A microbial safari: finding evidence of <i>Mycobacterium bovis</i> DNA in soil from the Kruger National Park, South Africa
Bibliographic record
Abstract
ABSTRACT The primary pathogen causing animal tuberculosis (TB), Mycobacterium bovis , can infect a wide range of mammals, including humans. This pathogen is considered endemic in the Kruger National Park (KNP), South Africa, where it threatens the health and conservation of African wildlife, including endangered species. This mycobacterial pathogen is spread through close contact with an infected host by aerosols or ingestion but may also be transmitted indirectly through the environment. Detecting environmental M. bovis is challenging due to the complexity of the sample matrix and may require culture-independent techniques due to biosecurity restrictions associated with sample movement. In this study, DNA was extracted from soil near water sources in the KNP ( n = 180) and screened for Mycobacterium tuberculosis complex (MTBC) DNA using the hsp65 polymerase chain reaction (PCR) followed by Sanger amplicon sequencing and the GeneXpert MTB/RIF Ultra (GXU) qPCR assay. The region of difference (RD)-PCR was used to confirm whether M. bovis DNA was present. Sanger hsp65 amplicon sequencing and GXU detected MTBC DNA in three and zero samples, respectively. Moreover, Sanger sequencing detected organisms belonging to the Mycobacterium genus in 44 samples and non-tuberculous Mycobacterium species in 21 samples. The RD-PCR confirmed M. bovis DNA presence in 2/3 MTBC-positive samples. The presence of M. bovis DNA in KNP soil suggests potential environmental contamination by shedding from infected animals. Further research is required to confirm the viability of MTBC and the role of environmental contamination in the TB epidemiology of this multi-host system. IMPORTANCE This article describes the first evidence that DNA from the bacterial pathogen, Mycobacterium bovis , which causes animal tuberculosis (TB) in wildlife, can be detected in soil from the Kruger National Park (KNP). Animal TB threatens wildlife conservation, including threatened and endangered species, in areas such as the KNP. Pathogenic Mycobacterium are spread primarily through direct contact with infected hosts. However, the presence of M. bovis DNA in KNP soil could indicate a role for the environment in disease transmission. This complements the growing evidence from European regions that M. bovis can be shed by infected animals into water, soil, or plant material and potentially infect animals in the surrounding environment. This indirect route of spread has implications for disease management strategies and warrants further scientific investigation. Moreover, the direct DNA-based detection techniques described in this study may provide a tool for detecting Mycobacterium pathogens using non-invasive sampling (sampling the environment rather than animals directly) when culturing is not possible.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".