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Volume 8, Issue 1

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

Abstract

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 , 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genomics , pathogen spread , R package , regional transmission , software and whole genome sequencing
Funding
This study was supported by the:
  • Michigan Institute for Clinical and Health Research Postdoctoral Translational Scholars Program
    • Principle Award Recipient: JoyceWang
  • Canadian Institutes of Health Research (Award 201711MFE-396343-165736)
    • Principle Award Recipient: JoyceWang
  • National Science Foundation (Award DGE 1256260)
    • Principle Award Recipient: ZenaLapp
  • National Institutes of Health (Award 1R01AI148259-01)
    • Principle Award Recipient: EvanS Snitkin
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-01-17
2024-04-19
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regentrans: a framework and R package for using genomics to study regional pathogen transmission
M Gen 8, 000747 (2022); https://doi.org/10.1099/mgen.0.000747
/content/journal/mgen/10.1099/mgen.0.000747
/content/journal/mgen/10.1099/mgen.0.000747
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