Culture-Independent PCR Detection and Differentiation of Mycobacteria spp. in Antemortem Respiratory Samples from African Elephants (Loxodonta Africana) and Rhinoceros (Ceratotherium Simum, Diceros Bicornis) in South Africa
Abstract
:1. Introduction
2. Results
2.1. Mycobacterial Culture Results
2.2. Presence of ESAT-6/CFP-10 in All Mycobacterial Cultures
2.3. Nucleic Acid Amplification Test Results on Raw Respiratory Samples
2.3.1. Ultra and Hain LPA for MTBC DNA Detection
2.3.2. Hain LPA NTM DNA Detection and Species Differentiation
2.3.3. Ku and rpoB Amplicon Sequencing for Mycobacterium Genus Detection and Speciation
3. Discussion
4. Materials and Methods
4.1. Animals
4.2. Antemortem Sample Collection and Mycobacterial Culture
4.3. Nucleic Acid Amplification Tests (NAAT) for Mycobacteria spp. Detection and Differentiation
4.4. Data Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Mycobacterial Culture Result from Antemortem Respiratory Specimens | Nucleic Acid Amplification Test Results from Antemortem Respiratory Specimens | ||||||||
---|---|---|---|---|---|---|---|---|---|
Mycobacterial spp. Present | Species (#Animals) | Sample Type (Animal ID) | Location (South Africa) | Combined MGIT and MGIT-TiKa Result | ESAT-6 and CFP-10 Virulence Determination | GeneXpert MTB/RIF Ultra Result | Hain CMdirect V1.0 LPA Result | rpoB PCR Result | ku PCR Result |
Confirmed MTBC-positive | African elephants n = 5 | BALF (18/85) | Zoo | M. tuberculosis | Positive | MTB DETECTED Medium; RIF resistance indeterminate | MTBC | M. tuberculosis | M. tuberculosis |
BALF (18/177) | Zoo | M. tuberculosis | Positive | MTB TRACE DETECTED | Mixed NTM | M. tuberculosis | M. tuberculosis | ||
BALF (18/177) | Zoo | M. africanum | Positive | MTB TRACE DETECTED | M. avium and/or M. interjectum | M. africanum | M. africanum | ||
TW (18/177) | Zoo | M. elephantis strain | Positive | MTB NOT DETECTED | M. fortuitum group | M. elephantis | M. fortuitum group | ||
BALF (18/527) | KNP | M. stomatepiae | Negative | MTB NOT DETECTED | MTBC and/or M. fortuitum group | M. stomatepiae | mixed NTMs-M. smegmatis | ||
TW (18/527) | KNP | M. bovis | Positive | MTB TRACE DETECTED | Mixed NTM | M. bovis | M. bovis | ||
TW (18/533) | KNP | M. bovis | Positive | MTB TRACE DETECTED | MTBC and/or mixed NTM infection | M. bovis | M. bovis | ||
TW (18/538) | KNP | M. bovis | Positive | MTB TRACE DETECTED | M. fortuitum group | M. bovis | M. bovis | ||
White rhinoceros n = 1 | BALF (19/46) | KNP | M. bovis | Positive | MTB TRACE DETECTED | MTBC and/or mixed NTM infection | M. bovis | M. bovis | |
Confirmed NTM-positive | African elephants n = 8 | TW (18/173) | KNP | M. avium complex strain | Positive | MTB TRACE DETECTED | MTBC and/or mixed NTM infection | M. avium complex | Mycobacteria spp. |
BALF (18/176) | Zoo | M. foliorum | Positive | MTB NOT DETECTED | M. fortuitum group | M. fortuitum group | M. fortuitum group | ||
BALF (19/460) | KNP | M. mantenii | Positive | MTB TRACE DETECTED | MTBC and/or mixed NTM infection | M. mantenii | M. mantenii | ||
TW (19/460) | KNP | M. abscessus strain | Positive | MTB NOT DETECTED | M. fortuitum group and/or M. abscessus | M. abscessus | M. abscessus | ||
BALF (18/530) | KNP | M. interjectum strain | Positive | MTB NOT DETECTED | Mixed NTM | M. interjectum strain | mixed NTMs-M. avium complex | ||
TW (18/530) | KNP | M. avium strain | Negative | MTB NOT DETECTED | Mixed NTM | M. avium complex | M. elephantis strain | ||
TW (18/532) | KNP | M. mageritense strain | Negative | MTB NOT DETECTED | M. fortuitum group | Negative | Negative | ||
TW (18/534) | KNP | M. intracellulare | Positive | MTB TRACE DETECTED | MTBC and/or mixed NTM infection | M. avium complex | M. intracellulare | ||
TW (18/539) | KNP | M. intracellulare | Negative | MTB NOT DETECTED | M. fortuitum group | M. intracellulare | mixed NTMs-M. avium complex | ||
TW (21/496) | KNP | M. fortuitum strain | Positive | MTB NOT DETECTED | M. fortuitum group | M. fortuitum | M. elephantis strain | ||
White rhinoceros n = 1 | BALF (18/31) | KNP | M. scrofulaceum strain | Positive | MTB NOT DETECTED | Mixed NTM | M. avium subsp. Paratuberculosis | mixed NTMs-M. avium subsp. Paratuberculosis |
Test and Combinations | rpoB PCR | ku PCR | Hain LPA | Culture | rpoB/ku | rpoB/Hain LPA | ku/Hain LPA | rpoB/ku/Hain LPA |
---|---|---|---|---|---|---|---|---|
rpoB PCR | 1 | |||||||
ku PCR | 0.91 (0.81–1.00, 0.05) | 1 | ||||||
Hain LPA | 0.94 (0.85–1.00, 0.04) | 0.88 (0.76–0.99, 0.06) | 1 | |||||
Culture | 0.47 (0.29–0.66, 0.09) | 0.50 (0.31–0.68, 0.09) | 0.32 (0.16–0.48, 0.09) | 1 | ||||
rpoB/ku PCRs | 0.97 (0.91–1.00, 0.03) | 0.94 (0.86–1.00, 0.04) | 0.97 (0.91–1.00, 0.03) | 0.45 (0.27–0.63, 0.09) | 1 | |||
rpoB/Hain LPA | 0.94 (0.85–1.00, 0.04) | 0.94 (0.85–1.00, 0.04) | 1.00 (0.95–1.00, 0.03) | 0.46 (0.29–0.64, 0.09) | 0.94 (0.85–1.00, 0.04) | 1 | ||
ku/Hain LPA | 0.94 (0.85–1.00, 0.04) | 0.94 (0.85–1.00, 0.04) | 1.00 (0.95–1.00, 0.03) | 0.46 (0.29–0.64, 0.09) | 0.94 (0.85–1.00, 0.04) | 1.00 (0.95–1.00, 0.03) | 1 | |
rpoB/Ku/Hain LPA | 0.94 (0.85–1.00, 0.04) | 0.94 (0.85–1.00, 0.04) | 1.00 (0.95–1.00, 0.03) | 0.46, (0.29–0.64, 0.09) | 0.94 (0.85–1.00, 0.04) | 1.00 (0.95–1.00, 0.03) | 1.00 (0.95–1.00, 0.03) | 1 |
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Goosen, W.J.; Clarke, C.; Kleynhans, L.; Kerr, T.J.; Buss, P.; Miller, M.A. Culture-Independent PCR Detection and Differentiation of Mycobacteria spp. in Antemortem Respiratory Samples from African Elephants (Loxodonta Africana) and Rhinoceros (Ceratotherium Simum, Diceros Bicornis) in South Africa. Pathogens 2022, 11, 709. https://doi.org/10.3390/pathogens11060709
Goosen WJ, Clarke C, Kleynhans L, Kerr TJ, Buss P, Miller MA. Culture-Independent PCR Detection and Differentiation of Mycobacteria spp. in Antemortem Respiratory Samples from African Elephants (Loxodonta Africana) and Rhinoceros (Ceratotherium Simum, Diceros Bicornis) in South Africa. Pathogens. 2022; 11(6):709. https://doi.org/10.3390/pathogens11060709
Chicago/Turabian StyleGoosen, Wynand J., Charlene Clarke, Léanie Kleynhans, Tanya J. Kerr, Peter Buss, and Michele A. Miller. 2022. "Culture-Independent PCR Detection and Differentiation of Mycobacteria spp. in Antemortem Respiratory Samples from African Elephants (Loxodonta Africana) and Rhinoceros (Ceratotherium Simum, Diceros Bicornis) in South Africa" Pathogens 11, no. 6: 709. https://doi.org/10.3390/pathogens11060709
APA StyleGoosen, W. J., Clarke, C., Kleynhans, L., Kerr, T. J., Buss, P., & Miller, M. A. (2022). Culture-Independent PCR Detection and Differentiation of Mycobacteria spp. in Antemortem Respiratory Samples from African Elephants (Loxodonta Africana) and Rhinoceros (Ceratotherium Simum, Diceros Bicornis) in South Africa. Pathogens, 11(6), 709. https://doi.org/10.3390/pathogens11060709