Detection of Mycobacterium bovis in nasal swabs from communal goats (Capra hircus) in rural KwaZulu-Natal, South Africa

Deborah M Cooke; Charlene Clarke; Tanya J Kerr; Robin M Warren; Carmel Witte; Michele A Miller; Wynand J Goosen

doi:10.3389/fmicb.2024.1349163

Detection of Mycobacterium bovis in nasal swabs from communal goats (Capra hircus) in rural KwaZulu-Natal, South Africa

Front Microbiol. 2024 Feb 14:15:1349163. doi: 10.3389/fmicb.2024.1349163. eCollection 2024.

Authors

Deborah M Cooke¹, Charlene Clarke², Tanya J Kerr¹, Robin M Warren¹, Carmel Witte^{1

3}, Michele A Miller¹, Wynand J Goosen¹

Affiliations

¹ Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa.
² Faculty of Natural and Agricultural Sciences, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa.
³ The Center for Wildlife Studies, South Freeport, ME, United States.

Abstract

Animal tuberculosis, caused by Mycobacterium bovis, presents a significant threat to both livestock industries and public health. Mycobacterium bovis tests rely on detecting antigen specific immune responses, which can be influenced by exposure to non-tuberculous mycobacteria, test technique, and duration and severity of infection. Despite advancements in direct M. bovis detection, mycobacterial culture remains the primary diagnostic standard. Recent efforts have explored culture-independent PCR-based methods for identifying mycobacterial DNA in respiratory samples. This study aimed to detect M. bovis in nasal swabs from goats (Capra hircus) cohabiting with M. bovis-infected cattle in KwaZulu-Natal, South Africa. Nasal swabs were collected from 137 communal goats exposed to M. bovis-positive cattle and 20 goats from a commercial dairy herd without M. bovis history. Swabs were divided into three aliquots for analysis. The first underwent GeneXpert® MTB/RIF Ultra assay (Ultra) screening. DNA from the second underwent mycobacterial genus-specific PCR and Sanger sequencing, while the third underwent mycobacterial culture followed by PCR and sequencing. Deep sequencing identified M. bovis DNA in selected Ultra-positive swabs, confirmed by region-of-difference (RD) PCR. Despite no other evidence of M. bovis infection, viable M. bovis was cultured from three communal goat swabs, confirmed by PCR and sequencing. Deep sequencing of DNA directly from swabs identified M. bovis in the same culture-positive swabs and eight additional communal goats. No M. bovis was found in commercial dairy goats, but various NTM species were detected. This highlights the risk of M. bovis exposure or infection in goats sharing pastures with infected cattle. Rapid Ultra screening shows promise for selecting goats for further M. bovis testing. These techniques may enhance M. bovis detection in paucibacillary samples and serve as valuable research tools.

Keywords: Capra hircus; GeneXpert® MTB/RIF Ultra; Ion Torrent Genexus sequencing; Mycobacterium bovis; animal tuberculosis; culture-independent detection; hsp65; rpoB.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the Wellcome Foundation (grant #222941/Z/21/Z), the South African Medical Research Council Centre for TB research, American Association of Zoo Veterinarians Wild Animal Health Fund (S005651 and S007355), the National Research Foundation South African Research Chair Initiative (grant #86949), and the European Union Global Health EDCTP3 Joint undertaking and its members (project 101103171).