regentrans: a framework and R package for using genomics to study regional pathogen transmission

Increasing evidence of regional pathogen transmission networks highlights the importance of investigating the dissemination of multidrug-resistant organisms (MDROs) across a region to identify where transmission is happening and how pathogens move across regions. We developed a framework for investigating MDRO regional transmission dynamics using whole-genome sequencing data and created regentrans, an easy-to-use, open source R package that implements these methods (https://github.com/Snitkin-Lab-Umich/regentrans). Using a dataset of over 400 carbapenem-resistant Klebsiella pneumoniae isolates collected from patients in 21 long-term acute care hospitals (LTACHs) over a one-year period, we demonstrate how to use our framework to gain insights into differences in inter- and intra-facility transmission across different LTACHs and over time. These tools will allow investigators to better understand the origins and transmission patterns of MDROs, which is the first step in understanding how to stop transmission at the regional level.