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Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial infection occurs in resource-restricted settings where barriers to transmission are lower. Here, we study the flux and genetic diversity of MRSA on ward and individual patient levels in a hospital where transmission was common. We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates from 46 patients and five members of staff, including the first MRSA-positive screen isolates and up to two repeat isolates where available. Phylogenetic analysis identified a flux of distinct ST 239 clades over time in each intensive care unit. In total, five main clades were identified, which varied in the carriage of plasmids encoding antiseptic and antimicrobial resistance determinants. Sequence data confirmed intra- and interwards transmission events and identified individual patients who were colonized by more than one clade. One patient on each unit was the source of numerous transmission events, and deep sampling of one of these cases demonstrated colonization with a "cloud" of related MRSA variants. The application of whole-genome sequencing and analysis provides novel insights into the transmission of MRSA in under-resourced healthcare settings and has relevance to wider global health.

Original publication

DOI

10.1101/gr.174730.114

Type

Journal article

Journal

Genome research

Publication Date

01/2015

Volume

25

Pages

111 - 118

Addresses

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; Menzies School of Health Research, Darwin, Northern Territory 0811, Australia;

Keywords

Humans, Staphylococcal Infections, Cross Infection, DNA, Bacterial, Bacterial Typing Techniques, Linear Models, Prospective Studies, Sequence Analysis, DNA, Computational Biology, Disease Outbreaks, Phylogeny, Polymorphism, Single Nucleotide, Adult, Child, Methicillin-Resistant Staphylococcus aureus, High-Throughput Nucleotide Sequencing