Journal article

Systematic analysis of key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria

Claire Gorrie, Anders Goncalves Da Silva, Danielle Ingle, Charlie Higgs, Torsten Seemann, Timothy Stinear, Deborah Williamson, Jason Kwong, Lindsay Grayson, Norelle Sherry, Benjamin Howden

Cold Spring Harbor Laboratory | Published : 2020

Abstract

ABSTRACT Background Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone for genomic approaches to multidrug-resistant organisms (MDROs) transmission inference in hospitals. However, the impact of key analysis parameters on these inferences has not been systematically analysed. Methods We conducted a multi-hospital 15-month prospective study, sequencing 1537 MDRO genomes for comparison; methicillin-resistant Staphylococcus aureus , vancomycin-resistant Enterococcus faecium , and extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae . We systematically assessed the impact of sample and reference genome diversity, masking of prophage and regions of ..

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