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Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

Paterson, Gavin K.; Harrison, Ewan M.; Murray, Gemma G. R.; Welch, John J.; Warland, James H.; Holden, Matthew T. G.; Morgan, Fiona J. E.; Ba, Xiaoliang; Koop, Gerrit; Harris, Simon R.; Maskell, Duncan J.; Peacock, Sharon J.; Herrtage, Michael E.; Parkhill, Julian; Holmes, Mark A.


Fiona J.E. Morgan

Xiaoliang Ba

Michael E. Herrtage

Julian Parkhill

Ewan M. Harrison

Gemma G. R. Murray

John J. Welch

James H. Warland

Matthew T. G. Holden

Fiona J. E. Morgan

Gerrit Koop

Simon R. Harris

Duncan J. Maskell

Sharon J. Peacock

Mark A. Holmes

Gemma G.R. Murray

Matthew T.G. Holden


Genome sequencing is revolutionizing clinical microbiology and our understanding of infectious diseases. Previous studies have largely relied on the sequencing of a single isolate from each individual. However, it is not clear what degree of bacterial diversity exists within, and is transmitted between individuals. Understanding this ‘cloud of diversity’ is key to accurate identification of transmission pathways. Here, we report the deep sequencing of methicillin-resistant Staphylococcus aureus among staff and animal patients involved in a transmission network at a veterinary hospital. We demonstrate considerable within-host diversity and that within-host diversity may rise and fall over time. Isolates from invasive disease contained multiple mutations in the same genes, including inactivation of a global regulator of virulence and changes in phage copy number. This study highlights the need for sequencing of multiple isolates from individuals to gain an accurate picture of transmission networks and to further understand the basis of pathogenesis.

Journal Article Type Article
Publication Date Jan 1, 2015
Journal Nature communications
Electronic ISSN 2041-1723
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
Volume 6
Issue 1
Keywords Biological sciences, Evolution, Medical research, Microbiology
Publisher URL
Copyright Statement This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit
Additional Information Copy of article first published in: Nature communications, 2015, v.6


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