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Billions of genomic sequences and records of species occurrence are available in public repositories (e.g. National Center for Biotechnology Information, NCBI and the Global Biodiversity Information Facility, GBIF). By implementing analytical tools from different scientific disciplines, data mining these databases can aid in the global surveillance of zoonotic pathogens that circulate among wildlife. We illustrate this by investigating the Hantavirus–rodent system in the Americas, i.e. New World Hantaviruses (NWH). First, we considered the circulation of pathogenic NWH among Cricetidae rodents, by inferring the phylogenetic links among 277 genomic samples of the S segment (N protein) of NWH found in 55 species. Second, we used machine learning to assess the impact of land use on the probability of presence of the rodent species linked with reservoirs of pathogenic Hantaviruses. Our results show that hosts are widely present across the Americas. Some hosts are present in the primary forest and agricultural land, but not in the secondary forest, whereas other hosts are present in secondary forest and agricultural land. The diversity of host species allows Hantavirus to circulate in a wide spectrum of habitats, in particular rural rather than urban. We highlight that public repositories of genomic data and species occurrence are very useful resources for monitoring potential enzootic transmission and spillover of zoonotic viruses in relation with the changes that humans produce in the biosphere.

Land-use change has a direct impact on species survival and reproduction, altering their spatio-temporal distributions. It acts as a selective force that favours the abundance and diversity of reservoir hosts and affects host–pathogen dynamics and prevalence. This has led to land-use change being a significant driver of infectious diseases emergence. Here, we predict the presence of rodent taxa and map the zoonotic hazard (potential sources of harm) from rodent-borne diseases in the short and long term (2025 and 2050). The study considers three different land-use scenarios based on the shared socioeconomic pathways narratives (SSPs): sustainable (SSP1-Representative Concentration Pathway (RCP) 2.6), fossil-fuelled development (SSP5-RCP 8.5) and deepening inequality (SSP4-RCP 6.0). We found that cropland expansion into forest and pasture may increase zoonotic hazards in areas with high rodent-species diversity. Nevertheless, a future sustainable scenario may not always reduce hazards. All scenarios presented high heterogeneity in zoonotic hazard, with high-income countries having the lowest hazard range. The SSPs narratives suggest that opening borders and reducing cropland expansion are critical to mitigate current and future zoonotic hazards globally, particularly in middle- and low-income economies. Our study advances previous efforts to anticipate the emergence of zoonotic diseases by integrating past, present and future information to guide surveillance and mitigation of zoonotic hazards at the regional and local scale. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Understanding the ecology of environmentally acquired and multi-host pathogens affecting humans and wildlife has been elusive in part because fluctuations in the abundance of host and pathogen species may feed back onto pathogen transmission. Complexity of pathogen-host dynamics emerges from processes driving local extinction of the pathogen, its hosts and non-hosts. While the extinction of species may entail losses in pathogen–host interactions and decrease the proportion of hosts infected by a pathogen (prevalence), some studies suggest the opposite pattern. Niche-based extinction, based on the species tolerance to environmental conditions, may increase prevalence of infection because the pathogen and its hosts persist, while other species go extinct. Hence, understanding prevalence of infection requires disentangling random- and niche-based extinction processes occurring simultaneously. To contribute to this exercise, we analysed the prevalence of an environmentally acquired, multi-host pathogen, Mycobacterium ulcerans (MU), in a unique dataset of 16 communities of freshwater animals, surveyed during 12 months in Akonolinga, Cameroon in equatorial Africa. Two different ecosystems were identified: rivers (lotic) and swamps and flooded areas (lentic). Increased prevalence of MU infection was correlated with niche-based extinction of aquatic host invertebrates and vertebrates in the lentic ecosystems, whereas decreased prevalence was associated with random disassembly of the lotic ecosystems. This finding suggests that random and niche-based extinction of host taxa are key to assessing the effect of local extinction of species on the ecology of environmentally acquired and multi-host pathogens.

High-profile epidemics such as Ebola, avian influenza, and severe acute respiratory syndrome (SARS) repeatedly thrust infectious diseases into the limelight. Because the emergence of dis-eases involves so many factors, the need for interdisciplinary approaches to studying emerging infections, particularly those originating from animals (i.e., zoonoses), is frequently discussed. However, effective integration across disciplines is challenging in practice. Ecological ideas, for example, are rarely considered in biomedical research, while insights from biomedicine are often neglected in ecological studies of infectious diseases. One practical reason for this is that researchers in these fields focus on vastly different scales of biological organization, which are difficult to bridge both intellectually and methodologically. Nevertheless, integration across biological scales is increasingly needed for solving the complex problems zoonotic diseases pose to human and animal well-being. Motivated by current events, we use Ebola virusas a case study to highlight fundamental questions about zoonoses that can be addressed by integrating insights and approaches across scales.

The broad distribution of macroparasites and their thriving populations are matters of health and economic concern. Macroparasites cause damage both directly through their feeding habits, which impact host fitness, and indirectly through the transmission of various infectious diseases of relevance to human and domestic animal health and wildlife conservation. Because the impacts of macroparasites on host health and the risk of disease transmission are directly related to their abundance, understanding the drivers of macroparasite burden is of relevance. Various host traits and environmental factors have been associated with differences in macroparasite abundance. In addition to these variables, spatial scale is increasingly incorporated to understand how these drivers vary across space. However, variation in the relative importance of host traits and environmental factors as predictors of abundance at different scales is not well understood. To further clarify the relationship between scale and drivers of macroparasite abundance, we investigated the effects of host traits and environmental factors on flea abundance in rodents of the Chihuahuan Desert in northwestern Mexico on three levels: within a single site, between sampling sites with different vegetation types, and across the region. This partitioning allowed us to compare drivers at both local and regional scales. Fleas provide a natural model to assess the interplay between host and environmental variables across scales because their life cycles alternate between on‐host and off‐host environments and their hosts have varying ranges of distribution. We sampled 1311 fleas from 674 rodent individuals of 14 different species across 40 sampling plots between 2012 and 2013. Using generalized linear mixed models, we found that flea abundance was associated with different combinations of host traits such as size and sex. The specific combination of predictive variables differed across species, while the effects on flea abundance showed context and scale dependency, although this could only be tested at the full level of analysis on the most abundant species, Dipodomys merriami. Sampling season was the only variable consistently significant across scales, reflecting the far‐reaching effects of large‐scale, interannual environmental fluctuations. These results emphasize that integrating spatial scale can strengthen study design for monitoring macroparasite burden.

The potential for disease transmission at the interface of wildlife, domestic animals and humans has become a major concern for public health and conservation biology. Research in this subject is commonly conducted at local scales while the regional context is neglected. We argue that prevalence of infection at local and regional levels is influenced by three mechanisms occurring at the landscape level in a metacommunity context. First, (1) dispersal, colonization, and extinction of pathogens, reservoir or vector hosts, and nonreservoir hosts, may be due to stochastic and niche‐based processes, thus determining distribution of all species, and then their potential interactions, across local communities (metacommunity structure). Second, (2) anthropogenic processes may drive environmental filtering of hosts, nonhosts, and pathogens. Finally, (3) phylogenetic diversity relative to reservoir or vector host(s), within and between local communities may facilitate pathogen persistence and circulation. Using a metacommunity approach, public heath scientists may better evaluate the factors that predispose certain times and places for the origin and emergence of infectious diseases. The multidisciplinary approach we describe fits within a comprehensive One Health and Ecohealth framework addressing zoonotic infectious disease outbreaks and their relationship to their hosts, other animals, humans, and the environment. A metacommunity framework can help explain the occurrence patterns of diseases by linking the spatial, ecological, and evolutionary relationships between pathogens, hosts (including vectors), and non‐host species.

Zoonotic diseases transmitted by wildlife affect biological conservation, public and animal health, and the economy. Current research efforts are aimed at finding wildlife pathogens at a given location. However, a meta-analytical approach may reveal emerging macroecological patterns in the host–pathogen relationship at different temporal and spatial scales. West Nile virus (WNV) is a pathogen with worldwide detrimental impacts on bird populations. To understand macroecological patterns driving WNV infection, we aimed to recognize unknown competent reservoirs using three disease metrics—serological prevalence (SP), molecular prevalence (MP) and mortality (M)—and test if these metrics are correlated with the evolutionary history, geographical origin of bird species, viral strain, time–space and methodology. We performed a quantitative review of field studies on birds sampled for WNV. We obtained 4945 observations of 949 species from 39 countries. Our analysis supported the idea that MP and M are good predictors of reservoir competence, and allowed us to identify potential competent reservoirs. Furthermore, results indicated that the variability of these metrics was attributable to phylogeny, time–space and sample size. A macroecological approach is needed to recognize susceptible species and competent reservoirs, and to identify other factors driving zoonotic diseases originating from wildlife.

Hantaviruses are transmitted by rodents producing the hantavirus pulmonary syndrome (HPS) in the Americas. Today, no human cases of HPS have been reported in Mexico in spite of similar environmental conditions with Central America and the USA where several cases have occurred. To understand the current situation of hantaviruses in Mexico and the public health risk, a systematic review of studies was conducted reporting hantaviruses in rodents to known state seroprevalence and hantavirus genotypes. Simultaneously, this study identified the potential hantaviruses based on the phylogenetic diversity (PD) of hantaviruses reported in the Americas in hosts with the distribution in Mexico. A total 3862 rodents belonging to 82 species have been tested since 1999 to 2017. Overall, 392 individuals representing 43 rodent species were seropositive, and the seroprevalence ranged from 0 to 69.22%. Seven hantaviruses genotypes have been described in Mexico and three are zoonotic. Four host species of rodents are widely distributed in Mexico harboring the highest PD of viruses. According to the hosts distribution, 16 genotypes could be circulating in Mexico and some of these represent a potential risk for public health. This study proposed multidisciplinary and interinstitutional collaborations to implement systematic surveillance in rodents.

Land-use change can raise the risk of human exposure to zoonotic diseases by increasing abundance of reservoir hosts. In this study, we conducted a meta-analysis on the associations between land-use change and the abundance of rodent species in relation to their reservoir status for rodent-borne diseases. Using the PREDICT database, we analyzed 58 case studies comprising 54 species from eight countries. In general, rodent reservoirs were significantly more abundant in modified habitats (anthropogenically altered sites), whereas non-reservoir species were more abundant in non-modified habitats. To our knowledge, this is the first meta-analysis that evaluates the response of rodents to land-use change with a focus on the potential implications for epidemiological risks. Our findings give further evidence that land-use change generally impacts biodiversity in ways that might imply higher risk of zoonotic pathogen transmission.

An understanding of the factors driving the distribution of pathogens is useful in preventing disease. Often we achieve this understanding at a local microhabitat scale; however the larger scale processes are often neglected. This can result in misleading inferences about the distribution of the pathogen, inhibiting our ability to manage the disease. One such disease is Buruli ulcer, an emerging neglected tropical disease afflicting many thousands in Africa, caused by the environmental pathogen Mycobacterium ulcerans. Herein, we aim to describe the larger scale landscape process describing the distribution of M. ulcerans. Following extensive sampling of the community of aquatic macroinvertebrates in Cameroon, we select the 5 dominant insect Orders, and conduct an ecological niche model to describe how the distribution of M. ulcerans positive insects changes according to land cover and topography. We then explore the generalizability of the results by testing them against an independent dataset collected in a second endemic region, French Guiana. We find that the distribution of the bacterium in Cameroon is accurately described by the land cover and topography of the watershed, that there are notable seasonal differences in distribution, and that the Cameroon model does not predict the distribution of M. ulcerans in French Guiana. Future studies of M. ulcerans would benefit from consideration of local structure of the local stream network in future sampling, and further work is needed on the reasons for notable differences in the distribution of this species from one region to another. This work represents a first step in the identification of large-scale environmental drivers of this species, for the purposes of disease risk mapping.