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

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.Funding Agencies|IMB PAS as part of the statutory research; Knut and Alice Wallenberg Foundation</p

Number of VF features and their function in the K and U populations.

<p>K, strains isolated from children with diarrhea; U, strains isolated from patients with urinary tract infections. (grey zone–VFs underrepresented, not included for prediction).</p

Predicting pathogenicity behavior in <i>Escherichia coli</i> population through a state dependent model and TRS profiling - Fig 5

<p>The transition rates between states–<i>q</i>₀₁, <i>q</i>₁₀ for collection of strains isolated from stool (A) and urine (B). Open bars–non-pathogenic direction (<i>q</i>₁₀); hatched bars–pathogenic direction (<i>q</i>₀₁).</p

The concept of the investigation.

<p>Each strain of <i>E</i>. <i>coli</i> has been assigned an individual profile of the TRS-PCR and a set of virulence traits (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005931#sec002" target="_blank">Materials and Methods</a>). The method of predicting pathogenicity relies on using BiSSE model and microsatellites TRS-PCR profiling. Additionally the wrapper scripts calculate probability of pathogenicity.</p

Graphical representation of the BiSSE model [11].

<p>On each arrows the particular parameters of the BiSSE model were placed: <i>q</i>₀₁, <i>q</i>10 –the transition between states; <i>λ</i>₀, <i>λ</i>₁ –the speciation rates; <i>μ</i>₀, <i>μ</i>₁ –the extinction rates. The state diagram has two states labeled 0 (non-pathogenic) and 1 (pathogenic).</p

The comparison of parameter <i>P</i>₁ to the different proportions: <i>N</i>₁/(<i>N</i>₁+<i>N</i>₀); <i>q</i>₀₁/<i>λ</i>₀; <i>λ</i>₀/<i>λ</i>₁ for particular virulence factors (VF gene).

<p>The <i>P</i>₁ denotes probability of maintaining the virulence factors in <i>E</i>. <i>coli</i> strains. K and U define the isolation environment, stool and urine, respectively.</p

The Probability (<i>P</i>₁) of maintaining the virulence factors in <i>E</i>. <i>coli</i> strains isolated from stool (hatched bars) and urine samples (open bars).

<p>Values above 0,5 (horizontal black line) indicate higher than 50% chance for being maintained.</p