In this article, we first update a classical framework for understanding wildlife disease to integrate better these principles. Within this framework, we explore the evolutionary implications of environment-disease interactions. Subsequently, we synthesize areas where applied evolution can be employed in wildlife disease management. Finally, we discuss some future directions and challenges. Here, we underscore that despite some evolutionary principles currently playing an important role in our understanding of disease in wild animals, considerable opportunities remain for fostering the practice of evolutionarily enlightened wildlife disease management.

A walk on the tundra: Host-parasite interactions in an extreme environment

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Climate change is altering host–parasite interactions in the Arctic.

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Changing ecological barriers reflect climate warming.

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Metabolic Theory of Ecology advances understanding of host–parasite interactions.

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Diversity emerges from host/parasite biogeographic/ecologic history.

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Insights gained from the Arctic apply to more complex systems.

Climate change is occurring very rapidly in the Arctic, and the processes that have taken millions of years to evolve in this very extreme environment are now changing on timescales as short as decades. These changes are dramatic, subtle and non-linear. In this article, we discuss the evolving insights into host–parasite interactions for wild ungulate species, specifically, muskoxen and caribou, in the North American Arctic. These interactions occur in an environment that is characterized by extremes in temperature, high seasonality, and low host species abundance and diversity. We believe that lessons learned in this system can guide wildlife management and conservation throughout the Arctic, and can also be generalized to more broadly understand host–parasite interactions elsewhere. We specifically examine the impacts of climate change on host–parasite interactions and focus on: (I) the direct temperature effects on parasites; (II) the importance of considering the intricacies of host and parasite ecology for anticipating climate change impacts; and (III) the effect of shifting ecological barriers and corridors. Insights gained from studying the history and ecology of host–parasite systems in the Arctic will be central to understanding the role that climate change is playing in these more complex systems.

Parasites in ungulates of Arctic North America and Greenland: a view of contemporary diversity, ecology, and impact in a world under change

Parasites play an important role in the structure and function of arctic ecosystems, systems that are currently experiencing an unprecedented rate of change due to various anthropogenic perturbations, including climate change. Ungulates such as muskoxen, caribou, moose and Dall's sheep are also important components of northern ecosystems and are a source of food and income, as well as a focus for maintenance of cultural traditions, for northerners. Parasites of ungulates can influence host health, population dynamics and the quality, quantity and safety of meat and other products of animal origin consumed by people. In this article, we provide a contemporary view of the diversity of nematode, cestode, trematode, protozoan and arthropod parasites of ungulates in arctic and subarctic North America and Greenland. We explore the intricate associations among host and parasite assemblages and identify key issues and gaps in knowledge that emerge in a regime of accelerating environmental transition.

Insights into the complex associations between MHC class II DRB polymorphism and multiple gastrointestinal parasite infestations in the striped mouse

Differences in host susceptibility to different parasite types are largely based on the degree of matching between immune genes and parasite antigens. Specifically the variable genes of the major histocompatibility complex (MHC) play a major role in the defence of parasites. However, underlying genetic mechanisms in wild populations are still not well understood because there is a lack of studies which deal with multiple parasite infections and their competition within. To gain insights into these complex associations, we implemented the full record of gastrointestinal nematodes from 439 genotyped individuals of the striped mouse, Rhabdomys pumilio. We used two different multivariate approaches to test for associations between MHC class II DRB genotype and multiple nematodes with regard to the main pathogen-driven selection hypotheses maintaining MHC diversity and parasite species-specific co-evolutionary effects. The former includes investigations of a 'heterozygote advantage', or its specific form a 'divergent-allele advantage' caused by highly dissimilar alleles as well as possible effects of specific MHC-alleles selected by a 'rare allele advantage' (= negative 'frequency-dependent selection'). A combination of generalized linear mixed models (GLMMs) and co-inertia (COIA) analyses made it possible to consider multiple parasite species despite the risk of type I errors on the population and on the individual level. We could not find any evidence for a 'heterozygote' advantage but support for 'divergent-allele' advantage and infection intensity. In addition, both approaches demonstrated high concordance of positive as well as negative associations between specific MHC alleles and certain parasite species. Furthermore, certain MHC alleles were associated with more than one parasite species, suggesting a many-to-many gene-parasite co-evolution. The most frequent allele Rhpu-DRB*38 revealed a pleiotropic effect, involving three nematode species. Our study demonstrates the co-existence of specialist and generalist MHC alleles in terms of parasite detection which may be an important feature in the maintenance of MHC polymorphism.

Northern host-parasite assemblages: history and biogeography on the borderlands of episodic climate and environmental transition

Diversity among assemblages of mammalian hosts and parasites in northern terrestrial ecosystems was structured by a deep history of biotic and abiotic change that overlies a complex geographic arena. Since the Pliocene, Holarctic ecosystems assembled in response to shifting climates (glacial and interglacial stages). Cycles of episodic dispersal/isolation and diversification defined northern diversity on landscape to regional scales. Episodes of geographic expansion and colonisation linked Eurasia and North America across Beringia and drove macroevolutionary structure of host and parasite associations. Asynchronous dispersal from centres of origin in Eurasia into the Nearctic resulted in gradients in parasite diversity in the carnivoran, lagomorph, rodent and artiodactyl assemblages we reviewed. Recurrent faunal interchange and isolation in conjunction with episodes of host colonisation have produced a mosaic structure for parasite faunas and considerable cryptic diversity among nematodes and cestodes. Mechanisms of invasion and geographic colonisation leading to the establishment of complex faunal assemblages are equivalent in evolutionary and ecological time, as demonstrated by various explorations of diversity in these high-latitude systems. Our ability to determine historical responses to episodic shifts in global climate may provide a framework for predicting the cascading effects of contemporary environmental change.

New species of Arostrilepis (Eucestoda: Hymenolepididae) in members of Cricetidae and Geomyidae (Rodentia) from the western Nearctic

Abstract : Specimens originally identified as Arostrilepis horrida from the Nearctic are revised, contributing to the recognition of a complex of cryptic species distributed across the Holarctic region. Previously unrecognized species are described based on specimens in cricetid (Neotominae) and geomyid rodents. Arostrilepis mariettavogeae n. sp. in Peromyscus californicus from Monterey County, California and Arostrilepis schilleri n. sp. in Thomomys bulbivorus from Corvallis, Oregon are characterized. Consistent with recent studies defining diversity in the genus, form, size, and spination (pattern, shape, and size) of the cirrus are diagnostic; species are further distinguished by the relative position and length of the cirrus sac and arrangement of the testes. Species of Arostrilepis have not previously been described in rodents outside of the Arvicolinae or from localities in the Nearctic. These studies emphasize the need for routine deposition of archival specimens and information, from survey, ecological, and biogeographic studies, in museum collections to serve as self-correcting records for biodiversity at local, regional, and continental scales.

Ecology of the gastrointestinal parasites of Colobus vellerosus at Boabeng-Fiema, Ghana: possible anthropozoonotic transmission

Parasite richness and prevalence in wild animals can be used as indicators of population and ecosystem health. In this study, the gastrointestinal parasites of ursine colobus monkeys (Colobus vellerosus) at the Boabeng-Fiema Monkey Sanctuary (BFMS), Ghana, were investigated. BFMS is a sacred grove where monkeys and humans have long lived in relatively peaceful proximity. Fecal samples (n = 109) were collected opportunistically from >27 adult and subadult males in six bisexual groups and one all-male band from July 2004 to August 2005. Using fecal floatation, we detected three protozoans (two Entamoeba sp., Isospora sp.), five nematodes (Ascaris sp., Enterobius sp., Trichuris sp., two strongyle sp.), and one digenean trematode. Using fluorescein labeled antibodies, we detected an additional protozoan (Giardia sp.), and with PCR techniques, we characterized this as G. duodenalis Assemblage B and also identified a protistan (Blastocystis sp., subtype 2). The most prevalent parasite species were G. duodenalis and Trichuris sp. Parasites were more prevalent in the long wet season than the long dry. Parasite prevalence did not vary by age, and average parasite richness did not differ by rank for males whose status remained unchanged. However, males that changed rank tended to show higher average parasite richness when they were lower ranked. Individuals that spent more time near human settlements had a higher prevalence of Isospora sp. that morphologically resembled the human species I. belli. The presence of this parasite and G. duodenalis Assemblage B indicates possible anthropozoonotic and/or zoonotic transmission between humans and colobus monkeys at this site.

Integrated approaches and empirical models for investigation of parasitic diseases in northern wildlife

A decade of research has yielded a multidisciplinary approach for detection, prediction, and potential mitigation measures.

The North is a frontier for exploration of emerging infectious diseases and the large-scale drivers influencing distribution, host associations, and evolution of pathogens among persons, domestic animals, and wildlife. Leading into the International Polar Year 2007–2008, we outline approaches, protocols, and empirical models derived from a decade of integrated research on northern host–parasite systems. Investigations of emerging infectious diseases associated with parasites in northern wildlife involved a network of multidisciplinary collaborators and incorporated geographic surveys, archival collections, historical foundations for diversity, and laboratory and field studies exploring the interface for hosts, parasites, and the environment. In this system, emergence of parasitic disease was linked to geographic expansion, host switching, resurgence due to climate change, and newly recognized parasite species. Such integrative approaches serve as cornerstones for detection, prediction, and potential mitigation of emerging infectious diseases in wildlife and persons in the North and elsewhere under a changing global climate.