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Genomic Surveillance of Antimicrobial Resistant Bacterial Colonisation and Infection in Intensive Care Patients by Wyres, Kelly L. (author);Hawkey, Jane (author);Mirčeta, Mirianne (author);Judd, Louise M. (author);Wick, Ryan R. (author);Gorrie, Claire L. (author);Pratt, Nigel F. (author);Garlick, Jill S. (author);Watson, Kerrie M. (author);Pilcher, David V. (author);McGloughlin, Steve A. (author);Abbott, Iain J. (author);Macesic, Nenad (author);Spelman, Denis W. (author);Jenney, Adam W. J. (author);Holt, Kathryn E. (author) is a Medicine article available to read on EtoBox.

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## Background Third-generation cephalosporin-resistant Gram-negatives (3GCR-GN) and vancomycin-resistant enterococci (VRE) are common causes of multi-drug resistant healthcare-associated infections, for which gut colonisation is considered a prerequisite. However, there remains a key knowledge gap about colonisation and infection dynamics in high-risk settings such as the intensive care unit (ICU), thus hampering infection prevention efforts. ## Methods We performed a three-month prospective genomic survey of infecting and gut-colonising 3GCR-GN and VRE among patients admitted to an Australian ICU. Bacteria were isolated from rectal swabs (__n__ = 287 and __n__ = 103 patients ≤2 and > 2 days from admission, respectively) and diagnostic clinical specimens between Dec 2013 and March 2014. Isolates were subjected to Illumina whole-genome sequencing (__n__ = 127 3GCR-GN, __n__ = 41 VRE). Multi-locus sequence types (STs) and antimicrobial resistance determinants were identified from de novo assemblies. Twenty-three isolates were selected for sequencing on the Oxford Nanopore MinION device to generate completed reference genomes (one for each ST isolated from ≥2 patients). Single nucleot

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Author

Wyres, Kelly L. (author);Hawkey, Jane (author);Mirčeta, Mirianne (author);Judd, Louise M. (author);Wick, Ryan R. (author);Gorrie, Claire L. (author);Pratt, Nigel F. (author);Garlick, Jill S. (author);Watson, Kerrie M. (author);Pilcher, David V. (author);McGloughlin, Steve A. (author);Abbott, Iain J. (author);Macesic, Nenad (author);Spelman, Denis W. (author);Jenney, Adam W. J. (author);Holt, Kathryn E. (author)

Publisher

Springer Science and Business Media LLC

Published

2021

Language

EN

Field

Medicine (Health Sciences)