A Bayesian model of acquisition and clearance of bacterial colonization

11/27/2018
by   Marko Järvenpää, et al.
0

Bacterial populations that colonize a host play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of acquisition and clearance of colonizing populations. Studies of colonization dynamics have been based on assessment of whether serial samples represent a single population or distinct colonization events. A common solution to estimate acquisition and clearance rates is to use a fixed genetic distance threshold. However, this approach is often inadequate to account for the diversity of the underlying within-host evolving population, the time intervals between consecutive measurements, and the uncertainty in the estimated acquisition and clearance rates. Here, we summarize recently submitted work jarvenpaa2018named and present a Bayesian model that provides probabilities of whether two strains should be considered the same, allowing to determine bacterial clearance and acquisition from genomes sampled over time. We explicitly model the within-host variation using population genetic simulation, and the inference is done by combining information from multiple data sources by using a combination of Approximate Bayesian Computation (ABC) and Markov Chain Monte Carlo (MCMC). We use the method to analyse a collection of methicillin resistant Staphylococcus aureus (MRSA) isolates.

READ FULL TEXT

page 1

page 2

page 3

page 4

research
04/08/2008

On the underestimation of model uncertainty by Bayesian K-nearest neighbors

When using the K-nearest neighbors method, one often ignores uncertainty...
research
04/09/2018

Bayesian Predictive Inference For Finite Population Quantities Under Informative Sampling

We investigate Bayesian predictive inference for finite population quant...
research
05/27/2021

Bayesian Inference for Population Attributable Measures from Under-identified Models

Population attributable risk (PAR) is used in epidemiology to predict th...
research
06/29/2019

A Data-Validated Host-Parasite Model for Infectious Disease Outbreaks

The use of model experimental systems and mathematical models is importa...
research
05/15/2020

Hierarchical Bayesian state-space modeling of age- and sex-structured wildlife population dynamics

Biodiversity is declining at alarming rates worldwide, including for lar...
research
06/05/2023

Branching model with state dependent offspring distribution for Chlamydia spread

Chlamydiae are bacteria with an interesting unusual developmental cycle....

Please sign up or login with your details

Forgot password? Click here to reset