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Study areaThe NCA encompasses an area of 8292 km2 and in 2020 had approximately 87,000 inhabitants23, who are primarily dependent on livestock for their livelihoods. It is a multiple-use area where people coexist with wildlife and livestock, and practise pastoralism with transhumance, characterised by seasonal movements of livestock for accessing resources such as grazing areas and water. The NCA comprises eleven administrative wards: Alailelai, Endulen, Eyasi, Laitole, Kakesio, Misigiyo, Ngorongoro, Naiyobi, Nainokanoka, Ngoile and Olbalbal (Fig. 1). The NCA was chosen for our study as it is known to be hyperendemic for anthrax4,17,20. In addition, informal consultations we held prior to the study, as well as tailored data collection at the community and household level, indicated that local communities have a good understanding of the disease in humans and animals, and of practices around carcass and livestock management that increase risks, particularly in certain locations and periods of the year24.Figure 1Locations of participatory mapping. Map showing the 11 administrative wards of the Ngorongoro Conservation Area in northern Tanzania and the locations where participatory mapping sessions took place (red dots). The maps were produced in QGIS 2.18.2 using data from the National Bureau of Statistics, Tanzania (http://www.nbs.go.tz/).Full size imageEthics approval and consent to participateThe study received approval from the National Institute for Medical Research, Tanzania, with reference number NIMRJHQ/R.8a/Vol. IX/2660; the Tanzania Commission for Science and Technology (numbers 2016-94-NA-2016-88 (O. R. Aminu), 2016-95-NA-2016-45 (T. L. Forde) and 2018-377-NA-2016-45 (T. Lembo)); Kilimanjaro Christian Medical University College Ethics Review Committee (certificate No. 2050); and the University of Glasgow College of Medical Veterinary & Life Sciences Ethics Committee (application number 200150152). Approval and permission to access communities and participants were also obtained from relevant local authorities. Written informed consent was obtained from all participants involved in the study. All data collected were analysed anonymously, ensuring the confidentiality of participants. All research activities were performed in accordance with relevant guidelines and regulations.Participatory mappingA participatory mapping approach based on methodology previously tested in East Africa25 was employed to define areas of anthrax risk for animals in the NCA based on community knowledge. Georeferenced maps of the NCA were produced using data from Google and DigitalGlobe (2016). The maps used datum Arc 1960/UTM zone 36S and grid intervals of 1000 km and were produced at 1:10,000 and 1:50,000 scales, in order to provide participants with a choice. Ten participatory mapping focus groups were held at ward administrative level (Fig. 1) in order to identify areas in the NCA that communities perceive as posing a high risk of anthrax. One mapping exercise was held in each ward. Ngoile and Olbalbal wards were covered at the same time and treated as one, as they had only recently (in 2015) been split from one ward (Olbalbal). Each session had between ten and thirteen participants, who consisted of village and ward administrators, animal health professionals (including community animal health workers and livestock field officers), community leaders, and selected community members. These participants represented members of the community concerned with animal health and owning livestock and, as such, were likely to hold in-depth knowledge relating to community experience of animal health and disease, including anthrax. Participants were recruited by consulting with animal health professionals as well as village and ward administrators, who gave permission to conduct the mapping sessions.The mapping sessions were conducted in Swahili and translated into English by an interpreter. Participants’ general knowledge of the area was first verified by testing whether they could correctly identify popular locations such as health centres, places of worship, markets and schools. Subsequently, participants discussed among themselves and came to a consensus about areas they considered to be at high risk of anthrax. Specifically, we asked them to identify locations they perceived as areas where they considered their animals to be at risk of being exposed to anthrax. These areas were drawn on the maps provided (Fig. 2). While they did not locate areas where the animals had succumbed to disease, we also asked for generic information on locations where anthrax outbreaks had occurred in the past to define areas that could be targeted for active surveillance of cases. In order to improve the fidelity of the data, participants defined risk areas in relation to their own locality (ward) and locations where their animals access resources. Therefore, the areas were not defined by administrative boundaries, as communities may access locations outside their wards, for instance for grazing or watering. The resulting maps were scanned, digitised and analysed as detailed in the following sections. Further detail on the participatory mapping process is provided in the Supplementary Methods (Additional File 1).Figure 2Participatory mapping of anthrax risk areas in the Ngorongoro Conservation Area. Images show (A) the set-up of a mapping session, (B) participants engaged during a session and (C) an example of a 1:50,000 scale map annotated by participants. The map was created with QGIS opensource mapping software. The basemap used was a scanned and geo-referenced full colour 1:50,000 scale topographic map produced by the Surveys & Mapping Division, Ministry of Lands, Housing & Human Settlements, Dar es Salaam, Tanzania. The grid is based on the Arc1960 UTM 36S projection and datum. The map was exported from QGIS in Acrobat Pdf format to enable it to be printed at suitable sizes for using in the fieldwork and to be manually annotated during the participatory mapping.Full size imageDigitisation of maps and generation of random pointsScanned maps were saved as PDF files and converted to high resolution TIFF files for digitisation in QGIS 2.18.2-Las Palmas free OpenSource software26. All maps were georeferenced with geographical coordinates during production and reference points were available to enable the precise mapping of all locations. The digitization was carried out using the QGIS digitizing tools and by creating polygon layers of the defined risk areas.Sourcing data on the environmental predictors of anthraxAvailable soil and environmental data (250 m grid) for Tanzania were obtained from various sources (Table 1). From the available data, we selected the following seven variables which have previously been shown to contribute to or explain the risk of anthrax based on the biology of B. anthracis (Table 1).Table 1 Environmental factors with potential to influence anthrax occurrence.Full size tableCation exchange capacity (CEC)Measured in cmol/kg, CEC is the total capacity of the soil to retain exchangeable cations such as Ca2+, Mg2+ etc. It is an inherent soil characteristic and is difficult to alter significantly. It influences the soil’s ability to hold on to essential nutrients and provides a buffer against soil acidification27. CEC has been reported to be positively correlated with anthrax risk. In addition, CEC is a proxy for calcium content, which may contribute to anthrax risk in a pH-dependent manner as explained below19,22.Predicted topsoil pH (pH)Soil pH below 6.0 (acidic soil) is thought to inhibit the viability of spores19 thus a positive effect of higher pH on the risk of anthrax is expected. It has been suggested that the exosporium of B. anthracis is negatively charged in soils with neutral to slightly alkaline pH. This negative charge attracts positively charged cations in soil, mainly calcium, enabling the spores to be firmly attached to soil particles and calcium to be maintained within the spore core, thereby promoting the viability of B. anthracis19,28.Distance to inland water bodies (DOWS)Both the distance from water and proximity to water may increase anthrax risk. Distance to inland water may indicate the degree to which an area is dry/arid. Anthrax outbreaks have been shown to occur in areas with very dry conditions19. Although anthrax occurrence has also been associated with high soil moisture, this relates more to the spore germination in the environment (a mechanism that is disputed) and the concentration of spores in moist humus that amount to an infectious dose18,29. Spores will survive much longer in soils with low moisture content19. Low moisture may also be associated with low vegetation which results in animals grazing close to the soil, increasing the risk of ingesting soil with spores. Hampson et al. reported that anthrax outbreaks occurred close to water sources in the Serengeti ecosystem of Tanzania in periods of heavy rainfall20, and Steenkamp et al. found that close proximity to water bodies was key to the transmission of B. anthracis spores in Kruger National Park, South Africa22. Water is an important resource for livestock and a large number of animals may congregate at water sources during dry seasons. The close proximity of a water source to a risk area may increase the chance of infection, particularly during periods of high precipitation which might unearth buried spores.Average enhanced vegetation index (EVI)Vegetation density may influence the likelihood of an animal ingesting soil or inhaling dust that may be contaminated with spores. Grazing animals are more likely to encounter bacteria in soil with low vegetation density20, although there is a possibility that spores can be washed onto higher vegetation by the action of water19. Vegetation index may also reflect the moisture content of soil. Arid/dry conditions favour the formation and resistance of spores in the environment, thus lower vegetation may be associated with the occurrence of anthrax.Average daytime land surface temperature (LSTD)Anthrax has been more commonly reported to occur in regions with warmer climates worldwide. Minett observed that under generally favourable conditions and at 32 °C to 37 °C, sporulation of B. anthracis occurs readily but vegetative cells are more likely to disintegrate at temperatures below 21 °C30. Another hypothesis for the association of high temperature with anthrax occurrence is altered host immune response to disease due to stress caused by elevated temperatures19. In addition, elevated temperatures are usually associated with arid areas where vegetation is low, limiting access to adequate nutrition, which in turn affects immunity. Similarly, in hotter climates where infectious diseases occur more often, host interactions with other pathogens may modulate immune response to anthrax31. In this case, a lower infectious and lethal dose of spores would be sufficient to cause infection and death, respectively19. Contact with and ingestion of soil, spores and abrasive pasture is also higher with low vegetation in hot and arid areas19,32. In boreal regions such as in northern Canada, where anthrax occurs in wood bison, and Siberia, the disease is more commonly reported in the summer19. We therefore hypothesised a positive effect of LSTD on the risk of anthrax.SlopeSpores of B. anthracis are hypothesized to persist more easily in flat landscapes that are characterised by shallow slopes19, as it is thought that wind and water may disperse spores more easily along areas with a higher slope gradient, thereby decreasing the density of spores to levels that may be insufficient to cause infection in a susceptible host. Therefore, we expected a negative relationship between slope and the risk of anthrax.Predicted topsoil organic carbon content (SOC)Organic matter (g/kg) may aid spore persistence by providing mechanical support. The negatively charged exosporium of spores is attracted to the positive charges on hummus-rich soil, thus anthrax is thought to persist in soil rich in organic matter18. Based on available evidence, we expected a positive effect of SOC on the risk of anthrax.Creating the datasetThe annotated and digitised maps yielded polygons of high-risk areas within the NCA (Fig. 3). After digitization, 5000 random points were generated33 to cover the 8292 km2 area of the NCA. This enabled us to obtain distinct points allowed by the 250 m grid resolution of the environmental variables. Points falling within the defined risk areas were selected to represent risk areas while those falling outside represented low-risk areas. Measures of the environmental characteristics associated with individual points were obtained with the ‘add Raster data to points’ feature in QGIS.Figure 3Ngorongoro Conservation Area map showing (A) defined risk areas (in red) and (B) distance to settlements. For analysis, 5000 random points were generated throughout the area; points falling within 4.26 km of human settlements (the average distance herds are moved from settlements in a day as determined through interviews of resident livestock owners) were retained for analysis (n = 2173, shown in blue in 3a). The maps were created in QGIS 2.18.2 using data from the National Bureau of Statistics, Tanzania (http://www.nbs.go.tz/).Full size imageIn order to focus on areas of greatest risk to humans and livestock and to exclude locations that are not accessible, only points within a certain range of distance from settlements were included (Fig. 3). On average, herders in the NCA move their livestock 4.26 km away from settlements for grazing and watering during the day (unpublished data obtained through a cross-sectional survey of 209 households). Thus, only points falling within this distance from settlements were selected, providing us with data on areas where infection is most likely to occur. Data on locations of settlements were obtained from satellite imagery and included permanent residences as well as temporary settlements (e.g. seasonal camps set up after long distance movement away from permanent settlements, typically in the dry season, in search of pasture and water). These data were collated from the Center for International Earth Science Information Network (CIESIN).After adjusting for accessibility of resource locations using the average distance moved by livestock, 2173 points were retained for analysis, of which 239 (11%) fell within high-risk areas.Data analysisAll statistical analyses were carried out in R (v 4.1.0) within the RStudio environment34. The aims of the statistical analysis were to infer the relationship between anthrax risk areas as determined through participatory mapping and the environmental factors identified in Table 1, and to use this relationship to make spatial predictions of anthrax risk across the study area. We achieved both aims by modelling the binary risk status (high or low) of the randomly generated points as a function of their environmental characteristics in a Bayesian spatial logit-binomial generalised linear mixed-effects model (GLMM), implemented in the package glmmfields35. Spatial autocorrelation (residual non-independence between nearby points) was accounted for by including spatial random effects in the GLMM. We chose relatively non-informative priors for the intercept and the covariates, using Student’s t-distributions centred at 0 and wide variances (intercept: df = 3, location = 0, scale = 10; betas: df = 3, location = 0, scale = 3). For the spatial Gaussian Process and the observation process scale parameters, we adopted the default glmmfields settings and used half-t priors (both gp_theta and gp_sigma: df = 3, location = 0, scale = 5), and 12 knots. To achieve convergence, the models were run for 5000 iterations35.First, univariable models were fitted to estimate unadjusted associations between each environmental factor (CEC, pH, DOWS, EVI, LSTD, slope, and SOC; Table 1; Supplementary Table S1) and high- and low-risk areas. Second, we constructed multivariable models by fitting multiple environmental variables (Supplementary Table S2). Three variables, SOC, slope and EVI showed a strongly right-skewed distribution and were therefore log-transformed prior to GLMM analysis to prevent excessive influence of outliers. All predictor variables were centred to zero mean and scaled to unit standard deviation for analysis, and odds ratios were rescaled back to the original units for ease of interpretation. Prior to fitting the multivariable GLMM, the presence of collinearity among the predictor variables—which were all continuous—was assessed using variance inflation factors (VIFs)36, calculated with the car package and illustrated using scatter plots (Supplementary Fig. S1)36. Three predictor variables showed a VIF greater than 3 (LSTD, ln EVI and pH with VIFs of 6.8, 4.2 and 3.5, respectively). Removal of LSTD and ln EVI reduced all VIFs to below 3, therefore these two variables were excluded from the multivariable regression analysis37.The model performance was assessed by calculating the area under the receiver operating characteristic curve. The predicted probability of being an anthrax high-risk area was determined and depicted on a map of the NCA using a regular grid of points generated throughout the NCA with one point sampled every 500 m.Consent for publicationPermission to publish was granted by the National Institute for Medical Research, Tanzania. More

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Genome’s collection and phylogenetic analysisThe study examined the genomes of 139 isolates, 61 of environmental samples (ENV) and 78 clinical (CLI) (Supplementary Table 1, Supplementary Fig. 1), with origin in 21 countries: USA (23/139, 17%), UK, Portugal and Spain (each 15/139, 33%), China (14/139, 10%), Germany (13/139, 9%), Thailand (11/139, 8%) and other countries (each  More

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