Journal article

Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis

Claire L Gorrie, Anders Gonçalves Da Silva, Danielle J Ingle, Charlie Higgs, Torsten Seemann, Timothy P Stinear, Deborah A Williamson, Jason C Kwong, M Lindsay Grayson, Norelle L Sherry, Benjamin P Howden

The Lancet Microbe | Elsevier BV | Published : 2021

Abstract

Background Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone of genomic approaches to the inference of transmission of multidrug-resistant (MDR) organisms in hospitals. However, the impact of many key analytical approaches on these inferences has not yet been systematically assessed. This study aims to make such a systematic assessment. Methods We conducted a 15-month prospective study (2-month pilot phase, 13-month implementation phase), across four hospital networks including eight hospitals in Melbourne, VIC, Australia. Patient clinical and screening samples containing one or more isolates of meticillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus fa..

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