| Literature DB >> 29377918 |
Pieter Johan Steenkamp1, Henriette van Heerden2, Ockert Louis van Schalkwyk2.
Abstract
The spores of the soil-borne bacterium, Bacillus anthracis, which causes anthrax are highly resistant to adverse environmental conditions. Under ideal conditions, anthrax spores can survive for many years in the soil. Anthrax is known to be endemic in the northern part of Kruger National Park (KNP) in South Africa (SA), with occasional epidemics spreading southward. The aim of this study was to identify and map areas that are ecologically suitable for the harboring of B. anthracis spores within the KNP. Anthrax surveillance data and selected environmental variables were used as inputs to the maximum entropy (Maxent) species distribution modeling method. Anthrax positive carcasses from 1988-2011 in KNP (n = 597) and a total of 40 environmental variables were used to predict and evaluate their relative contribution to suitability for anthrax occurrence in KNP. The environmental variables that contributed the most to the occurrence of anthrax were soil type, normalized difference vegetation index (NDVI) and precipitation. Apart from the endemic Pafuri region, several other areas within KNP were classified as ecologically suitable. The outputs of this study could guide future surveillance efforts to focus on predicted suitable areas for anthrax, since the KNP currently uses passive surveillance to detect anthrax outbreaks.Entities:
Mesh:
Year: 2018 PMID: 29377918 PMCID: PMC5788353 DOI: 10.1371/journal.pone.0191704
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Environmental variables used for the final Maxent model.
| Variable | Type of data | Source | References |
|---|---|---|---|
| Integrated NDVI (indvi) | Reflectance derived | MODIS-TERRA | [ |
| Elevation (altitude) | Elevation derived | Aster-DEM | [ |
| Distance to permanent water (permdist) | Distance metrics | ArcGIS Spatial Analyst extension | [ |
| Distance to seasonal water (seasdist) | Distance metrics | ArcGIS Spatial Analyst extension | [ |
| Distance to ephemeral water (ephdist) | Distance metrics | ArcGIS Spatial Analyst extension | [ |
| Geology (geologyventer) | Soils | KNP Scientific Services Skukuza | [ |
| SOTER Soil ID (sotersoilid) | Soils | SOTER database | [ |
| Land Type (ltypeventer) | Soils | KNP Scientific Services Skukuza | [ |
| Landscape (landscapegert) | Soils | KNP Scientific Services Skukuza | [ |
| Calcium (caventer) | Soils | Interpolated from Venter database | [ |
| Precipitation of driest quarter (preqdryq) | Climate | Worldclim | [ |
| Temperature seasonality (tempseasonality) | Climate | Worldclim | [ |
a Variable name as used in model included in parenthesis
b Measure of overall productivity and biomass as derived through the small seasonal integral of time-integrated NDVI images between 2000–2009 and is not extracted for each case’s time of death.
c Venter [25] classified the soils of Kruger National Park into 15 major classes and described the chemical composition of each.
d Precipitation is the 50 year average 1950–2000 from the Worldclim dataset.
Accuracy metrics for the predicted distribution for Maxtent model using 12 variables.
| Metric | Model specifications |
|---|---|
| Overall accuracy | 79.5% |
| 165 | |
| 54 | |
| Total omission | 25.8% |
| Average omission | 23.5% |
| Total commission | 79.8% |
| Average commission | 79.5% |
| TSS | 0.562 |
| AUC | 0.857 |
a N indicates the number of positive point occurrences and was divided into 25% testing:75% training locations at each model subset
TSS = true skill statistic; AUC = area under curve.
Threshold point values (>0.8) for the twelve environmental variables and the three most suitable areas identified by the model in Kruger National Park for Bacillus anthracis occurrence (see Fig 1).
| Section | Pafuri | Shingwedzi | Letaba | Kruger National Park mean (range) |
|---|---|---|---|---|
| 1646 | 3834 | 4447 | 18921 | |
| 302 | 131 | 81 | 597 | |
| 68 | 90 | 26 | 219 | |
| 75 | 50 | 4 | 134 | |
| Altitude (altitude) | 228.806 | 281 | 225.933 | 292 (145–570) |
| Calcium (caventer) | 171.835 | 184.626 | 198.049 | 148 (10–282) |
| Ephemeral Water Distance (ephdist) | 2069.046 | 0 | 13181.526 | 3618 (0 – |
| Seasonal Water Distance (seasdist) | 3169.587 | 0 | 7038.007 | 4124 (0–14764) |
| Permanent Water Distance (permdist) | 2190.000 | 46840.200 | 733.333 | 12461 (0–53450) |
| Geology Venter (geologyventer) | LB, CS, AL | AL | EC | LB, CS, AL, EC |
| INDVI (indvi) | 8.589 | 9.368 | 8.868 | 7.34 (-775–15) |
| Landscape (landscapegert) | 25,28 | 35 | 21,22 | 21, 22, 25, 28, 35 |
| Landtype (ltypeventer) | Pa04,Pa05 | Le05 | Le01 | Le01, Le05, Pa04, Pa05 |
| Precipitation Driest Quarter (precdryq) | 9 | 14 | 23.733 | 14.7 (8–36) |
| SOTER Soil ID (sotersoilid) | ZA21,ZA22 | ZA115 | ZA282 | ZA21, ZA22, ZA115, ZA282 |
| Temperature Seasonality (tempseasonality) | 3389.097 | 3687 | 3759.9333 | 3439 (2838–3828) |
LB–Karoo system; Olivine rich basalts, sub-ordinate alkali basalts, shoshonites [41]. CS–Karoo system; Fine grained sandstone, mudstone, chert (Cave sandstone and redbed stages) [41]. AL–Quarternary; Alluvium [41]. EC–Karoo system; Shale with coal seams, mudstone, grit (Ecca series) [41]. 15 –Colophospermum mopane forest. 21 –Combretum / Acacia nigrescens rugged veld. 22 –Combretum / Colophospermum mopane rugged veld. 25 –Adansonia digitata / Colophospermum mopane rugged veld. 28 –Limpopo / Luvuvhu floodplain. 35 –Salvadora angustifolia floodplains. ZA21, ZA115 –Eutric cambisols (A cambisol (CM) can be defined as having either a cambic or a mollic horizon. A cambic horizon is a weakly developed mineral soil horizon and a mollic horizon is a surface horizon of mineral soil that is dark in colour, relatively deep and contains (dry weight) at least 1% organic matter or 0.6% organic carbon) [28]. Le01: Letaba landtype; Le05: Shingwedzi Landtype; includes the Shingwedzi river; Pa04 and 05: Pafuri Landtype [25]. ZA22 –Eutric leptosols (A leptosol (LP) can be defined through a limit in depth by continuous hard rock within 25 cm from the soil surface, overlying material with a calcium carbonate equivalent of more than 40 percent within 25 cm from the soil surface or less than 10 percent (by weight) fine earth to a depth of 75 cm or more from the soil surface) [28]. ZA282 –Leptic phaeozems (Continuous rock starting between 50 and 100 cm from the soil surface with a mollic horizon and (1) a base saturation of 50 percent or more and no secondary carbonates, at least to a depth of 100 cm from the soil surface and (2) with no diagnostic horizons other than an albic, argic, cambic or vertic horizon) [28].
Fig 1Predicted ecological suitability (>80%) for Bacillus anthracis.
The red areas (greater than 0.8 probability) indicate areas of increased Bacillus anthracis ecological suitability and black rectangles indicate the three most suitable areas (A. Pafuri, B. Shingwedzi, C. Letaba) for B. anthracis detection in Kruger National Park.
Fig 2Three most ecologically suitable habitats for Bacillus anthracis areas in Kruger National Park.
The following suitable areas for the harbouring of B. anthracis spores within the soil was identified using maximum entropy as a statistical model, a range of environmental predictors and anthrax occurrence data: (A) Pafuri in the northern Kruger National Park, (B) Shingwedzi river system and (C) Letaba / Olifants sections.