Characterizing reservoirs of infection and the maintenance of pathogens in ecosystems

Tracking potential Leptospira sources following human cases of leptospirosis: A One Health approach applied to an ecosystem in Brittany, France

Pathogenic Leptospira can cause leptospirosis: a widespread, potentially fatal bacterial zoonosis whose risk is mediated by the soil and water features, animal host distributions, meaning the local ecosystem. When human cases of leptospirosis occur, it is challenging to track down their source because ecosystem-level epidemiological knowledge on Leptospira is needed. Between 2016 and 2019 in a focal riparian ecosystem, the human population experienced an outbreak and successive cases of leptospirosis attributable to L. kirschneri and L. interrogans. The epidemiological investigation was carried out using the One Health approach, as described in international health guidelines. As a first step in this process, we investigated leptospiral carriage in the main animal hosts found in the region. We sampled 143 nutrias, 17 muskrats, and 10 Norway rats using convenient trapping. DNA was extracted from their kidneys, lungs, and urine and subjected to real-time PCR (RT-PCR) targeting the Leptospira 16S rDNA and lfb1 genes. In the farms along the river's stretch of interest, we sampled serum from 439 cattle and used a microscopic agglutination test to detect the presence of antibodies against Leptospira. Urine samples were concomitantly obtained from 145 cattle and were used in two analyses: RT-PCR targeting the Leptospira 16S rDNA gene and Leptospira culturing. We found th, wt rodents were the most likely source of the L. interrogans behind the human cases. The cattle tested negative for Leptospira DNA but positive for antibodies against the serogroups implicated in the human cases. We failed to identify the potential source of the L. kirschneri responsible for several human cases of leptospirosis. Our results call for further clarification of the Leptospira maintenance community, which may comprise known maintenance hosts, such as rodents, as well as taxa not commonly considered to be maintenance hosts but that can still spread Leptospira. The resulting research network will collaboratively conduct future eco-epidemiological surveys to illuminate the leptospirosis risks faced by humans and animals within ecosystems.

Exploring the influence of host community composition on the outbreak potential of Anaplasma phagocytophilum and Borrelia burgdorferi s.l

In large parts of the northern hemisphere, multiple deer species coexist, and management actions can strongly influence wild deer communities. Such changes may also indirectly influence other species in the community, such as small mammals and birds, because deer can have strong effects on their habitats and resources. Deer, small mammals and birds play an important role in the dynamics of tick-borne zoonotic diseases. It is, however, relatively underexplored how the abundance and composition of vertebrate communities may affect the outbreak potential, maintenance and circulation of tick-borne pathogens. In this study we focus on the outbreak potential by exploring how the basic reproduction number R0 for different tick-borne pathogens depends on host community composition. We used published data on co-varying roe deer (Capreolus capreolus) and fallow deer (Dama dama) densities following a hunting ban, and different small mammal and bird densities, to investigate how the change in host community influences the R0 of four tick-borne pathogens: one non-zoonotic, namely Anaplasma phagocytophilum ecotype 2, and three zoonotic, namely A. phagocytophilum ecotype 1, Borrelia afzelii and Borrelia garinii. We calculated R0 using a next generation matrix approach, and used elasticities to quantify the contributions to R0 of the different groups of host species. The value of R0 for A. phagocytophilum ecotype 1 was higher with high fallow deer density and low roe deer density, while it was the other way round for A. phagocytophilum ecotype 2. For B. afzelii, R0 was mostly related to the density of small mammals and for B. garinii it was mostly determined by bird density. Our results show that the effect of species composition is substantial in the outbreak potential of tick-borne pathogens. This implies that also management actions that change this composition, can (indirectly and unintentionally) affect the outbreak potential of tick-borne diseases.

Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats

Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.

RACCOONS (PROCYON LOTOR) SHOW HIGHER TRYPANOSOMA CRUZI DETECTION RATES THAN VIRGINIA OPOSSUMS (DIDELPHIS VIRGINIANA) IN SOUTH CAROLINA, USA

Chagas disease, a significant public health concern in the Americas, is caused by a protozoan parasite, Trypanosoma cruzi. The life cycle of T. cruzi involves kissing bugs (Triatoma spp.) functioning as vectors and mammalian species serving as hosts. Raccoons (Procyon lotor) and opossums (Didelphis virginiana) have been identified as important reservoir species in the life cycle of T. cruzi, but prevalence in both species in the southeastern US is currently understudied. We quantified T. cruzi prevalence in these two key reservoir species across our study area in South Carolina, US, and identified factors that may influence parasite detection. We collected whole blood from 183 raccoons and 126 opossums and used PCR to detect the presence of T. cruzi. We then used generalized linear models with parasite detection status as a binary response variable and predictor variables of land cover, distance to water, sex, season, and species. Our analysis indicated that raccoons experienced significantly higher parasite detection rates than Virginia opossums, with T. cruzi prevalence found to be 26.5% (95% confidence interval [CI], 20.0-33.8) in raccoons and 10.5% (95% CI, 5.51-17.5) in opossums. Overall, our results concur with previous studies, in that T. cruzi is established in reservoir host populations in natural areas of the southeastern US.

Using mechanistic models to highlight research priorities for tick-borne zoonotic diseases: Improving our understanding of the ecology and maintenance of Kyasanur Forest Disease in India

The risk of spillover of zoonotic diseases to humans is changing in response to multiple environmental and societal drivers, particularly in tropical regions where the burden of neglected zoonotic diseases is highest and land use change and forest conversion is occurring most rapidly. Neglected zoonotic diseases can have significant impacts on poor and marginalised populations in low-resource settings but ultimately receive less attention and funding for research and interventions. As such, effective control measures and interventions are often hindered by a limited ecological evidence base, which results in a limited understanding of epidemiologically relevant hosts or vectors and the processes that contribute to the maintenance of pathogens and spillover to humans. Here, we develop a generalisable next generation matrix modelling framework to better understand the transmission processes and hosts that have the greatest contribution to the maintenance of tick-borne diseases with the aim of improving the ecological evidence base and framing future research priorities for tick-borne diseases. Using this model we explore the relative contribution of different host groups and transmission routes to the maintenance of a neglected zoonotic tick-borne disease, Kyasanur Forest Disease Virus (KFD), in multiple habitat types. The results highlight the potential importance of transovarial transmission and small mammals and birds in maintaining this disease. This contradicts previous hypotheses that primates play an important role influencing the distribution of infected ticks. There is also a suggestion that risk could vary across different habitat types but currently more research is needed to evaluate this relationship. In light of these results, we outline the key knowledge gaps for this system and future research priorities that could inform effective interventions and control measures.

Seroprevalence of Coxiella burnetii antibodies in wild deer populations in eastern Australia

Coxiella burnetii causes significant reproduction losses in livestock and the disease Q fever in humans. Transmission of C. burnetii is facilitated by the stability of the bacterium in the environment and the susceptibility of a variety of host species to infection. Consequently, inter-species transmission occurs frequently through either direct or indirect contact. Wildlife may represent reservoirs of C. burnetii and could therefore be a source of infection for domestic animals. Understanding the prevalence of C. burnetii infections at the wildlife-livestock interface is important for disease control. This study aimed to investigate the extent of C. burnetii exposure in wild deer in eastern Australia. Serum samples were obtained from 413 wild deer from seven regions in four eastern Australian states from 2017 to 2020. Antibodies were detected using a commercial Q fever antibody kit validated for ruminants. Seroprevalence of C. burnetii antibodies in deer was determined and true prevalence estimated, for each region. The overall seroprevalence of C. burnetii antibodies in wild deer was 3.4% (14 seropositive of 413 deer sampled) with true prevalence estimated to be 4.3% (95% credible interval: 0.6%, 10.9%). Seropositive deer were identified only in Queensland (7/108 seropositive) and northern New South Wales (7/120 seropositive). This geospatial distribution is consistent with seropositivity in other animal species and indicative of the level of C. burnetii in the environment. The low seroprevalence suggests that wild deer are unlikely to be a major reservoir species for C. burnetii in eastern Australia but may still be implicated in inter-species transmission cycles.

Identification of Pathogenic Leptospira kirschneri Serogroup Grippotyphosa in Water Voles (Arvicola terrestris) from Ruminant Pastures in Puy-de-Dôme, Central France

Rodents are the primary reservoirs for pathogenic Leptospira species, which cause leptospirosis. Among the key potential carriers are water voles, whose population outbreaks can consequently pose a major threat to human and animal health. We studied the prevalence, prominence, and epidemiology of pathogenic Leptospira species in water voles in central France. First, 46 voles were captured, and DNA was extracted from kidney, lung, liver, blood, and urine and tested for the presence of Leptospira using three molecular methods: PCR, O-antigen typing, and variable number tandem repeat (VNTR) typing. We also attempted to culture leptospires from kidney and urine samples. In addition, we investigated leptospiral antibodies in serum samples from 60 sheep using microscopic agglutination testing. These animals co-occurred with the voles, so we sought to assess their degree of exposure and involvement in pathogen dynamics. The overall prevalence of infection was 76.1% (CI_95% [61.2%, 87.4%]). The only strain found was L. kirschneri serogroup Grippotyphosa and a similar VNTR profile was acquired. Leptospires were successfully cultured from kidney and urine samples for four voles. Three sheep had low antibody titers against the Leptospira serogroup Grippotyphosa. Taken together, our results suggest the exclusive carriage of L. kirschneri serogroup Grippotyphosa among water voles in central France. Nevertheless, their ability to act as reservoir hosts that transmit the pathogen to co-occurring livestock remains unclear and merits further research.

Modeling the effectiveness of One Health interventions against the zoonotic hookworm Ancylostoma ceylanicum

Hookworm disease is a major global public health concern, annually affecting 500-700 million of the world's poorest people. The World Health Organization is targeting the elimination of hookworm as a public health problem by 2030 using a strategy of mass drug administration (MDA) to at-risk human populations. However, in Southeast Asia and the Pacific the zoonotic hookworm species, Ancylostoma ceylanicum, is endemic in dogs and commonly infects people. This presents a potential impediment to the effectiveness of MDA that targets only humans. Here, we develop a novel multi-host (dog and human) transmission model of A. ceylanicum and compare the effectiveness of human-only and "One Health" (human plus dog) MDA strategies under a range of eco-epidemiological assumptions. We show that One Health interventions-targeting both dogs and humans-could suppress prevalence in humans to ≤ 1% by the end of 2030, even with only modest coverage (25-50%) of the animal reservoir. With increasing coverage, One Health interventions may even interrupt transmission. We discuss key unresolved questions on the eco-epidemiology of A. ceylanicum, the challenges of delivering MDA to animal reservoirs, and the growing importance of One Health interventions to human public health.

Bitesize Epidemiology for General Awareness of All Students - I

This is the first part of a two-part series article. Recently, we have been in the middle of a difficult time due to the Covid-19 pandemic. Pandemics or global epidemics are not new to humankind; they have occurred many times in history. The discourse of epidemiology describes mainly the causal factors which need to be mitigated to prevent or combat the effects of epidemics. In epidemiology, we are not concerned for a person, but rather every individual globally, to make life healthier for all. In this article, we will discuss the basics of epidemiological practice that scientists have used for centuries to prevent epidemics with great results. Overall, we plan for better global health aided by epidemiology.

SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City

There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.

High prevalence does not necessarily equal maintenance species: Avoiding biased claims of disease reservoirs when using surveillance data

1. Many pathogens of public health and conservation concern persist in host communities. Identifying candidate maintenance and reservoir species is therefore a central component of disease management. The term maintenance species implies that if all species but the putative maintenance species were removed, then the pathogen would still persist. In the absence of field manipulations, this statement inherently requires a causal or mechanistic model to assess. 2. However, we lack a systematic understanding of i) how often conclusions are made about maintenance and reservoir species without reference to mechanistic models ii) what types of biases may be associated with these conclusions and iii) how explicitly invoking causal or mechanistic modeling can help ameliorate these biases. Filling these knowledge gaps is critical for robust inference on pathogen persistence and spillover in multihost parasite systems, with clear implications for human and wildlife health. 3. To address these gaps, we performed a literature review on the evidence previous studies have used to make claims regarding maintenance or reservoir species. We then developed a multihost-parasite model to explore and demonstrate common biases that could arise when inferring maintenance potential from observational prevalence data. Finally, we developed new theory to show how model-driven inference of maintenance species can minimize and eliminate emergent biases. 4. In our review, we found that 83% of studies used some form of observational prevalence data to draw conclusions on maintenance potential and only 6% of these studies combined observational data with mechanistic modeling. Using our model, we demonstrate how the community, spatial, and temporal context of observational data can lead to substantial biases in inferences of maintenance potential. Importantly, our theory identifies that model-driven inference of maintenance species elucidates other streams of observational data that can be leveraged to correct these biases. 5. Model-driven inference is an essential, yet underused, component of multidisciplinary studies that make inference on host reservoir and maintenance species. Better integration of wildlife disease surveillance and mechanistic models is necessary to improve the robustness and reproducibility of our conclusions regarding maintenance and reservoir species.

Transmission history of SARS-CoV-2 in humans and white-tailed deer

The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human–animal interface.

Once a reservoir, always a reservoir? Seasonality affects the pathogen maintenance potential of amphibian hosts

Host species that can independently maintain a pathogen in a host community and contribute to infection in other species are important targets for disease management. However, the potential of host species to maintain a pathogen is not fixed over time, and an important challenge is understanding how within- and across-season variability in host maintenance potential affects pathogen persistence over longer time scales relevant for disease management (e.g., years). Here, we sought to understand the causes and consequences of seasonal infection dynamics in leopard frogs (Rana sphenocephala and R. pipiens) infected with the fungal pathogen Batrachochytrium dendrobatidis (Bd). We addressed three questions broadly applicable to seasonal host-parasite systems. First, to what degree are observed seasonal patterns in infection driven by temperature-dependent infection processes compared to seasonal host demographic processes? Second, how does seasonal variation in maintenance potential affect long-term pathogen persistence in multihost communities? Third, does high deterministic maintenance potential relate to the long-term stochastic persistence of pathogens in host populations with seasonal infection dynamics? To answer these questions, we used field data collected over three years on >1400 amphibians across four geographic locations, laboratory and mesocosm experiments, and a novel mathematical model. We found that the mechanisms that drive seasonal prevalence were different than those driving seasonal infection intensity. Seasonal variation in Bd prevalence was driven primarily by changes in host contact rates associated with breeding migrations to and from aquatic habitat. In contrast, seasonal changes in infection intensity were driven by temperature-induced changes in Bd growth rate. Using our model, we found that the maintenance potential of leopard frogs varied significantly throughout the year and that seasonal troughs in infection prevalence made it unlikely that leopard frogs were responsible for long-term Bd persistence in these seasonal amphibian communities, highlighting the importance of alternative pathogen reservoirs for Bd persistence. Our results have broad implications for management in seasonal host-pathogen systems, showing that seasonal changes in host and pathogen vital rates, rather than the depletion of susceptible hosts, can lead to troughs in pathogen prevalence and stochastic pathogen extirpation.

Plant neighbours can make or break the disease transmission chain of a fungal root pathogen

Biodiversity can reduce or increase disease transmission. These divergent effects suggest that community composition rather than diversity per se determines disease transmission. In natural plant communities, little is known about the functional roles of neighbouring plant species in belowground disease transmission. Here, we experimentally investigated disease transmission of a fungal root pathogen (Rhizoctonia solani) in two focal plant species in combinations with four neighbour species of two ages. We developed stochastic models to test the relative importance of two transmission-modifying mechanisms: (1) infected hosts serve as nutrient supply to increase hyphal growth, so that successful disease transmission is self-reinforcing; and (2) plant resistance increases during plant development. Neighbouring plants either reduced or increased disease transmission in the focal plants. These effects depended on neighbour age, but could not be explained by a simple dichotomy between hosts and nonhost neighbours. Model selection revealed that both transmission-modifying mechanisms are relevant and that focal host-neighbour interactions changed which mechanisms steered disease transmission rate. Our work shows that neighbour-induced shifts in the importance of these mechanisms across root networks either make or break disease transmission chains. Understanding how diversity affects disease transmission thus requires integrating interactions between focal and neighbour species and their pathogens.

Challenges in modelling the dynamics of infectious diseases at the wildlife-human interface

The Covid-19 pandemic is of zoonotic origin, and many other emerging infections of humans have their origin in an animal host population. We review the challenges involved in modelling the dynamics of wildlife–human interfaces governing infectious disease emergence and spread. We argue that we need a better understanding of the dynamic nature of such interfaces, the underpinning diversity of pathogens and host–pathogen association networks, and the scales and frequencies at which environmental conditions enable spillover and host shifting from animals to humans to occur. The major drivers of the emergence of zoonoses are anthropogenic, including the global change in climate and land use. These, and other ecological processes pose challenges that must be overcome to counterbalance pandemic risk. The development of more detailed and nuanced models will provide better tools for analysing and understanding infectious disease emergence and spread.

The Bacterial Wilt Reservoir Host Solanum dulcamara Shows Resistance to Ralstonia solanacearum Infection

Ralstonia solanacearum causes bacterial wilt, a devastating plant disease, responsible for serious losses on many crop plants. R. solanacearum phylotype II-B1 strains have caused important outbreaks in temperate regions, where the pathogen has been identified inside asymptomatic bittersweet (Solanum dulcamara) plants near rivers and in potato fields. S. dulcamara is a perennial species described as a reservoir host where R. solanacearum can overwinter, but their interaction remains uncharacterised. In this study, we have systematically analysed R. solanacearum infection in S. dulcamara, dissecting the behaviour of this plant compared with susceptible hosts such as tomato cv. Marmande, for which the interaction is well described. Compared with susceptible tomatoes, S. dulcamara plants (i) show delayed symptomatology and bacterial progression, (ii) restrict bacterial movement inside and between xylem vessels, (iii) limit bacterial root colonisation, and (iv) show constitutively higher lignification in the stem. Taken together, these results demonstrate that S. dulcamara behaves as partially resistant to bacterial wilt, a property that is enhanced at lower temperatures. This study proves that tolerance (i.e., the capacity to reduce the negative effects of infection) is not required for a wild plant to act as a reservoir host. We propose that inherent resistance (impediment to colonisation) and a perennial habit enable bittersweet plants to behave as reservoirs for R. solanacearum.

Infection dynamics in ecosystems: on the interaction between red and grey squirrels, pox virus, pine martens and trees

Ecological and epidemiological processes and interactions influence each other, positively and negatively, directly and indirectly. The invasion potential of pathogens is influenced by the ecosystem context of their host species' populations. This extends to the capacity of (multiple) host species to maintain their (common) pathogen and the way pathogen dynamics are influenced by changes in ecosystem composition. This paper exemplifies these interactions and consequences in a study of red and grey squirrel dynamics in the UK. Differences and changes in background habitat and trophic levels above and below the squirrel species lead to different dynamic behaviour in many subtle ways. The range of outcomes of the different interactions shows that one has to be careful when drawing conclusions about the mechanisms and processes involved in explaining observed phenomena concerning pathogens in their natural environment. The dynamic behaviour also shows that planning interventions, for example for conservation purposes, benefits from understanding the complexity of interactions beyond the particular pathogen and its threatened host species.

Comparison of Japanese Encephalitis Force of Infection in Pigs, Poultry and Dogs in Cambodian Villages

Japanese encephalitis virus (JEV) is the main cause of human viral encephalitis in Asia, with a mortality rate reaching 30%, mostly affecting children. The traditionally described cycle involving wild birds as reservoirs, pigs as amplifying hosts and Culex mosquitoes as vectors is questioned, with increasing evidence of a more complex multi-host system involved in areas where densities of pigs are low, such as in Cambodia. In 2018, we examined pigs, chickens, ducks and dogs from Kandal province, Cambodia, for antibody response against JEV by hemagglutination inhibition and virus neutralization assays. Forces of infection (FOI) for flaviviruses and JEV were estimated per species and per unit of body surface area (BSA). JEV seroprevalence reached 31% (95% CI: 23-41%) in pigs, 1% (95% CI: 0.1-3%) in chickens, 12% (95% CI: 7-19%) in ducks and 35% (95% CI: 28-42%) in dogs. Pigs were most likely to be infected (FOI: 0.09 per month), but the FOI was higher in ducks than in pigs for a given BSA (ratio of 0.13). Dogs had a lower FOI than ducks but a higher FOI than chickens (0.01 per month). For a given BSA, dogs were less likely to be infected than pigs (ratio of 1.9). In Cambodia, the virus may be circulating between multiple hosts. Dogs live in close contact with humans, and estimating their exposure to JEV infection could be a relevant indicator of the risk for humans to get infected, which is poorly known due to underdiagnosis. Understanding the JEV cycle and developing tools to quantify the exposure of humans is essential to adapt and support control measures for this vaccine-preventable disease.

Disease hotspots or hot species? Infection dynamics in multi-host metacommunities controlled by species identity, not source location

Pathogen persistence in host communities is influenced by processes operating at the individual host to landscape-level scale, but isolating the relative contributions of these processes is challenging. We developed theory to partition the influence of host species, habitat patches and landscape connectivity on pathogen persistence within metacommunities of hosts and pathogens. We used this framework to quantify the contributions of host species composition and habitat patch identity on the persistence of an amphibian pathogen across the landscape. By sampling over 11 000 hosts of six amphibian species, we found that a single host species could maintain the pathogen in 91% of observed metacommunities. Moreover, this dominant maintenance species contributed, on average, twice as much to landscape-level pathogen persistence compared to the most influential source patch in a metacommunity. Our analysis demonstrates substantial inequality in how species and patches contribute to pathogen persistence, with important implications for targeted disease management.