Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates

Lupolova, N., Dallman, T. J., Matthews, L. , Bono, J. L. and Gally, D. L. (2016) Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates. Proceedings of the National Academy of Sciences of the United States of America, 113(40), pp. 11312-11317. (doi: 10.1073/pnas.1606567113) (PMID:27647883) (PMCID:PMC5056084)

Abstract

Sequence analyses of pathogen genomes facilitate the tracking of disease outbreaks and allow relationships between strains to be reconstructed and virulence factors to be identified. However, these methods are generally used after an outbreak has happened. Here, we show that support vector machine analysis of bovine E. coli O157 isolate sequences can be applied to predict their zoonotic potential, identifying cattle strains more likely to be a serious threat to human health. Notably, only a minor subset (less than 10%) of bovine E. coli O157 isolates analyzed in our datasets were predicted to have the potential to cause human disease; this is despite the fact that the majority are within previously defined pathogenic lineages I or I/II and encode key virulence factors. The predictive capacity was retained when tested across datasets. The major differences between human and bovine E. coli O157 isolates were due to the relative abundances of hundreds of predicted prophage proteins. This finding has profound implications for public health management of disease because interventions in cattle, such a vaccination, can be targeted at herds carrying strains of high zoonotic potential. Machine-learning approaches should be applied broadly to further our understanding of pathogen biology.

• Item Type: Articles
• Additional Information: This work was supported by Food Standards Scotland and the Food Standards Agency Grant FS101055 (to D.L.G., T.J.D., and L.M.), which has allowed the continuation of significant EHEC O157 research in the UK. This research was also supported by a University of Edinburgh studentship (N.L.) and core Biotechnology and Biological Sciences Research Council strategic programme Grant BB/J004227/ 1 (to D.L.G.). T.J.D. was funded by the National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections at the University of Liverpool in partnership with Public Health England, University of East Anglia, University of Oxford, and the Institute of Food Research.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Matthews, Professor Louise
• Authors: Lupolova, N., Dallman, T. J., Matthews, L., Bono, J. L., and Gally, D. L.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Proceedings of the National Academy of Sciences of the United States of America
• Publisher: National Academy of Sciences
• ISSN: 0027-8424
• ISSN (Online): 1091-6490
• Published Online: 19 September 2016
• Copyright Holders: Copyright © 2016 National Academy of Sciences
• First Published: First published in Proceedings of the National Academy of Sciences of the United States of America 113(40):11312-11317
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher