Journal article
Identifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data
- Abstract:
- Streptococcus pneumoniae, a normal commensal of the upper respiratory tract, is a major public health concern, responsible for substantial global morbidity and mortality due to pneumonia, meningitis and sepsis. Why some pneumococci invade the bloodstream or CSF (so-called invasive pneumococcal disease; IPD) is uncertain. In this study we identify genes associated with IPD. We transform whole genome sequence (WGS) data into a sequence typing scheme, while avoiding the caveat of using an arbitrary genome as a reference by substituting it with a constructed pangenome. We then employ a random forest machine-learning algorithm on the transformed data, and find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of the genes we identified as associated with IPD, we find 23 genes previously shown to be directly relevant to IPD, as well as 18 uncharacterized genes. We suggest that these uncharacterized genes identified by us are also likely to be relevant for IPD.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 1.1MB, Terms of use)
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- Publisher copy:
- 10.1038/s41598-019-40346-7
Authors
- Publisher:
- Nature Research
- Journal:
- Scientific Reports More from this journal
- Volume:
- 9
- Issue:
- 2019
- Article number:
- 4049
- Publication date:
- 2019-03-11
- Acceptance date:
- 2019-02-04
- DOI:
- EISSN:
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2045-2322
- Keywords:
- Pubs id:
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pubs:972965
- UUID:
-
uuid:ddf77e80-dd72-46c6-9a58-aa8e8b7791bd
- Local pid:
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pubs:972965
- Source identifiers:
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972965
- Deposit date:
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2019-02-14
Terms of use
- Copyright holder:
- Obolski et al
- Copyright date:
- 2019
- Notes:
- © Author(s) 2019. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
- Licence:
- CC Attribution (CC BY)
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