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regentrans: a framework and R package for using genomics to study regional pathogen transmission
Sophie Hoffman1, Zena Lapp1, Joyce Wang2
1Department of Computational Medicine and Bioinformatics, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109-5680, USA.
Microbial Genomics
|January 17, 2022
Summary
Understanding multidrug-resistant organism (MDRO) spread is crucial. A new framework and R package, regentrans, analyze pathogen transmission dynamics using whole-genome sequencing to identify regional spread patterns.
Area of Science:
- Genomic epidemiology
- Infectious disease dynamics
- Computational biology
Background:
- Regional pathogen transmission networks are increasingly recognized.
- Investigating the spread of multidrug-resistant organisms (MDROs) is vital for public health.
- Understanding transmission dynamics is key to controlling MDROs.
Purpose of the Study:
- To develop a framework for analyzing regional MDRO transmission dynamics.
- To create an open-source R package (regentrans) for implementing these methods.
- To provide tools for investigating pathogen movement across healthcare facilities.
Main Methods:
- Utilized whole-genome sequencing data.
- Developed a novel analytical framework for transmission dynamics.
- Applied the framework to a dataset of carbapenem-resistant *Klebsiella pneumoniae*.
Main Results:
- Demonstrated insights into inter- and intra-facility transmission patterns.
- Analyzed over 400 carbapenem-resistant *Klebsiella pneumoniae* isolates.
- Showcased the utility of the regentrans package for regional MDRO analysis.
Conclusions:
- The developed framework and regentrans package facilitate understanding of MDRO origins and transmission.
- This approach aids in identifying transmission hotspots and patterns at a regional level.
- Enables informed strategies for interrupting MDRO transmission in healthcare settings.
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