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A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak

Authors :
Frances Wallach
Ramona Karam-Howlin
Brianne Ciferri
Gintaras Deikus
Harm van Bakel
Martha Lewis-Sandari
Elizabeth Webster
Theodore R. Pak
Flora Samaroo
Kathleen Gibbs
Angela Rendo
Ali Bashir
Andrew Kasarskis
Deena R. Altman
Camille Hamula
Tanis C. Dingle
Colleen Beckford
Mitchell J. Sullivan
Kieran I. Chacko
Zenab Khan
Eric E. Schadt
Robert Sebra
Gopi Patel
Source :
Journal of Clinical Microbiology
Publication Year :
2019
Publisher :
American Society for Microbiology, 2019.

Abstract

Whole-genome sequencing (WGS) of Staphylococcus aureus is increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant Staphylococcus aureus (MRSA) blood infections at a major urban hospital.<br />Whole-genome sequencing (WGS) of Staphylococcus aureus is increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant Staphylococcus aureus (MRSA) blood infections at a major urban hospital. A survey of 132 MRSA genomes assembled from long reads enabled detailed characterization of an outbreak lasting several months of a CC5/ST105/USA100 clone among 18 infants in a neonatal intensive care unit (NICU). Available hospital-wide genome surveillance data traced the origins of the outbreak to three patients admitted to adult wards during a 4-month period preceding the NICU outbreak. The pattern of changes among complete outbreak genomes provided full spatiotemporal resolution of its progression, which was characterized by multiple subtransmissions and likely precipitated by equipment sharing between adults and infants. Compared to other hospital strains, the outbreak strain carried distinct mutations and accessory genetic elements that impacted genes with roles in metabolism, resistance, and persistence. This included a DNA recognition domain recombination in the hsdS gene of a type I restriction modification system that altered DNA methylation. Transcriptome sequencing (RNA-Seq) profiling showed that the (epi)genetic changes in the outbreak clone attenuated agr gene expression and upregulated genes involved in stress response and biofilm formation. Overall, our findings demonstrate the utility of long-read sequencing for hospital surveillance and for characterizing accessory genomic elements that may impact MRSA virulence and persistence.

Details

ISSN :
1098660X and 00951137
Volume :
57
Database :
OpenAIRE
Journal :
Journal of Clinical Microbiology
Accession number :
edsair.doi.dedup.....a687c904c52ebc81dc02710f81ad675d