Diversity of Bacillus anthracis and Clostridium species in livestock and wildlife in selected regions in South Africa

Bacteria from the genera Clostridium and Bacillus form part of the phylum Firmicutes and produce endospores. Both are soil-borne, toxin producing bacteria with the ability of causing diseases in animals. One of the most effective ways to combat these diseases is through vaccination. In this study, the characterisation of both the Bacillus anthracis and Clostridium species have led to a better understanding of the different species (Clostridium) and genotypes (B. anthracis) that are circulating in the country, both in livestock and wildlife. Through data mining, Clostridium species responsible for animal death in South Africa for the past four years (2013–2016) have been identified using the Universal Veterinary Information System (UVIS) of the Faculty of Veterinary Science, University of Pretoria. Clostridium species responsible for deaths in wildlife and livestock recorded in the UVIS database were identified from a combination of culture, fluorescent antibody technique as well as pathology results. A variety of Clostridium species causing diseases in both livestock and wildlife were identified, of which the most common were Clostridium perfringens and Clostridium. septicum. The mined data revealed that the percentage of confirmed Clostridium cases between livestock and wildlife were similar, namely 53.8% for livestock versus 50% for wildlife. These results identified prominent Clostridium species causing disease in animals. The results could indicate that there is a lack of vaccination as clostridial disease was found equally in livestock and wildlife since vaccination is not possible in wildlife due to costs and practicality. The incorrect usage of clostridial vaccine and not maintaining cold chain for vaccines could also contribute towards disease in livestock. Multiplex polymerase chain reaction (PCR) assays for the detection of Clostridium species (Clostridium botulinum, Clostridium tetani, Clostridium perfringens, Clostridium novyi, Clostridium chauvoei, Clostridium septicum and Clostridium sordellii) were developed and used to screen both animals and the environment of the Kruger National Park using passive surveillance samples. The screening revealed numerous Clostridium species in the environment with C. perfringens type A, C. sordellii and C. septicum being the most prominent species, while C. novyi, C. chauvoei and C. tetani were less prominent and no C. botulinum detected in the tested samples. This assay can be used to monitor Clostridia in environments or to confirm culture, histopathology and/or fluorescent antibody technique results. Bacillus anthracis was isolated and characterised (phenotypically and genotypically) into lineages, clonal groups, and genotypes from two separate outbreaks (Pafuri and Singita) in the northern parts of the Kruger National Park (KNP) in 2014–2016 and compared with data from previous years. An existing panel (MLVA7) was expanded to MLVA10 for B. anthracis genotyping as the MLVA7 panel was developed using B. anthracis strains belonging to A-clade while KNP contains both A and B-clade strains. The MLVA10 could differentiate 28 genotypes among the 79 strains B. anthracis from Pafuri and Singita all belonging to the A-clade and include animal species such as greater kudu (Tragelaphus strepsiceros), nyala (Tragelaphus angassi), impala (Aepyceros melampus) and African elephant (Loxodonta africana). The information generated from this project has exhibited the different species of Clostridium and genotypes of B. anthracis that were located and circulating in the KNP in both the animals and the environment. This information can be used for epidemiological studies and to improve clostridial vaccination practices, verify Clostridium species identification, as well as, evaluating clostridial and anthrax vaccine combinations by determining the occurrence of the diseases in livestock and wildlife.