Bayesian reconstruction of a vancomycin-resistant Enterococcus transmission route using epidemiologic data and genomic variants from whole genome sequencing

We aimed to reconstruct the transmission model using sequence variants extracted from whole genome sequencing data and epidemiological information of patients involved in a VRE outbreak. In addition, we aimed to evaluate the applicability of this model through the identification of risk factors for VRE transmission. In this study, we used a Bayesian approach to infer the direction of VRE transmission. We applied BadTrIP, an open source program package that enabled the reconstruction of the transmission inference model to the BEAST2 (version 2.5.2) open source cross-platform program for Bayesian phylogenetic analysis of molecular sequences.