Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling.

Autor: Krzysztof Bartoszek, Marta Majchrzak, Sebastian Sakowski, Anna B Kubiak-Szeligowska, Ingemar Kaj, Pawel Parniewski
Jazyk: angličtina
Rok vydání: 2018
Předmět:
Zdroj: PLoS Computational Biology, Vol 14, Iss 1, p e1005931 (2018)
Druh dokumentu: article
ISSN: 1553-734X
1553-7358
DOI: 10.1371/journal.pcbi.1005931
Popis: The Binary State Speciation and Extinction (BiSSE) model is a branching process based model that allows the diversification rates to be controlled by a binary trait. We develop a general approach, based on the BiSSE model, for predicting pathogenicity in bacterial populations from microsatellites profiling data. A comprehensive approach for predicting pathogenicity in E. coli populations is proposed using the state-dependent branching process model combined with microsatellites TRS-PCR profiling. Additionally, we have evaluated the possibility of using the BiSSE model for estimating parameters from genetic data. We analyzed a real dataset (from 251 E. coli strains) and confirmed previous biological observations demonstrating a prevalence of some virulence traits in specific bacterial sub-groups. The method may be used to predict pathogenicity of other bacterial taxa.
Databáze: Directory of Open Access Journals
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