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PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks

16 Nov 2020

Abstract excerpt

BACKGROUND: Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology. METHODS: We developed the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT) to automate integration...

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PMID: 33198787
DOI: 10.1186/s13073-020-00798-3

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