Dokument: Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning
| Titel: | Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning | |||||||
| URL für Lesezeichen: | https://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=68032 | |||||||
| URN (NBN): | urn:nbn:de:hbz:061-20250106-093635-6 | |||||||
| Kollektion: | Publikationen | |||||||
| Sprache: | Englisch | |||||||
| Dokumententyp: | Wissenschaftliche Texte » Artikel, Aufsatz | |||||||
| Medientyp: | Text | |||||||
| Autoren: | Ren, Yunxiao [Autor] Li, Carmen [Autor] Zhu, Chendi [Autor] Spänig, Sebastian [Autor] Jamrozy, Dorota [Autor] Rothen, Julian [Autor] Daubenberger, Claudia A. [Autor] Bentley, Stephen D. [Autor] Ip, Margaret [Autor] Heider, Dominik [Autor] | |||||||
| Dateien: |
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| Stichwörter: | Cross-species transmission, Hosts prediction, Interpretable machine learning, Host adaptations | |||||||
| Beschreibung: | Background
Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), exhibits a broad host range, manifesting as both a beneficial commensal and an opportunistic pathogen across various species. In humans, it poses significant risks, causing neonatal sepsis and meningitis, along with severe infections in adults. Additionally, it impacts livestock by inducing mastitis in bovines and contributing to epidemic mortality in fish populations. Despite its wide host spectrum, the mechanisms enabling GBS to adapt to specific hosts remain inadequately elucidated. Therefore, the development of a rapid and accurate method differentiates GBS strains associated with particular animal hosts based on genome-wide information holds immense potential. Such a tool would not only bolster the identification and containment efforts during GBS outbreaks but also deepen our comprehension of the bacteria's host adaptations spanning humans, livestock, and other natural animal reservoirs. Methods and results Here, we developed three machine learning models—random forest (RF), logistic regression (LR), and support vector machine (SVM) based on genome-wide mutation data. These models enabled precise prediction of the host origin of GBS, accurately distinguishing between human, bovine, fish, and pig hosts. Moreover, we conducted an interpretable machine learning using SHapley Additive exPlanations (SHAP) and variant annotation to uncover the most influential genomic features and associated genes for each host. Additionally, by meticulously examining misclassified samples, we gained valuable insights into the dynamics of host transmission and the potential for zoonotic infections. Conclusions Our study underscores the effectiveness of random forest (RF) and logistic regression (LR) models based on mutation data for accurately predicting GBS host origins. Additionally, we identify the key features associated with each GBS host, thereby enhancing our understanding of the bacteria's host-specific adaptations. | |||||||
| Rechtliche Vermerke: | Originalveröffentlichung:
Ren, Y., Li, C., Nanayakkara Sapugahawatte, D., Zhu, C., Spänig, S., Jamrozy, D., Rothen, J., Daubenberger, C. A., Bentley, S. D., Ip, M., & Heider, D. (2024). Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning. Computers in Biology and Medicine, 171, Article 108185. https://doi.org/10.1016/j.compbiomed.2024.108185 | |||||||
| Lizenz: |  Dieses Werk ist lizenziert unter einer Creative Commons Namensnennung 4.0 International Lizenz | |||||||
| Fachbereich / Einrichtung: | Mathematisch- Naturwissenschaftliche Fakultät Medizinische Fakultät | |||||||
| Dokument erstellt am: | 06.01.2025 | |||||||
| Dateien geändert am: | 06.01.2025 |
