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

PLoS Comput Biol. 2018 Jan 31;14(1):e1005931. doi: 10.1371/journal.pcbi.1005931. eCollection 2018 Jan.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Computer Simulation
  • Diarrhea / microbiology
  • Escherichia coli / pathogenicity*
  • Escherichia coli Infections / microbiology
  • Extinction, Biological*
  • Gene Expression Regulation, Bacterial
  • Genetic Speciation*
  • Humans
  • Microsatellite Repeats
  • Models, Biological
  • Models, Genetic
  • Phenotype
  • Phylogeny
  • Polymerase Chain Reaction
  • Probability
  • Software
  • Trinucleotide Repeats*
  • Urinary Tract Infections / microbiology
  • Virulence Factors
  • Virulence*

Substances

  • Virulence Factors

Grants and funding

These studies were partially funded by IMB PAS as part of the statutory research. KB was supported by the Knut and Alice Wallenberg Foundation. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.