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

• Main Authors: Krzysztof Bartoszek, Marta Majchrzak, Sebastian Sakowski, Anna B Kubiak-Szeligowska, Ingemar Kaj, Pawel Parniewski
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2018-01-01
• Series: PLoS Computational Biology
• Online Access: http://europepmc.org/articles/PMC5809097?pdf=render

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.