Prediction of Klebsiella phage-host specificity at the strain level
- Author
- Dimitri Boeckaerts, Michiel Stock (UGent) , Celia Ferriol-González, Jesús Oteo-Iglesias, Rafael Sanjuán, Pilar Domingo-Calap, Bernard De Baets (UGent) and Yves Briers (UGent)
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- Project
- Abstract
- Phages are increasingly considered promising alternatives to target drug-resistant bacterial pathogens. However, their often-narrow host range can make it challenging to find matching phages against bacteria of interest. Current computational tools do not accurately predict interactions at the strain level in a way that is relevant and properly evaluated for practical use. We present PhageHostLearn, a machine learning system that predicts strain-level interactions between receptor-binding proteins and bacterial receptors for Klebsiella phage-bacteria pairs. We evaluate this system both in silico and in the laboratory, in the clinically relevant setting of finding matching phages against bacterial strains. PhageHostLearn reaches a cross-validated ROC AUC of up to 81.8% in silico and maintains this performance in laboratory validation. Our approach provides a framework for developing and evaluating phage-host prediction methods that are useful in practice, which we believe to be a meaningful contribution to the machine-learning-guided development of phage therapeutics and diagnostics.
- Keywords
- LANGUAGE, RANGE
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01HZ6X8V4M84E60Y0XHH62K4TB
- MLA
- Boeckaerts, Dimitri, et al. “Prediction of Klebsiella Phage-Host Specificity at the Strain Level.” NATURE COMMUNICATIONS, vol. 15, no. 1, 2024, doi:10.1038/s41467-024-48675-6.
- APA
- Boeckaerts, D., Stock, M., Ferriol-González, C., Oteo-Iglesias, J., Sanjuán, R., Domingo-Calap, P., … Briers, Y. (2024). Prediction of Klebsiella phage-host specificity at the strain level. NATURE COMMUNICATIONS, 15(1). https://doi.org/10.1038/s41467-024-48675-6
- Chicago author-date
- Boeckaerts, Dimitri, Michiel Stock, Celia Ferriol-González, Jesús Oteo-Iglesias, Rafael Sanjuán, Pilar Domingo-Calap, Bernard De Baets, and Yves Briers. 2024. “Prediction of Klebsiella Phage-Host Specificity at the Strain Level.” NATURE COMMUNICATIONS 15 (1). https://doi.org/10.1038/s41467-024-48675-6.
- Chicago author-date (all authors)
- Boeckaerts, Dimitri, Michiel Stock, Celia Ferriol-González, Jesús Oteo-Iglesias, Rafael Sanjuán, Pilar Domingo-Calap, Bernard De Baets, and Yves Briers. 2024. “Prediction of Klebsiella Phage-Host Specificity at the Strain Level.” NATURE COMMUNICATIONS 15 (1). doi:10.1038/s41467-024-48675-6.
- Vancouver
- 1.Boeckaerts D, Stock M, Ferriol-González C, Oteo-Iglesias J, Sanjuán R, Domingo-Calap P, et al. Prediction of Klebsiella phage-host specificity at the strain level. NATURE COMMUNICATIONS. 2024;15(1).
- IEEE
- [1]D. Boeckaerts et al., “Prediction of Klebsiella phage-host specificity at the strain level,” NATURE COMMUNICATIONS, vol. 15, no. 1, 2024.
@article{01HZ6X8V4M84E60Y0XHH62K4TB,
abstract = {{Phages are increasingly considered promising alternatives to target drug-resistant bacterial pathogens. However, their often-narrow host range can make it challenging to find matching phages against bacteria of interest. Current computational tools do not accurately predict interactions at the strain level in a way that is relevant and properly evaluated for practical use. We present PhageHostLearn, a machine learning system that predicts strain-level interactions between receptor-binding proteins and bacterial receptors for Klebsiella phage-bacteria pairs. We evaluate this system both in silico and in the laboratory, in the clinically relevant setting of finding matching phages against bacterial strains. PhageHostLearn reaches a cross-validated ROC AUC of up to 81.8% in silico and maintains this performance in laboratory validation. Our approach provides a framework for developing and evaluating phage-host prediction methods that are useful in practice, which we believe to be a meaningful contribution to the machine-learning-guided development of phage therapeutics and diagnostics.
}},
articleno = {{4355}},
author = {{Boeckaerts, Dimitri and Stock, Michiel and Ferriol-González, Celia and Oteo-Iglesias, Jesús and Sanjuán, Rafael and Domingo-Calap, Pilar and De Baets, Bernard and Briers, Yves}},
issn = {{2041-1723}},
journal = {{NATURE COMMUNICATIONS}},
keywords = {{LANGUAGE,RANGE}},
language = {{eng}},
number = {{1}},
pages = {{10}},
title = {{Prediction of Klebsiella phage-host specificity at the strain level}},
url = {{http://doi.org/10.1038/s41467-024-48675-6}},
volume = {{15}},
year = {{2024}},
}
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