© 2018 Bartoszek et al. 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.
Bartoszek, K., Majchrzak, M., Sakowski, S., Kubiak-Szeligowska, A. B., Kaj, I., & Parniewski, P. (2018). Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling. PLoS Computational Biology, 14(1). https://doi.org/10.1371/journal.pcbi.1005931