TY - JOUR T1 - Bayesian inference of infectious disease transmission from whole genome sequence data JF - bioRxiv DO - 10.1101/001388 SP - 001388 AU - Xavier Didelot AU - Jennifer Gardy AU - Caroline Colijn Y1 - 2013/01/01 UR - http://biorxiv.org/content/early/2013/12/16/001388.abstract N2 - Genomics is increasingly being used to investigate disease outbreaks, but an important question remains unanswered – how well do genomic data capture known transmission events, particularly for pathogens with long carriage periods or large within-host population sizes? Here we present a novel Bayesian approach to reconstruct densely-sampled outbreaks from genomic data whilst considering within-host diversity. We infer a time-labelled phylogeny using BEAST, then infer a transmission network via a Monte-Carlo Markov Chain. We find that under a realistic model of within-host evolution, reconstructions of simulated outbreaks contain substantial uncertainty even when genomic data reflect a high substitution rate. Reconstruction of a real-world tuberculosis outbreak displayed similar uncertainty, although the correct source case and several clusters of epidemiologically linked cases were identified. We conclude that genomics cannot wholly replace traditional epidemiology, but that Bayesian reconstructions derived from sequence data may form a useful starting point for a genomic epidemiology investigation. ER -