Accurate and robust classification of Mycobacterium bovis-infected cattle using peripheral blood RNA-seq data

O'Grady, J. F.; Ivich, A.; McHugo, G. P.; Khan, A.; Hall, T. J.; O'Donnell, S. L. F.; Correia, C. N.; Browne, J. A.; Riggio, V.; Prendergast, J. G. D.; Clark, E. L.; Pausch, H.; Meade, K. G.; Gormley, I. C.; Gormley, E.; Gordon, S. V.; Greene, C. S.; MacHugh, D. E.

doi:10.1101/2025.09.01.673540

bioRxiv · 10.1101/2025.09.01.673540

Accurate and robust classification of Mycobacterium bovis-infected cattle using peripheral blood RNA-seq data

O'Grady, J. F.·Ivich, A.·McHugo, G. P.·Khan, A.·Hall, T. J.·O'Donnell, S. L. F.·Correia, C. N.·Browne, J. A.·Riggio, V.·Prendergast, J. G. D.·Clark, E. L.·Pausch, H.·Meade, K. G.·Gormley, I. C.·Gormley, E.·Gordon, S. V.·Greene, C. S.·MacHugh, D. E.

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Abstract

Bovine tuberculosis (bTB) remains recalcitrant to eradication in many endemic countries where current diagnostics are suboptimal. Mycobacterium bovis causes bTB and is closely related to Mycobacterium tuberculosis, which causes human tuberculosis (hTB). Although blood-based mRNA biomarkers identified through machine learning can discriminate hTB-positive from hTB-negative individuals, similar approaches have not been explored for bTB. Here, we use RNA-seq and machine learning to investigate the utility of blood mRNA as a host-response biomarker for bTB. We identify a 30-gene signature and a 273-gene elastic net classifier that differentiate bTB-positive from bTB-negative cattle, achieving area under the curve (AUC) values of 0.986/0.900 for the former and 0.968/0.938 for the latter in training and testing, respectively. Additionally, we show that these classifiers distinguish bTB-positive cattle from cattle infected with other microbial pathogens (AUC [≥] 0.819). These mRNA-based classifiers represent a promising tool for augmenting current diagnostics to advance global bTB eradication efforts.

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O'Grady, J. F., Ivich, A., McHugo, G. P., Khan, A., Hall, T. J., O'Donnell, S. L. F., Correia, C. N., Browne, J. A., Riggio, V., Prendergast, J. G. D., Clark, E. L., Pausch, H., Meade, K. G., Gormley, I. C., Gormley, E., Gordon, S. V., Greene, C. S., MacHugh, D. E.. 2025-09-04. Accurate and robust classification of Mycobacterium bovis-infected cattle using peripheral blood RNA-seq data. https://doi.org/10.1101/2025.09.01.673540

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