Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence

Patterns, Drivers, and Challenges of Vector-Borne Disease Emergence

Vector-borne diseases are emerging at an increasing rate and comprise a disproportionate share of all emerging infectious diseases. Yet, the key ecological and evolutionary dimensions of vector-borne disease that facilitate their emergence have not been thoroughly explored. This study reviews and synthesizes the existing literature to explore global patterns of emerging vector-borne zoonotic diseases (VBZDs) under changing global conditions. We find that the vast majority of emerging VBZDs are transmitted by ticks (Ixodidae) and mosquitoes (Culicidae) and the pathogens transmitted are dominated by Rickettsiaceae bacteria and RNA viruses (Flaviviridae, Bunyaviridae, and Togaviridae). The most common potential driver of these emerging zoonoses is land use change, but for many diseases, the driver is unknown, revealing a critical research gap. While most reported VBZDs are emerging in the northern latitudes, after correcting for sampling bias, Africa is clearly a region with the greatest share of emerging VBZD. We highlight critical gaps in our understanding of VBZD emergence and emphasize the importance of interdisciplinary research and consideration of deeper evolutionary processes to improve our capacity for anticipating where and how such diseases have and will continue to emerge.

Ecology and Infection Dynamics of Multi-Host Amdoparvoviral and Protoparvoviral Carnivore Pathogens

Amdoparvovirus and Protoparvovirus are monophyletic viral genera that infect carnivores. We performed surveillance for and sequence analyses of parvoviruses in mustelids in insular British Columbia to investigate parvoviral maintenance and cross-species transmission among wildlife. Overall, 19.1% (49/256) of the tested animals were parvovirus-positive. Aleutian mink disease virus (AMDV) was more prevalent in mink (41.6%, 32/77) than martens (3.1%, 4/130), feline panleukopenia virus (FPV) was more prevalent in otters (27.3%, 6/22) than mink (5.2%, 4/77) or martens (2.3%, 3/130), and canine parvovirus 2 (CPV-2) was found in one mink, one otter, and zero ermines (N = 27). Viruses were endemic and bottleneck events, founder effects, and genetic drift generated regional lineages. We identified two local closely related AMDV lineages, one CPV-2 lineage, and five FPV lineages. Highly similar viruses were identified in different hosts, demonstrating cross-species transmission. The likelihood for cross-species transmission differed among viruses and some species likely represented dead-end spillover hosts. We suggest that there are principal maintenance hosts (otters for FPV, raccoons for CPV-2/FPV, mink for AMDV) that enable viral persistence and serve as sources for other susceptible species. In this multi-host system, viral and host factors affect viral persistence and distribution, shaping parvoviral ecology and evolution, with implications for insular carnivore conservation.

Integration of shared-pathogen networks and machine learning reveals the key aspects of zoonoses and predicts mammalian reservoirs

Diseases that spread to humans from animals, zoonoses, pose major threats to human health. Identifying animal reservoirs of zoonoses and predicting future outbreaks are increasingly important to human health and well-being and economic stability, particularly where research and resources are limited. Here, we integrate complex networks and machine learning approaches to develop a new approach to identifying reservoirs. An exhaustive dataset of mammal–pathogen interactions was transformed into networks where hosts are linked via their shared pathogens. We present a methodology for identifying important and influential hosts in these networks. Ensemble models linking network characteristics with phylogeny and life-history traits are then employed to predict those key hosts and quantify the roles they undertake in pathogen transmission. Our models reveal drivers explaining host importance and demonstrate how these drivers vary by pathogen taxa. Host importance is further integrated into ensemble models to predict reservoirs of zoonoses of various pathogen taxa and quantify the extent of pathogen sharing between humans and mammals. We establish predictors of reservoirs of zoonoses, showcasing host influence to be a key factor in determining these reservoirs. Finally, we provide new insight into the determinants of zoonosis-sharing, and contrast these determinants across major pathogen taxa.

Zoonotic causes of febrile illness in malaria endemic countries: a systematic review

Fever is one of the most common reasons for seeking health care globally and most human pathogens are zoonotic. We conducted a systematic review to describe the occurrence and distribution of zoonotic causes of human febrile illness reported in malaria endemic countries. We included data from 53 (48·2%) of 110 malaria endemic countries and 244 articles that described diagnosis of 30 zoonoses in febrile people. The majority (17) of zoonoses were bacterial, with nine viruses, three protozoa, and one helminth also identified. Leptospira species and non-typhoidal salmonella serovars were the most frequently reported pathogens. Despite evidence of profound data gaps, this Review reveals widespread distribution of multiple zoonoses that cause febrile illness. Greater understanding of the epidemiology of zoonoses in different settings is needed to improve awareness about these pathogens and the management of febrile illness.

Molecular Survey on Vector-Borne Pathogens in Alpine Wild Carnivorans

In Europe, free-ranging wildlife has been linked to the emergence of several vector-borne diseases such as rodents for Borrelia burgdorferi s.l. In particular, wild carnivorans are one of the most important sources of emerging zoonotic pathogens worldwide, although little information is available regarding the epidemiology of vector-borne parasites in these animals. Thus, the aim of this paper was to investigate the prevalence of Babesia spp., Anaplasma spp., Ehrlichia spp., Hepatozoon spp. and Leishmania infantum in alpine wild canids and mustelids from Italy. For this study, spleen samples of 157 foxes (Vulpes vulpes), 45 badgers (Meles meles), and 33 wolves (Canis lupus) collected between 2009 and 2017 in Northwest Italy were examined by using conventional PCR. Logistic regression was used to identify possible risk factors for pathogen infections. DNA of any of the tested pathogens was found in more than 90% of the analyzed animals. In particular, Babesia spp. showed significantly higher prevalence in foxes (89.7%) and badgers (89.6%) than in wolves, while the latter were considerably more infected with Hepatozoon canis (75.8%) than foxes (5.1%). None of the badger tested positive for Hepatozoon spp., although they showed high prevalence of Leishmania infantum (53.3%). Sequencing results revealed the presence, among others, of Babesia vulpes, Babesia sp. isolate badger type A and B, and Anaplasma phagocytophilum. Moreover, previously unreported pathogen/host associations were observed, such as Babesia capreoli in wolves and badgers. The prevalence of vector-borne pathogens observed in the present study is one of the highest reported so far, suggesting the importance of free-ranging carnivorans in the epidemiology and maintenance of the sylvatic cycle of the pathogens. Moreover, several of these pathogens are of particular importance regarding human (A. phagocytophilum, L. infantum) and pet health (L. infantum, B. vulpes).

What do studies in wild mammals tell us about human emerging viral diseases in Mexico?

Multiple species of viruses circulate in wild mammals, some of them potentially causing zoonosis. Most of the suspected viral zoonotic diseases affecting human patients remain unidentified with regard to their aetiological agent. The aim of this study is to summarize the state of knowledge of the viral richness associated with wild mammals in Mexico throughout 1900-2018 and their relationship with human cases. We compiled two databases, one of them containing all available published studies on potentially zoonotic viruses in wild mammals and another with human cases related to zoonotic viruses. The database on wild mammals covers the period of 1900-2018; the human case database spans 2000-2013. We calculated the richness of viral potential zoonotic agents and evaluated their geographical distribution. We found 262 records of 42 potential zoonotic viral species associated with 92 wild mammal species in 28 states across Mexico. Records of human viral cases were only found in 29 states, which did not overlap with the reports in wild mammals. We detected 25.6% (42/164) of viral zoonotic agents reported worldwide. This analysis opens a relevant topic of discussion for public health attention.

Human Viruses: Emergence and Evolution

Many new viruses have emerged in the last five decades. These newer genetically active agents have a major impact on the public health systems worldwide. Most emerging infections appear to be caused by pathogens already present in the environment, brought out of obscurity or given a selective advantage by changing conditions and afforded an opportunity to infect new host populations. Also on rare occasions, a new variant may evolve and cause a new disease. Altered virus transmission because of deforestation and environment change, ecological changes and agricultural development, commerce, technology, microbial adaptation and change, breakdown of public health measures, and deficiencies in public health infrastructure are the reasons for emergence and reemergence of infectious diseases in general and viral infections in particular.

Specific factors precipitating disease emergence can be identified in virtually all cases. Moreover, these factors are increasing in prevalence. This increase, together with the ongoing evolution of viral and microbial variants and selection for drug resistance, suggests that infections will continue to emerge and probably increase and emphasize the urgent need for effective surveillance and control. These viruses are rich source of emerging diseases due to the introduction of infections from other species in the zoonotic pool. In the near future, there is an urgent need to monitor collaboration between human–animal interface so that public health risks can be understood. A number of activities increase microbial traffic from animals to humans or disseminate microbes from isolated groups into new populations and as a result promote emergence and epidemics. In some cases, including many of the most novel infections, the agents are zoonotic crossing from their natural hosts into the human population because of many similarities. Vector-borne diseases also have a natural advantage of dissemination.

Socioeconomic Predictors of Intestinal Parasitic Infections Among Under-Five Children in Rural Dembiya, Northwest Ethiopia: A Community-Based Cross-sectional Study

BACKGROUND

Soil-transmitted helminths and protozoan parasitic infections are endemic throughout the world. The problem of intestinal parasitic infection is higher among developing countries where children are the most vulnerable groups. Although health information related to parasitic infections is available globally, it is often limited in rural setups in least developed countries. This study was, therefore, conducted to assess socioeconomic predictors of intestinal parasitic infections among under-five children in rural Dembiya, Northwest Ethiopia.

METHODS

This cross-sectional study was conducted among 224 randomly selected households with under-five children. We used questionnaire to collect data and direct stool examination to identify intestinal parasitic infections. Adjusted odds ratio (AOR) with 95% confidence interval (CI) and P < .05 was used to identify socioeconomic predictors of parasitic infections.

RESULTS

We found that 25.4% (95% CI = [20.2, 31.1]) under-five children had intestinal parasitic infection. Ascaris lumbricoides was the leading infection, which accounted 44 of 224 (19.6%). The prevalence of childhood intestinal parasitic infections was higher among households with no members whose education level is secondary and above (AOR = 3.36, 95% CI = [1.23, 9.17]). Similarly, intestinal parasitic infections were statistically associated with presence of 2 under-five children in a household (AOR = 3.56, 95% CI = [1.29, 9.82]), absence of frequent health supervision (AOR = 3.49, 95% CI = [1.72, 7.09]), larger family size (AOR = 2.30, 95% CI = [1.09, 4.85]), and poor household economic status (AOR = 2.58, 95% CI = [1.23, 5.41]).

CONCLUSIONS

Significant proportion of children was infected with intestinal parasitic infection in rural Dembiya. Educational status of family members, number of under-five children in a household, health supervision, family size, and wealth index were statistically associated with parasitic infections. Provision of anthelmintic drugs, health supervision, and health education targeted with transmission and prevention of infections are recommended.

Tissue tropism and transmission ecology predict virulence of human RNA viruses

Novel infectious diseases continue to emerge within human populations. Predictive studies have begun to identify pathogen traits associated with emergence. However, emerging pathogens vary widely in virulence, a key determinant of their ultimate risk to public health. Here, we use structured literature searches to review the virulence of each of the 214 known human-infective RNA virus species. We then use a machine learning framework to determine whether viral virulence can be predicted by ecological traits, including human-to-human transmissibility, transmission routes, tissue tropisms, and host range. Using severity of clinical disease as a measurement of virulence, we identified potential risk factors using predictive classification tree and random forest ensemble models. The random forest approach predicted literature-assigned disease severity of test data with mean accuracy of 89.4% compared to a null accuracy of 74.2%. In addition to viral taxonomy, the ability to cause systemic infection was the strongest predictor of severe disease. Further notable predictors of severe disease included having neural and/or renal tropism, direct contact or respiratory transmission, and limited (0 < R₀ ≤ 1) human-to-human transmissibility. We present a novel, to our knowledge, comparative perspective on the virulence of all currently known human RNA virus species. The risk factors identified may provide novel perspectives in understanding the evolution of virulence and elucidating molecular virulence mechanisms. These risk factors could also improve planning and preparedness in public health strategies as part of a predictive framework for novel human infections.

Comparative analysis using machine learning shows that specificity of tissue tropism and transmission biology can act as predictive risk factors for the virulence of human RNA viruses.

Compositional and temporal stability of fecal taxon libraries for use with SourceTracker in sub-tropical catchments

Characterization of microbial communities using high-throughput amplicon sequencing is an emerging approach for microbial source tracking of fecal pollution. This study used SourceTracker software to examine temporal and geographical variability of fecal bacterial community profiles to identify pollutant sources in three freshwater catchments in sub-tropical Australia. Fecal bacterial communities from 10 animal species, humans, and composite wastewater samples from six sewage treatment plants were characterized and compared to freshwater samples using Illumina amplicon sequencing of the V5-V6 regions of the 16S rRNA gene. Source contributions were calculated in SourceTracker using new fecal taxon libraries as well as previously generated libraries to determine the effects of geographic and temporal variability on source assignments. SourceTracker determined 16S rRNA bacterial communites within freshwater samples, shared taxonomic similarities to that of wastewater at low levels (typically <3%). SourceTraker also predicted occasional fecal detection of deer and flying fox sources in the water samples. No significant differences in source contributions were observed within sequences from current and previously characterized fecal samples (P ≥ 0.107). However, significant differences were observed between previously characterized and newly characterized source communities (ANOSIM P ≤ 0.001), which shared <15% community composition. Results suggest temporal instability of fecal taxon libraries among tested sources and highlight continual evaluation of community-based MST using confirmatory qPCR analyses of marker genes.

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.

Genetic diversity of primate strongylid nematodes: Do sympatric nonhuman primates and humans share their strongylid worms?

The close phylogenetic relationship between humans and nonhuman primates (NHPs) can result in a high potential for pathogen exchange. In recent decades, NHP and human interactions have become more frequent due to increasing habitat encroachment and ecotourism. Strongylid communities, which include members of several genera, are typically found in NHPs. Using optimized high-throughput sequencing for strain-level identification of primate strongylids, we studied the structure of strongylid communities in NHPs and humans co-habiting a tropical forest ecosystem in the Central African Republic. General taxonomic assignment of 85 ITS-2 haplotypes indicated that the studied primates harbour at least nine genera of strongylid nematodes, with Oesophagostomum and Necator being the most prevalent. We detected both host-specific and shared strongylid haplotypes. Skin-penetrating Necator gorillaehaplotypes were shared between humans and gorillas but Necator americanus were much more restricted to humans. Strongylid communities of local hunter-gatherers employed as trackers were more similar to those of gorillas compared to their relatives, who spent more time in villages. This was due to lower abundance of human-origin N. americanus in both gorillas and trackers. Habituated gorillas or those under habituation did not show larger overlap of strongylids with humans compared to unhabituated. We concluded that the occurrence of the human-specific strongylids in gorillas does not increase with direct contact between gorillas and humans due to the habituation. Overall, our results indicate that the degree of habitat sharing between hosts, together with mode of parasite transmission, are important factors for parasite spillover among primates.

Genetic structure of Mycoplasma ovipneumoniae informs pathogen spillover dynamics between domestic and wild Caprinae in the western United States

Spillover diseases have significant consequences for human and animal health, as well as wildlife conservation. We examined spillover and transmission of the pneumonia-associated bacterium Mycoplasma ovipneumoniae in domestic sheep, domestic goats, bighorn sheep, and mountain goats across the western United States using 594 isolates, collected from 1984 to 2017. Our results indicate high genetic diversity of M. ovipneumoniae strains within domestic sheep, whereas only one or a few strains tend to circulate in most populations of bighorn sheep or mountain goats. These data suggest domestic sheep are a reservoir, while the few spillovers to bighorn sheep and mountain goats can persist for extended periods. Domestic goat strains form a distinct clade from those in domestic sheep, and strains from both clades are found in bighorn sheep. The genetic structure of domestic sheep strains could not be explained by geography, whereas some strains are spatially clustered and shared among proximate bighorn sheep populations, supporting pathogen establishment and spread following spillover. These data suggest that the ability to predict M. ovipneumoniae spillover into wildlife populations may remain a challenge given the high strain diversity in domestic sheep and need for more comprehensive pathogen surveillance.

Global Study of Social Odor Awareness

Olfaction plays an important role in human social communication, including multiple domains in which people often rely on their sense of smell in the social context. The importance of the sense of smell and its role can however vary inter-individually and culturally. Despite the growing body of literature on differences in olfactory performance or hedonic preferences across the globe, the aspects of a given culture as well as culturally universal individual differences affecting odor awareness in human social life remain unknown. Here, we conducted a large-scale analysis of data collected from 10 794 participants from 52 study sites from 44 countries all over the world. The aim of our research was to explore the potential individual and country-level correlates of odor awareness in the social context. The results show that the individual characteristics were more strongly related than country-level factors to self-reported odor awareness in different social contexts. A model including individual-level predictors (gender, age, material situation, education, and preferred social distance) provided a relatively good fit to the data, but adding country-level predictors (Human Development Index, population density, and average temperature) did not improve model parameters. Although there were some cross-cultural differences in social odor awareness, the main differentiating role was played by the individual differences. This suggests that people living in different cultures and different climate conditions may still share some similar patterns of odor awareness if they share other individual-level characteristics.

Host phylogenetic distance drives trends in virus virulence and transmissibility across the animal-human interface

Historically, efforts to assess 'zoonotic risk' have focused mainly on quantifying the potential for cross-species emergence of viruses from animal hosts. However, viruses clearly differ in relative burden, both in terms of morbidity and mortality (virulence) incurred and the capacity for sustained human-to-human transmission. Extending previously published databases, we delineated host and viral traits predictive of human mortality associated with viral spillover, viral capacity to transmit between humans following spillover and the probability of a given virus being zoonotic. We demonstrate that increasing host phylogenetic distance from humans positively correlates with human mortality but negatively correlates with human transmissibility, suggesting that the virulence induced by viruses emerging from hosts at high phylogenetic distance may limit capacity for human transmission. Our key result is that hosts most closely related to humans harbour zoonoses of lower impact in terms of morbidity and mortality, while the most distantly related hosts-in particular, order Chiroptera (bats)-harbour highly virulent zoonoses with a lower capacity for endemic establishment in human hosts. As a whole, our results emphasize the importance of understanding how zoonoses manifest in the human population and also highlight potential risks associated with multi-host transmission chains in spillover. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

The problem of scale in the prediction and management of pathogen spillover

Disease emergence events, epidemics and pandemics all underscore the need to predict zoonotic pathogen spillover. Because cross-species transmission is inherently hierarchical, involving processes that occur at varying levels of biological organization, such predictive efforts can be complicated by the many scales and vastness of data potentially required for forecasting. A wide range of approaches are currently used to forecast spillover risk (e.g. macroecology, pathogen discovery, surveillance of human populations, among others), each of which is bound within particular phylogenetic, spatial and temporal scales of prediction. Here, we contextualize these diverse approaches within their forecasting goals and resulting scales of prediction to illustrate critical areas of conceptual and pragmatic overlap. Specifically, we focus on an ecological perspective to envision a research pipeline that connects these different scales of data and predictions from the aims of discovery to intervention. Pathogen discovery and predictions focused at the phylogenetic scale can first provide coarse and pattern-based guidance for which reservoirs, vectors and pathogens are likely to be involved in spillover, thereby narrowing surveillance targets and where such efforts should be conducted. Next, these predictions can be followed with ecologically driven spatio-temporal studies of reservoirs and vectors to quantify spatio-temporal fluctuations in infection and to mechanistically understand how pathogens circulate and are transmitted to humans. This approach can also help identify general regions and periods for which spillover is most likely. We illustrate this point by highlighting several case studies where long-term, ecologically focused studies (e.g. Lyme disease in the northeast USA, Hendra virus in eastern Australia, Plasmodium knowlesi in Southeast Asia) have facilitated predicting spillover in space and time and facilitated the design of possible intervention strategies. Such studies can in turn help narrow human surveillance efforts and help refine and improve future large-scale, phylogenetic predictions. We conclude by discussing how greater integration and exchange between data and predictions generated across these varying scales could ultimately help generate more actionable forecasts and interventions. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

Multi-host disease management: the why and the how to include wildlife

In recent years, outbreaks caused by multi-host pathogens (MHP) have posed a serious challenge to public and animal health authorities. The frequent implication of wildlife in such disease systems and a lack of guidelines for mitigating these diseases within wild animal populations partially explain why the outbreaks are particularly challenging. To face these challenges, the French Ministry of Agriculture launched a multi-disciplinary group of experts that set out to discuss the main wildlife specific concepts in the management of MHP disease outbreaks and how to integrate wildlife in the disease management process.

This position paper structures the primary specific concepts of wildlife disease management, as identified by the working group. It is designed to lay out these concepts for a wide audience of public and/or animal health officers who are not necessarily familiar with wildlife diseases. The group’s discussions generated a possible roadmap for the management of MHP diseases. This roadmap is presented as a cycle for which the main successive step are: step 1-descriptive studies and monitoring; step 2-risk assessment; step 3-management goals; step 4-management actions and step 5-assessment of the management plan. In order to help choose the most adapted management actions for all involved epidemiological units, we integrated a decision-making framework (presented as a spreadsheet). This tool and the corresponding guidelines for disease management are designed to be used by public and health authorities when facing MHP disease outbreaks. These proposals are meant as an initial step towards a harmonized transboundary outbreak response framework that integrates current scientific understanding adapted to practical intervention.

Confronting models with data: the challenges of estimating disease spillover

For pathogens known to transmit across host species, strategic investment in disease control requires knowledge about where and when spillover transmission is likely. One approach to estimating spillover is to directly correlate observed spillover events with covariates. An alternative is to mechanistically combine information on host density, distribution and pathogen prevalence to predict where and when spillover events are expected to occur. We use several case studies at the wildlife-livestock disease interface to highlight the challenges, and potential solutions, to estimating spatio-temporal variation in spillover risk. Datasets on multiple host species often do not align in space, time or resolution, and may have no estimates of observation error. Linking these datasets requires they be related to a common spatial and temporal resolution and appropriately propagating errors in predictions can be difficult. Hierarchical models are one potential solution, but for fine-resolution predictions at broad spatial scales, many models become computationally challenging. Despite these limitations, the confrontation of mechanistic predictions with observed events is an important avenue for developing a better understanding of pathogen spillover. Systems where data have been collected at all levels in the spillover process are rare, or non-existent, and require investment and sustained effort across disciplines. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

Zoonotic nematodes of wild carnivores

For a long time, wildlife carnivores have been disregarded for their potential in transmitting zoonotic nematodes. However, human activities and politics (e.g., fragmentation of the environment, land use, recycling in urban settings) have consistently favoured the encroachment of urban areas upon wild environments, ultimately causing alteration of many ecosystems with changes in the composition of the wild fauna and destruction of boundaries between domestic and wild environments. Therefore, the exchange of parasites from wild to domestic carnivores and vice versa have enhanced the public health relevance of wild carnivores and their potential impact in the epidemiology of many zoonotic parasitic diseases. The risk of transmission of zoonotic nematodes from wild carnivores to humans via food, water and soil (e.g., genera Ancylostoma, Baylisascaris, Capillaria, Uncinaria, Strongyloides, Toxocara, Trichinella) or arthropod vectors (e.g., genera Dirofilaria spp., Onchocerca spp., Thelazia spp.) and the emergence, re-emergence or the decreasing trend of selected infections is herein discussed. In addition, the reasons for limited scientific information about some parasites of zoonotic concern have been examined. A correct compromise between conservation of wild carnivores and risk of introduction and spreading of parasites of public health concern is discussed in order to adequately manage the risk of zoonotic nematodes of wild carnivores in line with the 'One Health' approach.

The triad "dogs, conservation and zoonotic diseases" - An old and still neglected problem in Brazil

The presence of domestic/free-ranging dogs in Brazilian protected areas and native vegetation fragments is an important problem, mainly because these animals pose a threat to wild species that live in such areas. In addition, dogs constantly circulate between wildlife environments and urban regions, acting as "bridges" in spillover events. Dogs are traditionally recognized as vectors of zoonoses, which are correct, but their roles as facilitating agents for the "jump" of pathogens from wild animals to humans (and vice versa) are sparsely debated. In this context, this work briefly describes the different roles of dogs in the dynamics and ecology of infectious diseases, using the Brazilian scenario as a study model.

Infection dynamics of gastrointestinal helminths in sympatric non-human primates, livestock and wild ruminants in Kenya

BACKGROUND

Gastrointestinal parasites are neglected infections, yet they cause significant burden to animal and human health globally. To date, most studies of gastrointestinal parasites focus on host-parasite systems that involve either a single parasite or a host species. However, when hosts share habitat and resources, they may also cross-transmit generalist gastrointestinal parasites. Here we explore multi-host-parasite interactions in a single ecosystem to understand the infection patterns, especially those linked to livestock-wildlife interfaces and zoonotic risk.

METHODS

We used both coprological methods (flotation and sedimentation; N = 1,138 fecal samples) and molecular identification techniques (rDNA and mtDNA; N = 18 larvae) to identify gastrointestinal parasites in nine sympatric host species (cattle, sheep, goats, wildebeest, Grant's gazelles, Thomson's gazelles, impala, vervet monkeys and baboons) in the Amboseli ecosystem, Kenya.

RESULTS

We found that the host community harbored a diverse community of gastrointestinal helminths, including 22 species and/or morphotypes that were heterogeneously distributed across the hosts. Six zoonotic gastrointestinal helminths were identified: Trichuris spp., Trichostrongylus colubriformis, Enterobius spp. Oesophagostomum bifurcum, Strongyloides stercoralis and Strongyloides fuelleborni. The dominant parasite was Trichuris spp, whose ova occurred in two morphological types. Baboons were co-infected with Strongyloides fuelleborni and S. stercoralis.

CONCLUSIONS

We found that the interface zone shared by wild ungulates, livestock and non-human primates is rich in diversity of gastrointestinal helminths, of which some are extensively shared across the host species. Closely related host species were most likely to be infected by the same parasite species. Several parasites showed genetic sub-structuring according to either geography or host species. Of significance and contrary to expectation, we found that livestock had a higher parasite richness than wild bovids, which is a health risk for both conservation and livestock production. The zoonotic parasites are of public health risk, especially to pastoralist communities living in areas contiguous to wildlife areas. These results expand information on the epidemiology of these parasites and highlights potential zoonotic risk in East African savanna habitats.

Phylogeographical and cross-species transmission dynamics of SAT1 and SAT2 foot-and-mouth disease virus in Eastern Africa

Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Bayesian phylodynamic models were used to analyse SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (p = 0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (p = 0.72). Salient (Bayes factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife, with limited evidence that buffalo serve as reservoirs for cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities.

Topic modeling of major research themes in disease ecology of mammals

Disease ecology is a rapidly growing subdiscipline, and mammals and their parasites feature prominently in both historical and more recent research efforts. Nevertheless, the diversity of topics explored, and those not well explored, has not been systematically assessed. We conducted a systematic review of the published scientific literature in disease ecology of mammals and subjected the collection of original and review articles identified to a topic modeling approach, which is based on the words used in the published texts and their contexts (i.e., the frequency and strength of their semantic relationships with one another). In addition to concept maps identifying the most prominent research themes, we identified eight (not mutually exclusive) subcategories of studies, including experimental, theoretical, comparative, behavioral, immunological-microbiological, biogeographic-macroecological, vector-focused (e.g., mosquitoes), and disturbance-focused. The most prominent themes arising in review papers included the ecology of zoonotic diseases transmitted from non-human mammals, comparisons of pathogen prevalence between mammalian species, and pathogen discovery-disease surveillance studies, particularly of marine mammals and bats. For the original articles, the most prominent themes included ecology of rodent-transmitted viral and bacterial diseases and the population biology of zoonotic hosts. Most studies used comparative or descriptive approaches to investigate mammal-pathogen-disease relationships at a local scale, focusing on vector-borne diseases. Experimental, modeling, immunological, and behavioral approaches were strikingly underrepresented. Topics of strong conceptual importance, but that are underrepresented in the current literature, include: 1) the effects of the population density of mammalian hosts, and manipulations of density, on pathogen transmission; 2) macroecological studies that quantify effects of mammalian host species on parasite abundance and prevalence; and 3) effects of climate change on physiological and behavioral processes relevant to mammal-parasite interactions.

Host Specificity in Variable Environments

Host specificity encompasses the range and diversity of host species that a parasite is capable of infecting and is considered a crucial measure of a parasite's potential to shift hosts and trigger disease emergence. Yet empirical studies rarely consider that regional observations only reflect a parasite's 'realized' host range under particular conditions: the true 'fundamental' range of host specificity is typically not approached. We provide an overview of challenges and directions in modelling host specificity under variable environmental conditions. Combining tractable modelling frameworks with multiple data sources that account for the strong interplay between a parasite's evolutionary history, transmission mode, and environmental filters that shape host-parasite interactions will improve efforts to quantify emerging disease risk in times of global change.

Prevalence of parasites in working pig-tailed Macaques (Macaca nemestrina) in Kelantan, Malaysia

BACKGROUND

Coconut is an important commodity in Kelantan, and pig-tailed macaques (Macaca nemestrina) have been traditionally used for coconut-plucking for over a century. Most of these animals were sourced from the wild population, and the parasitic status of these macaques is unknown, plus the impacts caused by these parasites are usually underestimated by the owners.

METHODS

A total of 30 macaques were sampled for blood, faeces and hair plucks to detect parasite.

RESULTS

Out of 21 faecal samples examined, 11 (52%) were determined positive for one or more gastrointestinal parasites, namely Trichostrongylus spp., Strongyloides spp., Anatrichosoma spp., Capillaria spp., Trichuris spp. and Paramphisotomum spp. Filaria was detected in one (3%) of the blood samples. For ectoparasites, only lice, Pedicinus sp., were found in 9 (30%) macaques.

CONCLUSIONS

It is imperative that the parasitic status of these animals be determined so that necessary actions and preventive measures can be implemented to prevent zoonotic transmissions.

Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites

Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera.

Parasite sharing in wild ungulates and their predators: Effects of phylogeny, range overlap, and trophic links

Understanding factors that facilitate interspecific pathogen transmission is a central issue for conservation, agriculture, and human health. Past work showed that host phylogenetic relatedness and geographical proximity can increase cross-species transmission, but further work is needed to examine the importance of host traits, and species interactions such as predation, in determining the degree to which parasites are shared between hosts. Here we consider the factors that predict patterns of parasite sharing across a diverse assemblage of 116 wild ungulates (i.e., hoofed mammals in the Artiodactyla and Perissodactyla) and nearly 900 species of micro- and macroparasites, controlling for differences in total parasite richness and host sampling effort. We also consider the effects of trophic links on parasite sharing between ungulates and carnivores. We tested for the relative influence of range overlap, phylogenetic distance, body mass, and ecological dissimilarity (i.e., the distance separating species in a Euclidean distance matrix based on standardized traits) on parasite sharing. We also tested for the effects of variation in study effort as a potential source of bias in our data, and tested whether carnivores reported to feed on ungulates have more ungulate parasites than those that use other resources. As in other groups, geographical range overlap and phylogenetic similarity predicted greater parasite community similarity in ungulates. Ecological dissimilarity showed a weak negative relationship with parasite sharing. Counter to our expectations, differences, not similarity, in host body mass predicted greater parasite sharing between pairs of ungulate hosts. Pairs of well-studied host species showed higher overlap than poorly studied species, although including sampling effort did not reduce the importance of biological traits in our models. Finally, carnivores that feed on ungulates harboured a greater richness of ungulate helminths. Overall, we show that the factors that predict parasite sharing in wild ungulates are similar to those known for other mammal groups, and demonstrate the importance of controlling for heterogeneity in host sampling effort in future analyses of parasite sharing. We also show that ecological interactions, in this case trophic links via predation, can allow sharing of some parasite species among distantly related host species.

Molecular characterization of nodule worm in a community of Bornean primates

Strongyles are commonly reported parasites in studies of primate parasite biodiversity. Among them, nodule worm species are often overlooked as a serious concern despite having been observed to cause serious disease in nonhuman primates and humans. In this study, we investigated whether strongyles found in Bornean primates are the nodule worm Oesophagostomum spp., and to what extent these parasites are shared among members of the community. To test this, we propose two hypotheses that use the parasite genetic structure to infer transmission processes within the community. In the first scenario, the absence of parasite genetic substructuring would reflect high levels of parasite transmission among primate hosts, as primates' home ranges overlap in the study area. In the second scenario, the presence of parasite substructuring would suggest cryptic diversity within the parasite genus and the existence of phylogenetic barriers to cross-species transmission. By using molecular markers, we identify strongyles infecting this primate community as O. aculeatum, the only species of nodule worm currently known to infect Asian nonhuman primates. Furthermore, the little to no genetic substructuring supports a scenario with no phylogenetic barriers to transmission and where host movements across the landscape would enable gene flow between host populations. This work shows that the parasite's high adaptability could act as a buffer against local parasite extinctions. Surveys targeting human populations living in close proximity to nonhuman primates could help clarify whether this species of nodule worm presents the zoonotic potential found in the other two species infecting African nonhuman primates.

Long-term prevalence data reveals spillover dynamics in a multi-host (Artemia), multi-parasite (Microsporidia) community

In the study of multi-host parasites, it is often found that host species contribute asymmetrically to parasite transmission. Yet in natural populations, identifying which hosts contribute to parasite transmission and maintenance is a recurring challenge. Here, we approach this issue by taking advantage of natural variation in the composition of a host community. We studied the brine shrimps Artemia franciscana and Artemia parthenogenetica and their microsporidian parasites Anostracospora rigaudi and Enterocytospora artemiae. Previous laboratory experiments had shown that each host can transmit both parasites, but could not predict their actual contributions to the parasites' maintenance in the field. To resolve this, we gathered long-term prevalence data from a metacommunity of these species. Metacommunity patches could contain either or both of the Artemia host species, so that the presence of the hosts could be linked directly to the persistence of the parasites. First, we show that the microsporidian A. rigaudi is a spillover parasite: it was unable to persist in the absence of its maintenance host A. parthenogenetica. This result was particularly striking, as A. rigaudi displayed both high prevalence (in the field) and high infectivity (when tested in the laboratory) in both hosts. Moreover, the seasonal presence of A. parthenogenetica imposed seasonality on the rate of spillover, causing cyclical pseudo-endemics in the spillover host A. franciscana. Second, while our prevalence data was sufficient to identify E. artemiae as either a spillover or a facultative multi-host parasite, we could not distinguish between the two possibilities. This study supports the importance of studying the community context of multi-host parasites, and demonstrates that in appropriate multi-host systems, sampling across a range of conditions and host communities can lead to clear conclusions about the drivers of parasite persistence.

Emerging infectious diseases and biological invasions: a call for a One Health collaboration in science and management

The study and management of emerging infectious diseases (EIDs) and of biological invasions both address the ecology of human-associated biological phenomena in a rapidly changing world. However, the two fields work mostly in parallel rather than in concert. This review explores how the general phenomenon of an organism rapidly increasing in range or abundance is caused, highlights the similarities and differences between research on EIDs and invasions, and discusses shared management insights and approaches. EIDs can arise by: (i) crossing geographical barriers due to human-mediated dispersal, (ii) crossing compatibility barriers due to evolution, and (iii) lifting of environmental barriers due to environmental change. All these processes can be implicated in biological invasions, but only the first defines them. Research on EIDs is embedded within the One Health concept-the notion that human, animal and ecosystem health are interrelated and that holistic approaches encompassing all three components are needed to respond to threats to human well-being. We argue that for sustainable development, biological invasions should be explicitly considered within One Health. Management goals for the fields are the same, and direct collaborations between invasion scientists, disease ecologists and epidemiologists on modelling, risk assessment, monitoring and management would be mutually beneficial.

Rat-borne diseases at the horizon. A systematic review on infectious agents carried by rats in Europe 1995-2016

To investigate the spectrum of rat-borne pathogens circulating in Europe a systematic review spanning across 55 European countries during the years 1995-2016 was performed. The study surveyed viruses, bacteria, macroparasites and unicellular eukaryotes (protozoa). Fifty-three different infectious agents, all with zoonotic potential, were reported to be carried by commensal rats; 48 by the brown rat (Rattus norvegicus) and 20 by the black rat (R. rattus). There was a tendency for rural areas to harbour more rat-borne microbes than urban areas regarding the brown rat, but the opposite could be observed for the black rat. The study clearly indicated that an improved surveillance on wild rats is needed in Europe, and further indicated the pathogens and geographical areas where the major focus is required. For example, six zoonotic microbes seemed to be clearly more geographically widespread in Europe than others; virulent or resistant E. coli, pathogenic Leptospira spp., Hymenolepis diminuta, H. nana, Capillaria hepatica and Toxoplasma gondii.

One health insights to prevent the next HxNy viral outbreak: learning from the epidemiology of H7N9

Background

With an increased incidence of viral zoonoses, there is an impetus to strengthen collaborations between public health, agricultural and environmental departments. This interdisciplinary cooperation, also known as the ‘One Health’ approach, has received significant support from various stakeholders. However, current efforts and policies still fall short of those needed for an effective One Health approach towards disease control and prevention. The avian-origin H7N9 influenza A virus outbreak in China serves as an ideal case study to emphasise this point.

Discussion

Here, we present the features and epidemiology of human infections with H7N9 influenza virus. At the early stages of the H7N9 epidemic, there was limited virus surveillance and limited prevention measures implemented in live poultry markets. As a result, zoonotic infections with H7N9 influenza viruses continued to enlarge in both numbers and geographic distribution. It was only after the number of human infections with H7N9 influenza virus spiked in the 5th wave of the epidemic that inter-departmental alliances were formed. This resulted in the rapid control of the number of human infections. We therefore further discuss the barriers that prevented the implementation of an effective One Health approach in China and what this means for other emerging, zoonotic viral diseases.

Summary

Effective implementation of evidence-based disease management approaches in China will result in substantial health and economic gains. The continual threat of avian influenza, as well as other emerging zoonotic viral infections, emphasizes the need to remove the barriers that prevent the effective implementation of One Health policies in disease management.

Characterizing the phylogenetic specialism-generalism spectrum of mammal parasites

The distribution of parasites across mammalian hosts is complex and represents a differential ability or opportunity to infect different host species. Here, we take a macroecological approach to investigate factors influencing why some parasites show a tendency to infect species widely distributed in the host phylogeny (phylogenetic generalism) while others infect only closely related hosts. Using a database on over 1400 parasite species that have been documented to infect up to 69 terrestrial mammal host species, we characterize the phylogenetic generalism of parasites using standard effect sizes for three metrics: mean pairwise phylogenetic distance (PD), maximum PD and phylogenetic aggregation. We identify a trend towards phylogenetic specialism, though statistically host relatedness is most often equivalent to that expected from a random sample of host species. Bacteria and arthropod parasites are typically the most generalist, viruses and helminths exhibit intermediate generalism, and protozoa are on average the most specialist. While viruses and helminths have similar mean pairwise PD on average, the viruses exhibit higher variation as a group. Close-contact transmission is the transmission mode most associated with specialism. Most parasites exhibiting phylogenetic aggregation (associating with discrete groups of species dispersed across the host phylogeny) are helminths and viruses.

Mapping the epidemiological distribution and incidence of major zoonotic diseases in South Tigray, North Wollo and Ab'ala (Afar), Ethiopia

Zoonotic diseases continue to affect the health and livelihood of resource limited communities. In Ethiopia, despite the presence of a national master plan for prevention, control and elimination of some common zoonotic diseases, well-organized epidemiological data regarding incidence and distribution are lacking. A retrospective cross-sectional study based on a patient medical data recorded from 2012-2016 in selected districts of Southern Tigray, North Wollo zone of Amhara region and Ab'Ala district of Afar region was conducted to map the distribution and Incidence proportion of major zoonotic diseases. The incidence proportion of four major zoonotic diseases (helminthiasis, tuberculosis (TB), rabies and schistosomiasis) was mapped using qGIS software based on the Health Management Information System (HMIS) data collected from district health facilities. The result indicated that, out of a total 1,273,145 observed human disease cases, 53,614 (4.2%) of them were potential zoonotic diseases that include: helminthiasis (51,192), TB (2,085), rabies (227), schistosomiasis (105) and visceral leishmaniasis (7). The highest incidence proportion of TB (262.8 cases per 100,000 population) and rabies (33.2 cases per 100,000 population) were recorded in Gubalafto and Weldya followed by Raya Alamata (253.4 cases per 100,000 population %), and Ab'Ala and Raya Azebo (29 cases each per 100,000 population) for TB and rabies, respectively. The highest incidence proportion for schistosomiasis was reported in Raya Alamata (50.1 cases per 100,000 population) followed by Gubalafto and Weldya (10.8 cases per 100,000 population). The incidence proportion of visceral leishmaniasis per 100,000 population was 4.1, 1.3 and 1.2 cases for Ab'Ala, Gubalafto and Weldiya, and Raya Azebo districts, respectively. Except rabies, which showed high incidence proportion (p<0.0001) in 5-14 age groups, the other zoonotic diseases showed higher incidence proportion (p<0.0001) in age groups above 15 years. Rabies, helminthiasis and schistosomiasis showed statistically significant variation (p<0.0001) among seasons. Rabies and TB showed decreasing trend within the data recorded years. In animals, only 31 rabies cases and 15 anthrax cases were recorded from 2012 to 2016. This finding highlighted the distribution and incidence of some major zoonotic diseases in the study areas. Systematic and detailed research should be conducted in the future to map the distribution of major zoonotic diseases at regional and country level so as to initiate integrated effort from human and animal health authorities and professionals.

Conservation metagenomics: a new branch of conservation biology

Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.

Evolutionary Virology at 40

RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.

Response of antibiotic and heavy metal resistance genes to two different temperature sequences in anaerobic digestion of waste activated sludge

Response of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) to two different temperature sequences (i.e., mesophilic-thermophilic and thermophilic-mesophilic) were investigated. Higher removal of total ARGs (twenty-one targeted subtypes) and HMRGs (three targeted subtypes) was achieved by the mesophilic-thermophilic sequence than by the thermophilic-mesophilic sequence. The sequence of mesophilic-thermophilic showed the highest removal of total ARGs, but the sequence of thermophilic-mesophilic proved more suitable for removal of class 1 integrons (intI1). Correlation analysis indicated that intI1 correlated significantly with tetG, tetQ, tetX, sul2, aac(6')-lb-cr, bla_TEM, ermB and floR. High-throughput sequencing revealed that the mesophilic-thermophilic sequence TPAD removed more human bacterial pathogens (HBPs) than did the thermophilic-mesophilic sequence. Also, significantly positive correlation was observed between ARGs and HBPs. For instance, Mycoplasma pneumonia showed significantly positive correlation with several ARGs including tetE, tetQ, tetX, tetZ, sul1, sul2, aac(6')-lb-cr and floR.

Quantifying resilience of humans and other animals

All life requires the capacity to recover from challenges that are as inevitable as they are unpredictable. Understanding this resilience is essential for managing the health of humans and their livestock. It has long been difficult to quantify resilience directly, forcing practitioners to rely on indirect static indicators of health. However, measurements from wearable electronics and other sources now allow us to analyze the dynamics of physiology and behavior with unsurpassed resolution. The resulting flood of data coincides with the emergence of novel analytical tools for estimating resilience from the pattern of microrecoveries observed in natural time series. Such dynamic indicators of resilience may be used to monitor the risk of systemic failure across systems ranging from organs to entire organisms. These tools invite a fundamental rethinking of our approach to the adaptive management of health and resilience.

Vector population growth and condition-dependent movement drive the spread of plant pathogens

Plant viruses, often spread by arthropod vectors, impact natural and agricultural ecosystems worldwide. Intuitively, the movement behavior and life history of vectors influence pathogen spread, but the relative contribution of each factor has not been examined. Recent research has highlighted the influence of host infection status on vector behavior and life history. Here, we developed a model to explore how vector traits influence the spread of vector-borne plant viruses. We allowed vector life history (growth rate, carrying capacity) and movement behavior (departure and settlement rates) parameters to be conditional on whether the plant host is infected or healthy and whether the vector is viruliferous (carrying the virus) or not. We ran simulations under a wide range of parameter combinations and quantified the fraction of hosts infected over time. We also ran case studies of the model for Barley yellow dwarf virus, a persistently transmitted virus, and for Potato virus Y, a non-persistently transmitted virus. We quantified the relative importance of each parameter on pathogen spread using Latin hypercube sampling with the statistical partial rank correlation coefficient technique. We found two general types of mechanisms in our model that increased the rate of pathogen spread. First, increasing factors such as vector intrinsic growth rate, carrying capacity, and departure rate from hosts (independent of whether these factors were condition-dependent) led to more vectors moving between hosts, which increased pathogen spread. Second, changing condition-dependent factors such as a vector's preference for settling on a host with a different infection status than itself, and vector tendency to leave a host of the same infection status, led to increased contact between hosts and vectors with different infection statuses, which also increased pathogen spread. Overall, our findings suggest that vector population growth rates had the greatest influence on rates of virus spread, but rates of vector dispersal from infected hosts and from hosts of the same infection status were also very important. Our model highlights the importance of simultaneously considering vector life history and behavior to better understand pathogen spread. Although developed for plant viruses, our model could readily be utilized with other vector-borne pathogen systems.