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Antimicrobial resistance is a disseminated global health challenge because many of the genes that cause resistance can transfer horizontally between bacteria. Despite the central role of extrachromosomal DNA elements called plasmids in driving the spread of resistance, the detection and surveillance of plasmids remains a significant barrier in molecular epidemiology. We assessed two DNA sequencing platforms alone and in combination for laboratory diagnostics in Botswana by annotating antibiotic resistance genes and plasmids in extensively drug resistant bacteria from diarrhea in Botswana. Long-read Nanopore DNA sequencing and high accuracy basecalling effectively estimated the architecture and gene content of three plasmids in Escherichia coli HUM3355 and two plasmids in Klebsiella pneumoniae HUM7199. Polishing the assemblies with Illumina reads increased base calling precision with small improvements to gene prediction. All five plasmids encoded one or more antibiotic resistance genes, usually within gene islands containing multiple antibiotic and metal resistance genes, and four plasmids encoded genes associated with conjugative transfer. Two plasmids were almost identical to antibiotic resistance plasmids sequenced in Europe and North America from human infection and a pig farm. These One Health connections demonstrate how low-, middle-, and high-income countries collectively benefit from increased whole genome sequencing capacity for surveillance and tracking of infectious diseases and antibiotic resistance genes that can transfer between animal hosts and move across continents. Published version

Disease transmission can be strongly influenced by the manner in which conspecifics are connected across a landscape and the effects of land use upon these dynamics. In northern Botswana, the territorial and group‐living banded mongoose (Mungos mungo) lives across urban and natural landscapes and is infected with a novel Mycobacterium tuberculosis complex pathogen, M. mungi. Using microsatellite markers amplified from DNA derived from banded mongoose fecal and tissue samples (n = 168), we evaluated population genetic structure, individual dispersal, and gene flow for 12 troops. Genetic structure was detectable and moderately strong across groups (F ST = 0.086), with K = 7 being the best‐supported number of genetic clusters. Indications of admixture in certain troops suggest formation of new groups through recent fusion events. Differentiation was higher for troops inhabiting natural areas (F ST = 0.102) than for troops in urban landscapes (F ST = 0.081). While this suggests increased levels of gene flow between urban‐dwelling troops, the inclusion of a smaller number of study troops from natural land types may have influenced these findings. Of those individuals confirmed infected with M. mungi, the majority (73%, n = 11) were assigned to their natal group which is consistent with previous observations linking lower levels of dispersal with infection. Twenty‐one probable dispersing individuals were identified, with all suspected migrants originating from troops within the urban landscape. Findings suggest that urbanized landscapes may increase gene flow and dispersal behavior with a concomitant increase in the risk of pathogen spread. As urban landscapes expand, there is an increasing need to understand how land use and pathogen infection may change wildlife behavior and disease transmission potential., Using microsatellite markers amplified from DNA derived from banded mongoose fecal and tissue samples (n = 168), we evaluate gene flow in banded mongoose (Mungos mungo) in northern Botswana. This species lives across urban and natural landscapes and is infected with a novel Mycobacterium tuberculosis complex pathogen, M. mungi. Our results suggest that urban landscapes may increase mongoose movements between groups, gene flow, and potentially pathogen transmission potentially highlighting the critical influence urban landscapes may have on wildlife behavior and ecology.

Background Interference competition among sympatric carnivores can potentially influence species viability through population reduction or extinction, and has important implications for the structure and function of large carnivore communities. Carnivores may mitigate the risk of competition through fine-scaled spatial or temporal separation that subsequently affects predator interactions and community dynamics. Simultaneous telemetry records of sympatric carnivores allows for an in-depth analysis of individual space-use patterns and association metrics. Together with the application of a novel method for analyzing fine-scaled movement interactions, quantifying spatiotemporal separation between predator species provides insight into understanding the dynamic interactions among co-existing carnivores. Methods We analyzed GPS satellite relocation data from 17 lions (Panthera leo) and 14 spotted hyenas (Crocuta crocuta) over four-years, across two distinct ecosystems. Data were used to investigate lion and hyena space-use patterns and fine-scale movement of intra- and interspecific dyads. We assessed home range overlap among lion and spotted hyena, and applied a novel T-LoCoH (Time-Local Convex Hull) method to study species range overlaps from an interaction perspective. We also present the first application of our dyadic movement methodology to characterize the relative movement of lion and spotted hyena dyads. Results Heterospecific home-range overlap between lion prides and hyena clans was considerably greater than conspecific pride-pride and clan-clan overlap. Spatial overlaps among heterospecific competitors occurred mainly at the edge of home ranges, and were indicative of joint, contemporaneous space-use. Close encounters between individual lion and hyena provided opportunities to assess and compare interactions within home ranges and, even, core areas across seasons and ecosystems. At distances

Collaboration has been the key to success for urban forest management in Colorado, not only collaboration amongst agencies at all levels of government but also in engaging industry allies, coordinating education and outreach efforts and in fostering community support. A unique interagency team, the Emerging Pests in Colorado (EPIC) Workgroup, was formed in 2009 to address the immediate threat from Thousand Cankers Disease (TCD) of walnut and to plan for the arrival of other invasive urban forest pests to Colorado. When the emerald ash borer (Agrilus planipennis Fairmaire) (EAB) was detected in Boulder, Colorado in 2013, it marked the westernmost occurrence of EAB in the US, threatening millions of planted and naturalized ash trees representing over 25 percent of the tree canopy throughout Colorado’s urban and riparian forests. The detection in Boulder prompted the development of a second multi-agency group, the Colorado EAB Response Team (CORT). The preparedness and established working relationships between stakeholders and responsible authorities allowed for a quick, decisive and unified response. We review as a case study: (1) the formation and history of collaborative interagency groups in Colorado; (2) how the interagency collaborative planning and post-detection EAB response have supported community forestry programmes throughout the state; (3) development of the post-detection EAB management plan and economics behind the strategy in Boulder, Colorado; and (4) the proactive EAB planning and outreach efforts underway in Denver, Colorado.

Childhood diarrheal disease causes significant morbidity and mortality in low and middle-income countries, yet our ability to accurately predict diarrhea incidence remains limited. El Niño-Southern Oscillation (ENSO) has been shown to affect diarrhea dynamics in South America and Asia. However, understanding of its effects in sub-Saharan Africa, where the burden of under-5 diarrhea is high, remains inadequate. Here we investigate the connections between ENSO, local environmental conditions, and childhood diarrheal disease in Chobe District, Botswana. Our results demonstrate that La Niña conditions are associated with cooler temperatures, increased rainfall, and higher flooding in the Chobe region during the rainy season. In turn, La Niña conditions lagged 0–5 months are associated with higher than average incidence of under-5 diarrhea in the early rainy season. These findings demonstrate the potential use of ENSO as a long-lead prediction tool for childhood diarrhea in southern Africa., Here, Heaney et al. show that La Niña conditions are associated with higher than average incidence of childhood diarrheal disease in Botswana in the early rainy season. This finding could help to predict childhood diarrhea outbreaks in southern Africa.

Denning behavior is a critical life history attribute for many mammalian species and can be impacted by urbanization, affecting species’ reproductive success and survival in these landscapes. One significant factor that is influenced by this behavior is the spread of disease. Banded mongooses (Mungos mungo) in Northern Botswana are often infected with a novel Mycobacterium tuberculosis complex pathogen, M. mungi, that is transmitted through olfactory communication networks that allow the pathogen to move through the population by both direct and environmental transmission routes. We have studied characteristics of active banded mongoose den sites across 24 troops and 308 den sites in Northern Botswana (348 den nights from 2008 to 2010 and 281 den nights from 2016–2017). Dens were located across the human-wildlife interface (national park, lodge, urban, residential, and undeveloped). Cluster analysis and Classification and Regression Tree (CART) analysis of the den sites identified differences in den site characteristics across the land area designations. Habitat was the most important factor for den sites located at lodges, associated with the presence of gallery forest and teak woodlands. Distance to the nearest tar road was the most important variable separating the dens in the National Park from those in human-transformed landscapes. Den type was the most predictive of den sites located in human-modified environments. Sites that had the longest use were dominantly anthropogenic in nature (94% ± 6%, n = 67, used in 2008–2010 and 2016–2017). Natural dens, in contrast, appeared to be more vulnerable to destruction, shortening the period of structural soundness and use. Although banded mongoose are territorial, den use by troops other than the resident troop was observed, but only for anthropogenic dens sites (6%, n = 308). These space-sharing behaviors can significantly impact pathogen transmission dynamics and disease spread. Anthropogenic landscapes can have a critical influence on animal behavior and space use, potentially influencing infectious disease exposure and transmission potential.

A complex suite of drivers can influence infectious disease transmission with behavior and landscape spatial dynamics contributing importantly to epidemic patterns across host-pathogen-environmental systems. However, our understanding of the interaction between landscape and host behavior and its influence on spatial variability in pathogen transmission is limited. In the banded mongoose (Mungos mungo), a novel tuberculosis pathogen, Mycobacterium mungi, has emerged in Northern Botswana, which is transmitted through olfactory communication behaviors. We evaluated how associations between landscape type and mongoose behaviors affect the frequency of olfactory communication behaviors and pathogen transmission potential. We used remote sensing camera traps at den sites to eliminate observer influence across human-modified and natural landscapes (n=18 troops, 18,229 detections of banded mongooses from 7,497 photographs). Using generalized linear mixed models, we identified a significant effect of vigilance and the interactions between vigilance and landscape and vigilance and troop count on the frequency of olfactory behaviors. Interactions between troop count-vigilance interactions had a negative influence on olfactory communication. Vigilance, however, appeared to have a bidirectional association with olfactory communication depending on land type. In lodge areas, vigilance was associated with increased olfactory behaviors, but in landscapes with expected increases in predation risk (i.e., national park and urban land-use areas), vigilance had a negative association with olfactory behaviors. The interaction between behavior and landscape type may have the potential to create “super-spreading” environments, or transmission hotspots, where behavior-landscape interactions increase pathogen shedding and transmission potential.

Background Campylobacter is a common, but neglected foodborne-zoonotic pathogen, identified as a growing cause of foodborne disease worldwide. Wildlife and domestic animals are considered important reservoirs, but little is known about pathogen infection dynamics in free-ranging mammalian wildlife particularly in sub-Saharan Africa. In countries like Botswana, there is significant overlap between humans and wildlife, with the human population having one of the highest HIV infection rates in the world, increasing vulnerability to infection. Methodology/Principal findings We investigated Campylobacter occurrence in archived human fecal samples (children and adults, n = 122, 2011), feces from free-ranging banded mongooses (Mungos mungo, n = 201), surface water (n = 70), and river sediment samples (n = 81) collected in 2017 from the Chobe District, northern Botswana. Campylobacter spp. was widespread in humans (23.0%, 95% CI 13.9–35.4%), with infections dominantly associated with C. jejuni (82.1%, n = 28, 95% CI 55.1–94.5%). A small number of patients presented with asymptomatic infections (n = 6). While Campylobacter spp. was rare or absent in environmental samples, over half of sampled mongooses tested positive (56%, 95% CI 45.6–65.4%). Across the urban-wilderness continuum, we found significant differences in Campylobacter spp. detection associated with the type of den used by study mongooses. Mongooses utilizing man-made structures as den sites had significantly higher levels of C. jejuni infection (p = 0.019) than mongooses using natural dens. Conversely, mongooses using natural dens had overall higher levels of detection of Campylobacter at the genus level (p = 0.001). Conclusions These results suggest that landscape features may have important influences on Campylobacter species exposure and transmission dynamics in wildlife. In particular, data suggest that human-modified landscapes may increase C. jejuni infection, a primarily human pathogen, in banded mongooses. Pathogen circulation and transmission in urbanizing wildlife reservoirs may increase human vulnerability to infection, findings that may have critical implications for both public and animal health in regions where people live in close proximity to wildlife., Author summary Campylobacter infections are increasing worldwide but we still know little about the true burden of disease in the developing world, and even less about the role of wildlife and environmental reservoirs in human exposure and infection. Here we take a one-health approach evaluating Campylobacter infections in humans, banded mongooses (Mungos mungo), and the environment. We found evidence of widespread infection with Campylobacter spp. infecting nearly a quarter of sampled adults and children (23.0%, n = 122, 2011), dominantly with C. jejuni. Banded mongooses live in close association with humans in the area and over half of the animals sampled were found positive for Campylobacter spp. (56%, n = 201, 2017). Infection with C. jejuni was greater among mongooses utilizing human-made structures as den sites than those using natural dens. These data suggest that wildlife utilization of anthropogenic landscapes may increase C. jejuni exposure and infection. In turn, pathogen circulation and transmission in urbanizing wildlife reservoirs may increase human vulnerability to infection, particularly impoverished populations, where greater environmental exposures are expected.

Background Glucocorticoids mediate responses to perceived stressors, thereby restoring homeostasis. However, prolonged glucocorticoid elevation may cause homeostatic overload. Using extensive field investigations of banded mongoose (Mungos mungo) groups in northern Botswana, we assessed the influence of reproduction, predation risk, and food limitation on apparent homeostatic overload (n=13 groups, 1542 samples from 268 animals). We experimentally manipulated reproduction and regulated food supply in captive mongooses, and compared their glucocorticoid responses to those obtained from free-living groups. Results At the population level, variation in glucocorticoid levels in free-living mongooses was explained by food limitation: fecal organic matter, recent rainfall, and access to concentrated anthropogenic food resources. Soil macrofauna density and reproductive events explained less and predation risk very little variation in glucocorticoid levels. Reproduction and its associated challenges alone (under regulated feeding conditions) increased glucocorticoid levels 19-fold in a captive group. Among free-living groups, glucocorticoid elevation was seasonal (occurring in late dry season or early wet season when natural food resources were less available), but the timing of peak glucocorticoid production was moderated by access to anthropogenic resources (groups with fewer anthropogenic food sources had peaks earlier in dry seasons). Peak months represented 12- and 16-fold increases in glucocorticoids relative to nadir months with some animals exhibiting 100-fold increases. Relative to the captive group nadir, some free-living groups exhibited 60-fold increases in peak glucocorticoid levels with some animals exhibiting up to 800-fold increases. Most of these animals exhibited 1- to 10-fold increases relative to the captive animal peak. Conclusions Banded mongooses exhibit seasonal chronic glucocorticoid elevation, associated primarily with food limitation and secondarily with reproduction. Magnitude and duration of this elevation suggests that this may be maladaptive for some animals, with possible fitness consequences. In late dry season, this population may face a convergence of stressors (food limitation, agonistic encounters at concentrated food resources, evictions, estrus, mate competition, parturition, and predation pressure on pups), which may induce homeostatic overload.

Infectious disease emergence has increased significantly over the last 30 years, with mass mortality events (MMEs) associated with epizootics becoming increasingly common. Factors influencing these events have been widely studied in terrestrial systems, but remain relatively unexplored in marine mammals. Infectious disease-induced MMEs (ID MMEs) have not been reported ubiquitously among marine mammal species, indicating that intrinsic (host) and/or extrinsic (environmental) ecological factors may influence this heterogeneity. We assess the occurrence of ID MMEs (1955-2018) across extant marine mammals (n = 129) in relation to key life-history characteristics (sociality, trophic level, habitat breadth) and environmental variables (season, sea surface temperature [SST] anomalies, El Nino occurrence). Our results show that ID MMEs have been reported in 14% of marine mammal species (95% CI 9%-21%), with 72% (n = 36; 95% CI 56%-84%) of these events caused predominantly by viruses, primarily morbillivirus and influenza A. Bacterial pathogens caused 25% (95% CI 14%-41%) of MMEs, with only one being the result of a protozoan pathogen. Overall, virus-induced MMEs involved a greater number of fatalities per event compared to other pathogens. No association was detected between the occurrence of ID MMEs and host characteristics, such as sociality or trophic level, but ID MMEs did occur more frequently in semiaquatic species (pinnipeds) compared to obligate ocean dwellers (cetaceans; χ2 = 9.6, p = .002). In contrast, extrinsic factors significantly influenced ID MMEs, with seasonality linked to frequency (χ2 = 19.85, p = .0002) and severity of these events, and global yearly SST anomalies positively correlated with their temporal occurrence (Z = 3.43, p = 2.7e-04). No significant association was identified between El Nino and ID MME occurrence (Z = 0.28, p = .81). With climate change forecasted to increase SSTs and the frequency of extreme seasonal weather events, epizootics causing MMEs are likely to intensify with significant consequences for marine mammal survival.

Investigations into natural resource use and access are often limited to rural areas; such use is not considered an integral part of urban livelihood strategies, especially amongst the poor. With growing urban food insecurity, poverty, and unequal access to services, natural resource use may provide a viable alternative to cash-based resources, thus, allowing households to navigate the rural–urban continuum as they address livelihood needs. This may be especially pertinent for growing, but small, urban landscapes that are in transition. We investigated the use of and access to natural resources in households in rural (Lesoma), peri-urban (Kazungula), and urban (Kasane) settlements in northern Botswana. Semi-structured questionnaires for 85 households were used to investigate household demographics, variety of natural resources used, the availability, use, and importance of natural resources, threats to resources, harvesting locations, and extent of resource commercialization. Significant differences were identified in the mean number of resources used by households across the three settlements (Kruskal–Wallis Chi-squared = 9.29, df = 2, p = 0.01). Using the post hoc test Conover with Bonferroni adjustment, mean natural resource use between the urban and peri-urban villages did not differ significantly (p = 1). However, both types of villages differed from the rural village in mean resource use (urban p = 0.007 and peri-urban p = 0.012). Nevertheless, urban and peri-urban households reported use of a broad range of natural resources, highlighting the importance of these products in transitioning landscapes. Across the study villages, natural resource harvesting occurred predominantly on communal land. Primary barriers to resource access were perceived to be strict government regulations and decreasing resource availability. Natural resource commercialization was identified as a potential opportunity but was often carried out only on a small scale. The use of natural resources is intuitively thought to be associated with rural areas, but our results suggest that such resources form an important part of livelihoods across urban and peri-urban landscapes as well. This continued reliance on natural resources raises important planning questions about how to ensure both the ongoing conservation of forested and other natural areas, and the availability of associated resources for urban livelihoods. In this regard, small urban towns that are rapidly transitioning from rural landscapes provide a targeted opportunity for early intervention. Our findings underpin the vital role that natural areas play in supporting the livelihoods of the urban poor and highlight the need to encourage land designation and management of such areas not only for conservation but also as a safety net for vulnerable urban households.

In regions rich in natural resources, nature-based tourism is advancing rapidly. This form of development is identified as an important economic opportunity for local communities but can impact ecosystem services through rapid landscape transformation, threatening the livelihoods of the most impoverished sectors of a community. While it is accepted that communities should participate in the planning process, variation in community and household-level landscape dependencies and priorities can create a fractured viewpoint that is difficult to integrate into the land planning process. Power structures and special interests can subvert participatory processes and input at the community level. In the Chobe District, Northern Botswana, tourism, and other related developments had occurred at a rapid pace around the Chobe National Park creating access barriers, in some instances, to essential natural resource areas. We evaluate community landscape dependencies and participatory approaches to the development of inclusive land use maps. Spatial information on land use dependencies from household surveys were used to form the bases of reiterative village-level participatory mapping exercises (n = 179 households, six villages). The activities were conducted through traditional leadership structures. Landscape dependencies were widespread across study villages in both natural resource and agricultural sectors. Cluster and CART analysis of household data identified important variation in landscape dependencies between and within study villages. Fishing was the most important factor predicting gender of headship with male-headed households using this resource more frequently. Spatial data from these household consultations were used to create a draft map that was reiteratively refined through participatory map building exercises until final approval was provided by community members and their traditional leaders in a village. Scaled consultations and involvement of the traditional leadership limited the ability of power structures to control the process and/or subvert the interests of more vulnerable members of a community. Mapping outputs were later successfully used in land planning exercises and consultations. Development of inclusive community consensus on landscape dependencies should be undertaken before lucrative tourism ventures and land allocations are advanced in competition to the needs of more vulnerable and often voiceless sectors of a community.

The origin of ionic conductivity in bulk lithium lanthanum titanate, a promising solid electrolyte for Li-ion batteries, has long been under debate, with experiments showing lower conductivity than predictions. Using first-principles-based calculations, we find that experimentally observed type I boundaries are more stable compared with the type II grain boundaries, consistent with their observed relative abundance. Grain boundary stability appears to strongly anti-correlate with the field strength as well as the spatial extent of the space charge region. Ion migration is faster along type II grain boundaries than across, consistent with recent experiments of increased conductivity when type II densities were increased.

While there is agreement that ecosystem services provide critical life support, local communities can be disengaged from the process of conservation, allocation and decision-making. How do we move from concepts, which are often seen as hand waving by natural resource users and policymakers, to concrete valuation appreciated at the level of the household, community and policy maker? In this special issue, we explore examples from southern Africa where ecosystem services are engaged and identified by users as important and critical to improved livelihoods as well as advancing business outcomes. Two papers focus on how small, disenfranchised communities can be empowered to build a common vision of natural resource priority and identify a voice in the planning process. The second two papers in this issue investigate the role of two functional mammal guilds, bats and mesocarnivores, in reducing crop depredation. The final paper investigates how ecovolunteerism can fulfill conservation and community development gaps that occur when governments and NGO’s do not avail themselves to local communities. Together these research papers provide a holistic and synthetic view about the links between humans and ecosystems, help to assess community level capacity for sustainability and stewardship, and define what the metrics of success look like.

Epidemiological contact network models have emerged as an important tool in understanding and predicting the spread of infectious disease, due to their capacity to engage individual heterogeneity that may underlie essential dynamics of a particular host-pathogen system. Just as fundamental are the changes that real-world contact networks undergo over time, both independently of and in response to pathogen spreading. These dynamics play a central role in determining whether a disease will die out or become an epidemic within a population, known as the epidemic threshold. In this paper, we provide an overview of methods to predict the epidemic threshold for temporal contact network models, and discuss areas that remain unexplored., 22 pages

Bacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute infection that most significantly affects grazing livestock and wild ungulates, but also poses a threat to human health. The geographic extent of B. anthracis is poorly understood, despite multi-decade research on anthrax epizootic and epidemic dynamics; many countries have limited or inadequate surveillance systems, even within known endemic regions. Here, we compile a global occurrence dataset of human, livestock and wildlife anthrax outbreaks. With these records, we use boosted regression trees to produce a map of the global distribution of B. anthracis as a proxy for anthrax risk. We estimate that 1.83 billion people (95% credible interval (CI): 0.59-4.16 billion) live within regions of anthrax risk, but most of that population faces little occupational exposure. More informatively, a global total of 63.8 million poor livestock keepers (95% CI: 17.5-168.6 million) and 1.1 billion livestock (95% CI: 0.4-2.3 billion) live within vulnerable regions. Human and livestock vulnerability are both concentrated in rural rainfed systems throughout arid and temperate land across Eurasia, Africa and North America. We conclude by mapping where anthrax risk could disrupt sensitive conservation efforts for wild ungulates that coincide with anthrax-prone landscapes.

Diarrheal disease is the second largest cause of mortality in children younger than 5, yet our ability to anticipate and prepare for outbreaks remains limited. Here, we develop and test an epidemiological forecast model for childhood diarrheal disease in Chobe District, Botswana. Our prediction system uses a compartmental susceptible-infected-recovered-susceptible (SIRS) model coupled with Bayesian data assimilation to infer relevant epidemiological parameter values and generate retrospective forecasts. Our model inferred two system parameters and accurately simulated weekly observed diarrhea cases from 2007-2017. Accurate retrospective forecasts for diarrhea outbreaks were generated up to six weeks before the predicted peak of the outbreak, and accuracy increased over the progression of the outbreak. Many forecasts generated by our model system were more accurate than predictions made using only historical data trends. Accurate real-time forecasts have the potential to increase local preparedness for coming outbreaks through improved resource allocation and healthcare worker distribution. National Science Foundation Dynamics of Coupled Natural and Human Systems [1518486]; National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [T32 ES023770] This project was made possible by a grant from the National Science Foundation Dynamics of Coupled Natural and Human Systems (Award #1518486, KAA) and by a training grant from National Institutes of Health (T32 ES023770). We would also like to thank the Botswana Ministry of Health, the Chobe District Health Team, Dr. M. Vandewalle, R. Sut-cliffe, L. Nkwalale, M. Heneghan, K. Ramsden, T. Motseothata, S. Vandewalle, C. A. Nichols, and others who contributed importantly to the collection of the health data used in this study.

Background The impacts of climate change on surface water, waterborne disease, and human health remain a growing area of concern, particularly in Africa, where diarrheal disease is one of the most important health threats to children under 5 years of age. Little is known about the role of surface water and annual flood dynamics (flood pulse) on waterborne disease and human health nor about the expected impact of climate change on surface-water-dependent populations. Methods and findings Using the Chobe River in northern Botswana, a flood pulse river—floodplain system, we applied multimodel inference approaches assessing the influence of river height, water quality (bimonthly counts of Escherichia coli and total suspended solids [TSS], 2011–2017), and meteorological variability on weekly diarrheal case reports among children under 5 presenting to health facilities (n = 10 health facilities, January 2007–June 2017). We assessed diarrheal cases by clinical characteristics and season across age groups using monthly outpatient data (January 1998–June 2017). A strong seasonal pattern was identified, with 2 outbreaks occurring regularly in the wet and dry seasons. The timing of outbreaks diverged from that at the level of the country, where surface water is largely absent. Across age groups, the number of diarrheal cases was greater, on average, during the dry season. Demographic and clinical characteristics varied by season, underscoring the importance of environmental drivers. In the wet season, rainfall (8-week lag) had a significant influence on under-5 diarrhea, with a 10-mm increase in rainfall associated with an estimated 6.5% rise in the number of cases. Rainfall, minimum temperature, and river height were predictive of E. coli concentration, and increases in E. coli in the river were positively associated with diarrheal cases. In the dry season, river height (1-week lag) and maximum temperature (1- and 4-week lag) were significantly associated with diarrheal cases. During this period, a 1-meter drop in river height corresponded to an estimated 16.7% and 16.1% increase in reported diarrhea with a 1- and 4-week lag, respectively. In this region, as floodwaters receded from the surrounding floodplains, TSS levels increased and were positively associated with diarrheal cases (0- and 3-week lag). Populations living in this region utilized improved water sources, suggesting that hydrological variability and rapid water quality shifts in surface waters may compromise water treatment processes. Limitations include the potential influence of health beliefs and health seeking behaviors on data obtained through passive surveillance. Conclusions In flood pulse river—floodplain systems, hydrology and water quality dynamics can be highly variable, potentially impacting conventional water treatment facilities and the production of safe drinking water. In Southern Africa, climate change is predicted to intensify hydrological variability and the frequency of extreme weather events, amplifying the public health threat of waterborne disease in surface-water-dependent populations. Water sector development should be prioritized with urgency, incorporating technologies that are robust to local environmental conditions and expected climate-driven impacts. In populations with high HIV burdens, expansion of diarrheal disease surveillance and intervention strategies may also be needed. As annual flood pulse processes are predominantly influenced by climate controls in distant regions, country-level data may be inadequate to refine predictions of climate—health interactions in these systems., Kathleen Alexander and colleagues determine the effects of river flood height, water quality and amount of suspended solids in river water in Botswana in response to climate change and weather variability and the resultant cases of diarrhoea in children under 5., Author summary Why was this study done? Diarrheal disease remains a persistent global health threat for children under 5 years of age, particularly in Africa. In river—floodplain systems, annual floods or flood pulses can occur, with extreme flooding and drought a common threat to local populations. We do not know how surface water dynamics influence diarrheal disease and human health or how climate change will affect populations dependent on surface water resources in these regions. What did the researchers do and find? We conducted a study on the Chobe River floodplain system in northern Botswana, a system that floods annually and is the source of drinking water for 8 villages included in the study. We evaluated diarrheal outbreak patterns in children under 5 years of age (weekly, 2007–2017) and individuals of all ages (monthly, 1998–2017) reporting diarrheal disease at government health facilities (n = 10). Using multimodel inference approaches, we assessed how meteorology, river height, and water quality characteristics (2011–2017) were associated with reports of diarrheal disease in children under 5 years of age. Across individuals of all ages, diarrheal outbreaks occurred regularly in the wet and dry seasons. Season had an important influence on the type of diarrhea and age group of the patient. Increases in diarrheal case reports were closely tied to meteorology, flood recession, and decreases in surface water quality, with the highest number of cases occurring in the dry season. What do these findings mean? In flood pulse river—floodplain systems, rapid changes in surface water quality may influence the ability of water treatment plants to provide safe drinking water. Climate change is expected to increase hydrological variability, further influencing the vulnerability of populations in this region. There is an urgent need to strengthen water infrastructure to address current and future environmental impacts that can influence the production of safe water. In populations with high HIV infection levels, public health focus may need to be extended to include other at-risk groups beyond children under five, such as HIV-infected individuals and others that may also be immunocompromised. As distant weather patterns influence local flood dynamics, use of country-level data may not be adequate to predict climate impacts on human health in these types of systems.

SummaryBacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute and commonly lethal infection that most significantly affects grazing livestock, wild ungulates and other herbivorous mammals, but also poses a serious threat to human health1, 2. The geographic extent of B. anthracis endemism is still poorly understood, despite multi-decade research on anthrax epizootic and epidemic dynamics around the world3, 4. Several biogeographic studies have focused on modeling environmental suitability for anthrax at local or national scales5–9, but many countries have limited or inadequate surveillance systems, even within known endemic regions. Here we compile an extensive global occurrence dataset for B. anthracis, drawing on confirmed human, livestock, and wildlife anthrax outbreaks. With these records, we use boosted regression trees10, 11 to produce the first map of the global distribution of B. anthracis as a proxy for anthrax risk. Variable contributions to the model support pre-existing hypotheses that environmental suitability for B. anthracis depends most strongly on soil characteristics such as pH that affect spore persistence, and the extent of seasonal fluctuations in vegetation, which plays a key role in transmission for herbivores12, 13. We apply the global model to estimate that 1.83 billion people (95% credible interval: 0.59—4.16 billion) live within regions of anthrax risk, but most of that population faces little occupational exposure to anthrax. More informatively, a global total of 63.8 million rural poor livestock keepers (95% CI: 17.5—168.6 million) and 1.1 billion livestock (95% CI: 0.4—2.3 billion) live within vulnerable regions. Human risk is concentrated in rural areas, and human and livestock vulnerability are both concentrated in rainfed systems throughout arid and temperate land across Eurasia, Africa, and North America. We conclude by mapping where anthrax risk overlaps with vulnerable wild ungulate populations, and therefore could disrupt sensitive conservation efforts for species like bison, pronghorn, and saiga that coincide with anthrax-prone, mixed-agricultural landscapes. Anthrax is a zoonotic disease caused by the Gram-positive bacterium Bacillus anthracis, a generalist soil-transmitted pathogen found on every inhabited continent14, and several islands including Haiti and parts of the Philippines and Indonesia. Worldwide, an estimated 20,000 to 100,000 cases of anthrax occur annually, mostly in poor rural areas15. In clinical presentations of anthrax, case fatality rates are a function of exposure pathway. Respiratory exposure from spore inhalation is important the context of bioterrorism, but is highly uncommon, and accounts for a negligible fraction of the global burden of anthrax cases. Cutaneous exposure to B. anthracis accounts for the majority of human cases worldwide, and typically presents with low mortality; gastrointestinal exposure accounts for the remainder and presents with intermediate to high fatality rates. Cutaneous and gastrointestinal cases of anthrax are most commonly caused by handling and slaughtering infected livestock, or butchering and eating contaminated meat; untreated gastrointestinal cases likely account for most human mortality from anthrax.14–16

Limited understanding of disease in low resource communities continues to hamper improvements in health. We evaluated household pit latrine sampling as a non-invasive approach to investigate important fecal pathogens such as Giardia lamblia and Cryptosporidium spp. in impoverished communities where health-seeking behavior limits the sensitivity of health facility-based surveillance. Fecal samples were collected from pit latrines in randomly selected households and from patients presenting to the only hospital in the region during the same time periods. Samples were tested with a commercially available ELISA. Giardia household prevalence was 28.7% in 2016 and 48.4% in 2017, while individual samples from hospital submission had a Giardia prevalence of 2.4% in 2016 and 8.0% in 2017. Cryptosporidium was only found in one household. Results suggest that pit latrine surveillance for fecal-borne infections provide course estimates of community infection levels that are unbiased by health seeking behaviors and allow surveillance of vulnerable sectors of a population.

Novel diseases are increasingly emerging into human populations through the complex—and often, unseen—stepwise process of spillover from a combination of wildlife, livestock, vectors, and the abiotic environment. Characterizing and modeling the spillover interface are a key part of how eco-epidemiologists respond to the growing global burden of emerging infectious diseases; but the diversity of pathogen life cycles and transmission modes poses a complex challenge for ecologists and clinicians alike. We review our current understanding of the spillover process and present a framework that relates spillover rates and human-to-human transmissibility to the basic reproduction number (R0). Using pathogens that exemplify important transmission pathways (anthrax, Ebola, influenza, and Zika), we illustrate key aspects of the spillover interface and discuss implications to public health and management of emerging infectious disease.

Wild banded mongooses ( Mungos mungo) in northeastern Botswana and northwest Zimbabwe are infected with a novel Mycobacterium tuberculosis complex (MTC) pathogen, Mycobacterium mungi. We evaluated gross and histologic lesions in 62 infected mongooses (1999–2017). Many tissues contained multifocal irregular, lymphohistiocytic to granulomatous infiltrates and/or multifocal or coalescing noncaseating to caseating granulomas with variable numbers of intralesional acid-fast bacilli. Over one-third of nasal turbinates examined had submucosal lymphohistiocytic to granulomatous infiltrates, erosion and ulceration of the nasal mucosa, bony remodeling, and nasal distortion. Similar inflammatory cell infiltrates expanded the dermis of the nasal planum with frequent ulceration. However, even in cases with intact epidermis, acid-fast bacilli were present in variable numbers among dermal infiltrates and on the epidermal surface among desquamated cells and debris, most commonly in small crevices or folds. In general, tissue involvement varied among cases but was highest in lymph nodes (50/54, 93%), liver (39/53, 74%), spleen (37/51, 73%), and anal glands/sacs (6/8, 75%). Pulmonary lesions were present in 67% of sampled mongooses (35/52) but only in advanced disseminated disease. The pathological presentation of M. mungi in the banded mongoose is consistent with pathogen shedding occurring through scent-marking behaviors (urine and anal gland secretions) with new infections arising from contact with these contaminated olfactory secretions and percutaneous movement of the pathogen through breaks in the skin, nasal planum, and/or skin of the snout. Given the character and distribution of lesions and the presence of intracellular acid-fast bacilli, we hypothesize that pathogen spread occurs within the body through a hematogenous and/or lymphatic route. Features of prototypical granulomas such as multinucleated giant cells and peripheral fibrosis were rarely present in affected mongooses. Acid-fast bacilli were consistently found intracellularly, even in regions of necrosis. The mongoose genome has a unique deletion (RD1mon) that includes part of the encoding region for PPE68 (Rv3873), a gene co-operonic with PE35. These proteins can influence the host’s cellular immune response to mycobacterial infections, and it remains uncertain how this deletion might contribute to observed patterns of pathology. M. mungi infection in banded mongooses is characterized by both a unique transmission and exposure route, as well as accompanying pathological features, providing an opportunity to increase our understanding of MTC pathogenesis across host-pathogen systems.

The emergence of antimicrobial resistance is arguably the most important threat to human and animal health. The impacts of antimicrobial use can reach far from the site of prescription and wildlife may serve as a conduit for the movement of resistance across landscapes, contributing to the spread of antimicrobial resistance within and between different reservoirs. We compared antimicrobial resistance and life history among wild and domestic species in Chobe, Botswana to explore key attributes and behaviors that may increase exposure and allow resistance to move between humans, animals, and ecosystems. Among 150 fecal samples evaluated from African animals, 41.3% contained Escherichia coli isolates that were resistant to one or two of 10 tested antibiotics, and 13.3% of isolates demonstrated multidrug resistance (three or more antibiotics). Resistance to each of the 10 tested antibiotics was detected among wildlife fecal samples. Resistance was widespread, but not ubiquitous, and isolates from wildlife demonstrated similar patterns of resistance to human E. coli from environmental and clinical sources in the study area. Multidrug resistance was significantly higher in carnivores, water-associated species, and species inhabiting urban areas, suggesting that life history may be key to understanding exposure patterns and transmission dynamics in heterogeneous landscapes.

Technological improvements in battery life and physical dimensions of Global Positioning System (GPS) telemetry have increased the number of locations one can collect, but due to relatively unimproved GPS accuracy this also increases the number of locations with unacceptable measurement error. We propose and show an example of a new method for screening data for locations with unacceptable error. We also propose a new screening metric: estimated elevation error (EEE). EEE identifies unacceptable xy -coordinate error in some cases better than do methods that use horizontal dilution of precision (HDOP) or fix dimension (2-D or 3-D). Our screening method combines test data and a model-averaging information-theoretic framework that uses a priori candidate models of telemetry measurement error. We demonstrate this method using experimental data collected on banded mongooses ( Mungos mungo ). One can adapt this screening method to any GPS data.

Individual host behavior may be influenced by infectious disease in ways that can alter population-level disease dynamics. A novel pathogen in the Mycobacterium tuberculosis complex, Mycobacterium mungi, has emerged among banded mongooses (Mungos mungo) in Northeastern Botswana. This host–pathogen system provides an opportunity to study how individual behavior and social interactions in a group-living species might respond to infectious disease. We used repeated focal observations of known individuals with an extensive ethogram to identify behavioral differences and social interactions between healthy individuals and those with clinical signs of tuberculosis (TB). Clinically diseased banded mongooses exhibited a significantly smaller proportion of time active and alert, a larger proportion of time resting, and a slower behavioral transition rate compared to healthy individuals. They also showed lower reciprocation of allogrooming by approximately 50 %. Despite these strong behavioral differences that may serve as visible cues for healthy mongooses to avoid diseased conspecifics, we found no evidence for avoidance of clinically diseased mongooses by healthy individuals or vice versa: Clinically diseased individuals did not have lower levels of social behaviors than healthy individuals, and clinically diseased mongooses were allogroomed at the expected level despite their decreased reciprocation. Our results show that in contrast to prior studies of other species, avoidance of diseased conspecifics did not occur in this highly social species. We discuss hypotheses for this lack of avoidance and potential implications for pathogen transmission.

Background Variation in animal space use reflects fitness trade-offs associated with ecological constraints. Associated theories such as the metabolic theory of ecology and the resource dispersion hypothesis generate predictions about what drives variation in animal space use. But, metabolic theory is usually tested in macro-ecological studies and is seldom invoked explicitly in within-species studies. Full evaluation of the resource dispersion hypothesis requires testing in more species. Neither have been evaluated in the context of anthropogenic landscape change. Methods In this study, we used data for banded mongooses (Mungos mungo) in northeastern Botswana, along a gradient of association with humans, to test for effects of space use drivers predicted by these theories. We used Bayesian parameter estimation and inference from linear models to test for seasonal differences in space use metrics and to model seasonal effects of space use drivers. Results Results suggest that space use is strongly associated with variation in the level of overlap that mongoose groups have with humans. Seasonality influences this association, reversing seasonal space use predictions historically-accepted by ecologists. We found support for predictions of the metabolic theory when moderated by seasonality, by association with humans and by their interaction. Space use of mongooses living in association with humans was more concentrated in the dry season than the wet season, when historically-accepted ecological theory predicted more dispersed space use. Resource richness factors such as building density were associated with space use only during the dry season. We found negligible support for predictions of the resource dispersion hypothesis in general or for metabolic theory where seasonality and association with humans were not included. For mongooses living in association with humans, space use was not associated with patch dispersion or group size over both seasons. Conclusions In our study, living in association with humans influenced space use patterns that diverged from historically-accepted predictions. There is growing need to explicitly incorporate human–animal interactions into ecological theory and research. Our results and methodology may contribute to understanding effects of anthropogenic landscape change on wildlife populations.

Wildlife activity patterns tend to be defined by terms such as diurnal and nocturnal that might not fully depict the complexity of a species' life history strategy and behavior in a given system. These activity pattern categories often influence the methodological approaches employed, including the temporal period of study (daylight or nighttime). We evaluated banded mongoose (Mungos mungo) behavior in Northern Botswana through the use of remote sensing cameras at active den sites in order to characterize early morning behavior for this diurnal species. Our approach, however, provided the facility to capture unexpected nocturnal activity in a species that had otherwise only been studied during daylight hours. Camera traps were deployed for 215 trap days (24 hour data capture period) at den sites, capturing 5,472 photos over all events. Nocturnal activity was identified in 3% of trap days at study den sites with both vigilant and non-vigilant nocturnal behaviors identified. While vigilant behaviors involved troop fleeing responses, observations of non-vigilant behaviors suggest nonresident mongoose may investigate den sites of other troops during nocturnal time periods. There was no association between the occurrence of nocturnal activity and lunar phase (Fisher's exact test, n = 215, p = 0.638) and thus, increased moonlight was not identified as a factor influencing nocturnal behavior. The drivers and fitness consequences of these nocturnal activities remain uncertain and present intriguing areas for future research. Our findings highlight the need for ecological studies to more explicitly address and evaluate the potential for temporal variability in activity periods. Modifying our approach and embracing variation in wildlife activity patterns might provide new insights into the interaction between ecological phenomenon and species biology that spans the diurnal-nocturnal spectrum. National Science Foundation as part of the joint NSF-NIH-USDA Ecology and Evolution of Infectious Diseases program [1518663] This work was funded by the National Science Foundation (Grant Number #1518663) (KA) as part of the joint NSF-NIH-USDA Ecology and Evolution of Infectious Diseases program. The funders had no role in study design, data collection and analysis, or the decision to submit the work for publication, or preparation of the manuscript. https://www.nsf.gov/.