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

Microb Genom

Department of Microbiology and Immunology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5680, USA.

Published: January 2022

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 occurring 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 isolates of collected from patients in 21 long-term acute care hospitals 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 facilities and over time. This framework and corresponding R package 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.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8914358PMC
http://dx.doi.org/10.1099/mgen.0.000747DOI Listing

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