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The COVID-19 pandemic has underscored the need to strengthen national surveillance systems to protect a globally connected world. In low-income and middle-income countries, zoonotic disease surveillance has advanced considerably in the past two decades. However, surveillance efforts often prioritise urban and adjacent rural communities. Communities in remote rural areas have had far less support despite having routine exposure to zoonotic diseases due to frequent contact with domestic and wild animals, and restricted access to health care. Limited disease surveillance in remote rural areas is a crucial gap in global health security. Although this point has been made in the past, practical solutions on how to implement surveillance efficiently in these resource-limited and logistically challenging settings have yet to be discussed. We highlight why investing in disease surveillance in remote rural areas of low-income and middle-income countries will benefit the global community and review current approaches. Using semi-arid regions in Kenya as a case study, we provide a practical approach by which surveillance in remote rural areas can be strengthened and integrated into existing systems. This Viewpoint represents a transition from simply highlighting the need for a more holistic approach to disease surveillance to a solid plan for how this outcome might be achieved.

The emergence of COVID-19 has drawn the attention of health researchers sharply back to the role that food systems can play in generating human disease burden. But emerging pandemic threats are just one dimension of the complex relationship between agriculture and infectious disease, which is evolving rapidly, particularly in low-income and middle-income countries (LMICs) that are undergoing rapid food system transformation. We examine this changing relationship through four current disease issues. The first is that greater investment in irrigation to improve national food security raises risks of vector-borne disease, which we illustrate with the case of malaria and rice in Africa. The second is that the intensification of livestock production in LMICs brings risks of zoonotic diseases like cysticercosis, which need to be managed as consumer demand grows. The third is that the nutritional benefits of increasing supply of fresh vegetables, fruit, and animal-sourced foods in markets in LMICs pose new food-borne disease risks, which might undermine supply. The fourth issue is that the potential human health risks of antimicrobial resistance from agriculture are intensified by changing livestock production. For each disease issue, we explore how food system transition is creating unintentional infectious disease risks, and what solutions might exist for these problems. We show that successfully addressing all of these challenges requires a coordinated approach between public health and agricultural sectors, recognising the costs and benefits of disease-reducing interventions to both, and seeking win-win solutions that are most likely to attract broad policy support and uptake by food systems.

Increasingly intimate associations between human society and the natural environment are driving the emergence of novel pathogens, with devastating consequences for humans and animals alike. Prior to emergence, these pathogens exist within complex ecological systems that are characterized by trophic interactions between parasites, their hosts and the environment. Predicting how disturbance to these ecological systems places people and animals at risk from emerging pathogens-and the best ways to manage this-remains a significant challenge. Predictive systems ecology models are powerful tools for the reconstruction of ecosystem function but have yet to be considered for modelling infectious disease. Part of this stems from a mistaken tendency to forget about the role that pathogens play in structuring the abundance and interactions of the free-living species favoured by systems ecologists. Here, we explore how developing and applying these more complete systems ecology models at a landscape scale would greatly enhance our understanding of the reciprocal interactions between parasites, pathogens and the environment, placing zoonoses in an ecological context, while identifying key variables and simplifying assumptions that underly pathogen host switching and animal-to-human spillover risk. As well as transforming our understanding of disease ecology, this would also allow us to better direct resources in preparation for future pandemics.

Infectious diseases have the potential to extirpate populations of great apes. As the interface between humans and great apes expands, zoonoses pose an increasingly severe threat to already endangered great ape populations. Despite recognition of the threat posed by human pathogens to great apes, health monitoring is only conducted for a small fraction of the world's wild great apes (and mostly those that are habituated) meaning that outbreaks of disease often go unrecognized and therefore unmitigated. This lack of surveillance (even in sites where capacity to conduct surveillance is present) is the most significant limiting factor in our ability to quickly detect and respond to emerging infectious diseases in great apes when they first appear. Accordingly, we must create a surveillance system that links disease outbreaks in humans and great apes in time and space, and enables veterinarians, clinicians, conservation managers, national decision makers, and the global health community to respond quickly to these events. Here, we review existing great ape health surveillance programs in African range habitats to identify successes, gaps, and challenges. We use these findings to argue that standardization of surveillance across sites and geographic scales, that monitors primate health in real-time and generates early warnings of disease outbreaks, is an efficient, low-cost step to conserve great ape populations. Such a surveillance program, which we call "Great Ape Health Watch" would lead to long-term improvements in outbreak preparedness, prevention, detection, and response, while generating valuable data for epidemiological research and sustainable conservation planning. Standardized monitoring of great apes would also make it easier to integrate with human surveillance activities. This approach would empower local stakeholders to link wildlife and human health, allowing for near real-time, bidirectional surveillance at the great ape-human interface.

Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance.

One Health brings the powerful interrelationship between human and wildlife health together with ecosystem health. The initial concept of One Health was formulated decades ago and focused on disease transfer from wildlife to human populations. More recently, the concept has been used to associate resilience to disease with the health of the ecosystem and resilience to environmental stressors. The need for a One Health approach is particularly evident in the plight of Old World vultures, which are facing a conservation crisis due to drastic reductions in populations across their entire range. Moreover, vulture conservation exemplifies many contemporary tenets of One Health; vultures are critical to a sustainable and resilient ecosystem, which in turn is essential for the socio-ecological health of human communities. In this review, we examine the complex factors contributing to the demise of Old World vulture populations, using the lens of One Health to conceptualize the primary drivers impacting the health and sustainability of these populations. The One Health concept provides the basis for the development of a framework that incorporates a multidimensional approach and includes human health, wildlife health, environmental and disease-related stressors, disease incidences, societal pressures, and environmental contaminants. Integrating societal needs with management aimed at maintaining healthy vulture populations is key for successfully using a One Health framework to optimize the health of human and wildlife populations and ensure ecosystem health.

BACKGROUND: Antimicrobial resistance is one of the great challenges facing global health security in the modern era. Wildlife, particularly those that use urban environments, are an important but understudied component of epidemiology of antimicrobial resistance. We investigated antimicrobial resistance overlap between sympatric wildlife, humans, livestock, and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance.METHODS: 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (ie, the household and its perimeter; n=849), 13 livestock species (n=656), and humans (n=333), and from the external environment (n=288). Escherichia coli, our sentinel organism, was cultured and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of antimicrobial resistant phenotypes was compared between urban wildlife, humans, livestock, and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of antimicrobial resistant phenotypes and multidrug-resistant E coli carriage in urban wildlife is linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of antimicrobial resistance between humans, wildlife, and livestock.FINDINGS: E coli were isolated from 485 samples collected from wildlife between Sept 6,2015, and Sept 28, 2016. Wildlife carried a low prevalence of E coli isolates susceptible to all antibiotics tested (45 [9%] of 485 samples) and a high prevalence of clinically relevant multidrug resistance (252 [52%] of 485 samples), which varied between taxa and by foraging traits. Multiple isolates were resistant to one agent from at least seven antimicrobial classes tested for, and a single isolate was resistant to all antibiotics tested for in the study. The phenotypic diversity of antimicrobial-resistant E coli in wildlife was lower than in livestock, humans, and the environment. Within household compounds, statistical models identified two interfaces for exchange of antimicrobial resistance: between both rodents, humans and their rubbish, and seed-eating birds, humans and their rubbish; and between seed-eating birds, cattle, and bovine manure.INTERPRETATION: Urban wildlife carry a high burden of clinically relevant antimicrobial-resistant E coli in Nairobi, exhibiting resistance to drugs considered crucial for human medicine by WHO. Identifiable traits of the wildlife contribute to this exposure; however, compared with humans, livestock, and the environment, low phenotypic diversity in wildlife is consistent with the hypothesis that wildlife are a net sink rather than source of clinically relevant resistance. Wildlife that interact closely with humans, livestock, and both human and livestock waste within households, are exposed to more antimicrobial resistant phenotypes, and could therefore act as conduits for the dissemination of clinically relevant antimicrobial resistance to the wider environment. These results provide novel insight into the broader epidemiology of antimicrobial resistance in complex urban environments, characteristic of lower-middle-income countries.FUNDING: UK Medical Research Council and CGIAR Research Program on Agriculture for Nutrition and Health.

The keeping of livestock has been posited as a risk factor for the emergence of zoonoses and the spread of antimicrobial resistance. However, quantitative evidence regarding the major sources of pathogenic and drug-resistant bacteria and transmission routes between hosts remains lacking. In the largest epidemiological study of this nature to date, we sampled Escherichia coli from humans, livestock, food, wildlife and the environment of 99 households across Nairobi, Kenya to gain a deeper understanding of sharing of bacteria among hosts and potential reservoirs. By analysing whole genome sequencing data from 1,338 E. coli isolates, we reconstruct sharing patterns for the sampled E. coli and its antimicrobial resistance determinants. We find that the diversity and sharing patterns of E. coli is heavily structured by household, which is the primary epidemiological interface for bacterial strain sharing. Strain sharing within households was strongly shaped by host type. We also find evidence for inter-household and inter-host sharing, and importantly, between humans and animals, although this occurs much less frequently. We find similar strain sharing patterns for the E. coli accessory genome, suggesting that it is shaped by recent evolutionary history and is strongly associated with the core genome. Resistome similarity, however, were quite differently distributed across host and household, consistent with their being driven by shared exposure to antimicrobials. Our results indicate that there is potential for the exchange of bacteria between humans, livestock and wildlife in the same household in a tropical urban setting, with wider mixing occurring over a period of months or years, but this does not drive the distribution of antimicrobial resistance.

Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large‐scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co‐exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio‐ecological drivers occurring across the city. By characterizing landscape‐scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy., We live in a rapidly urbanizing world. Today, more than half of the human race lives in cities, and this number is set to continue to increase, as people migrate to urban areas in search of higher standards of living. Careful planning is required to ensure that detrimental impacts of urban development on the environment and human health are identified and addressed. In this study we use Nairobi—one of the world's fastest growing cities—as a case study with which to explore how and why people's co‐existence with wildlife and livestock varies across a rapidly developing urban landscape. By providing a detailed characterization of the patterns of human and animal co‐existence that emerge from urban socioeconomic and environmental change, and hypotheses for how this influences disease transmission, our results provide a framework within which continuing research on the ecological and epidemiological consequences of rapid urban development in the tropics can be framed.

Much of recent human development has come at the expense of Nature - undermining ecosystems, fragmenting habitats, reducing biodiversity, and increasing our exposure and vulnerability to emerging diseases. For example, as we push deeper into tropical forests, and convert more land to agriculture and human settlements, the rate at which people encounter new pathogens that may trigger the next public health, social and economic crisis, is likely to increase. Expanding and strengthening our understanding of the links between nature and human health is especially important in Africa, where nature brings economic prosperity and wellbeing to more than a billion people. Pandemics such as COVID are just one of a growing number of health challenges that humanity is facing as a result of our one-sided and frequently destructive relationship with nature. This report aims to inform professionals and decision-makers on how health outcomes emerge from human interactions with the natural world and identify how efforts to preserve the natural environment and sustainably manage natural resources could have an impact on human and animal health. While the report focuses on the African continent, it will also be of relevance to other areas of the world facing similar environmental pressures.

The effects of COVID-19 have gone undocumented in nomadic pastoralist communities across Africa, which are largely invisible to health surveillance systems despite the fact that they are of key significance in the setting of emerging infectious disease. We expose these landscapes as a “blind spot” in global health surveillance, elaborate on the ways in which current health surveillance infrastructure is ill-equipped to capture pastoralist populations and the animals with which they coexist, and highlight the consequential risks of inadequate surveillance among pastoralists and their livestock to global health. As a platform for further dialogue, we present concrete solutions to address this gap.

Highlights • First study of antimicrobial resistance (AMR) phenotypes in humans and urban livestock. • Highest AMR carriage in humans, pigs and poultry. • AMR more common in larger households. • Urban livestock keeping is not a risk factor for AMR in humans. • Use of animal manure affects the risk factor of AMR in humans., There are substantial limitations in understanding of the distribution of antimicrobial resistance (AMR) in humans and livestock in developing countries. This papers present the results of an epidemiological study examining patterns of AMR in Escherichia coli isolates circulating in sympatric human (n = 321) and livestock (n = 633) samples from 99 households across Nairobi, Kenya. E. coli isolates were tested for susceptibility to 13 antimicrobial drugs representing nine antibiotic classes. High rates of AMR were detected, with 47.6% and 21.1% of isolates displaying resistance to three or more and five or more antibiotic classes, respectively. Human isolates showed higher levels of resistance to sulfonamides, trimethoprim, aminoglycosides and penicillins compared with livestock (P0.05). These findings revealed a high prevalence of AMR E. coli circulating in healthy humans and livestock in Nairobi, with no evidence to suggest that keeping livestock, when treated as a single risk factor, contributed significantly to the burden of AMR in humans, although the presence of livestock waste was significant. These results provide an understanding of the broader epidemiology of AMR in complex and interconnected urban environments.

Mountain gorillas (Gorilla beringei beringei) are critically endangered primates surviving in two isolated populations in protected areas within the Virunga Massif of Rwanda, Uganda, the Democratic Republic of Congo, and in Bwindi Impenetrable National Park in Uganda. Mountain gorillas face intense ecologic pressures due to their proximity to humans. Human communities outside the national parks, and numerous human activities within the national parks (including research, tourism, illegal hunting, and anti-poaching patrols), lead to a high degree of contact between mountain gorillas and wildlife, domestic animals, and humans. To assess the pathogen transmission potential between wildlife and livestock, feces of mountain gorillas, forest buffalo (Syncerus caffer nanus), and domestic cattle (Bos taurus) in Rwanda were examined for the parasites Giardia and Cryptosporidium. Giardia was found in 9% of mountain gorillas, 6% of cattle, and 2% of forest buffalo. Our study represents the first report of Giardia prevalence in forest buffalo. Cryptosporidium-like particles were also observed in all three species. Molecular characterization of Giardia isolates identified zoonotic genotype assemblage B in the gorilla samples and assemblage E in the cattle samples. Significant spatial clustering of Giardia-positive samples was observed in one sector of the park. Although we did not find evidence for transmission of protozoa from forest buffalo to mountain gorillas, the genotypes of Giardia samples isolated from gorillas have been reported in humans, suggesting that the importance of humans in this ecosystem should be more closely evaluated.

Long-term studies of morbidity and mortality in free-ranging primates are scarce, but may have important implications for the conservation of extant populations. Infants comprise a particularly important age group, as variation in survival rates may have a strong influence on population dynamics. Since 1968, the Mountain Gorilla Veterinary Project (MGVP, Inc.) and government partners have conducted a comprehensive health monitoring and disease investigation program on mountain gorillas (Gorilla beringei beringei) in Rwanda, Uganda, and the Democratic Republic of the Congo. In an effort to better understand diseases in this species, we reviewed reliable field reports (n = 37), gross post-mortem (n = 66), and histopathology (n = 53) reports for 103 infants (less than 3.5 years) mountain gorillas in the Virunga Massif. Our aim was to conduct the first comprehensive analysis of causes of infant mortality and to correlate histological evidence with antemortem morbidity in infant mountain gorillas. Causes of morbidity and mortality were described, and compared by age, sex, and over time. Trauma was the most common cause of death in infants (56%), followed by respiratory infections and aspiration (13%). Gastrointestinal parasitism (33%), atypical lymphoid hyperplasia (suggestive of infectious disease) (31%), and hepatic capillariasis (25%) were the most significant causes of antemortem morbidity identified post-mortem. Identifying the causes of mortality and morbidity in infants of this critically endangered species will help to inform policy aimed at their protection and guide ante- and post-mortem health monitoring and clinical decision-making in the future.

Cysts morphologically resembling Balantidium coli were identified in the feces of a mountain gorilla (Gorilla beringei beringei). Confirmatory PCR and sequencing revealed two distinct B. coli-specific sequences (ITS-1, sub-types A0 and B1). This represents the first report of B. coli in this species, raising the possibility of infection from a reservoir host.