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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.


Gavin K. Paterson

Ewan M. Harrison

Gemma G. R. Murray

John J. Welch

James H. Warland

Matthew T. G. Holden

Fiona J. E. Morgan

Xiaoliang Ba

Gerrit Koop

Simon R. Harris

Duncan J. Maskell

Sharon J. Peacock

Michael E. Herrtage

Julian Parkhill

Mark A. Holmes


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.


Paterson, G. K., Harrison, E. M., Murray, G. G. R., Welch, J. J., Warland, J. H., Holden, M. T. G., …Holmes, M. A. (2015). Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nature communications, 6(1),

Acceptance Date Feb 6, 2015
Online Publication Date Mar 27, 2015
Publication Date Jan 1, 2015
Deposit Date Jun 23, 2015
Publicly Available Date Jun 23, 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
Public URL
Publisher URL
Additional Information Copy of article first published in: Nature communications, 2015, v.6


Paterson_Harrison_Nature_commm_2015.pdf (2.2 Mb)

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