Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a Bayesian framework
Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a Bayesian framework
Staphylococcus aureus is a common cause of infections that has undergone rapid global spread over recent decades. Formal phylogeographic methods have not yet been applied to the molecular epidemiology of bacterial pathogens because the limited genetic diversity of data sets based on individual genes usually results in poor phylogenetic resolution. Here, we investigated a whole-genome single nucleotide polymorphism (SNP) data set of health care-associated Methicillin-resistant S. aureus sequence type 239 (HA-MRSA ST239) strains, which we analyzed using Markov spatial models that incorporate geographical sampling distributions. The reconstructed timescale indicated a temporal origin of this strain shortly after the introduction of Methicillin, followed by global pandemic spread. The estimate of the temporal origin was robust to the molecular clock, coalescent prior, full/intergenic/synonymous SNP inclusion, and correction for excluded invariant site patterns. Finally, phylogeographic analyses statistically supported the role of human movement in the global dissemination of HA-MRSA ST239, although it was unable to conclusively resolve the location of the root. This study demonstrates that bacterial genomes can indeed contain sufficient evolutionary information to elucidate the temporal and spatial dynamics of transmission. Future applications of this approach to other bacterial strains may provide valuable epidemiological insights that may justify the cost of genome-wide typing.
bayes theorem, communicable diseases, microbiology, evolution, molecular genome-wide association, study methods, humans likelihood functions, markov chains methicillin-resistant staphylococcus aureus, genetics isolation & purification models, genetic phylogeny phylogeography, staphylococcal infections
1593-1603
Gray, R.R.
0865cf96-c9d9-4a13-b6ab-330e5b0b0185
Tatem, A. J.
6c6de104-a5f9-46e0-bb93-a1a7c980513e
Johnson, J.A.
f1bed820-de14-4ce9-9cef-e2a996f9437a
Alekseyenko, A.V.
3bcd49fe-a4d6-4dd0-a0f9-0b1f24b6d268
Pybus, O.G.
5fa128e1-8eb8-4d38-b925-1d7869a07f99
Suchard, M.A.
7927425a-5f75-4ddd-ba84-3c9eb06bc714
Salemi, M.
c7822d3e-11d0-4184-835a-68f3b7945afc
26 November 2011
Gray, R.R.
0865cf96-c9d9-4a13-b6ab-330e5b0b0185
Tatem, A. J.
6c6de104-a5f9-46e0-bb93-a1a7c980513e
Johnson, J.A.
f1bed820-de14-4ce9-9cef-e2a996f9437a
Alekseyenko, A.V.
3bcd49fe-a4d6-4dd0-a0f9-0b1f24b6d268
Pybus, O.G.
5fa128e1-8eb8-4d38-b925-1d7869a07f99
Suchard, M.A.
7927425a-5f75-4ddd-ba84-3c9eb06bc714
Salemi, M.
c7822d3e-11d0-4184-835a-68f3b7945afc
Gray, R.R., Tatem, A. J., Johnson, J.A., Alekseyenko, A.V., Pybus, O.G., Suchard, M.A. and Salemi, M.
(2011)
Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a Bayesian framework.
Molecular Biology and Evolution, 28 (5), .
(doi:10.1093/molbev/msq319).
(PMID:21112962)
Abstract
Staphylococcus aureus is a common cause of infections that has undergone rapid global spread over recent decades. Formal phylogeographic methods have not yet been applied to the molecular epidemiology of bacterial pathogens because the limited genetic diversity of data sets based on individual genes usually results in poor phylogenetic resolution. Here, we investigated a whole-genome single nucleotide polymorphism (SNP) data set of health care-associated Methicillin-resistant S. aureus sequence type 239 (HA-MRSA ST239) strains, which we analyzed using Markov spatial models that incorporate geographical sampling distributions. The reconstructed timescale indicated a temporal origin of this strain shortly after the introduction of Methicillin, followed by global pandemic spread. The estimate of the temporal origin was robust to the molecular clock, coalescent prior, full/intergenic/synonymous SNP inclusion, and correction for excluded invariant site patterns. Finally, phylogeographic analyses statistically supported the role of human movement in the global dissemination of HA-MRSA ST239, although it was unable to conclusively resolve the location of the root. This study demonstrates that bacterial genomes can indeed contain sufficient evolutionary information to elucidate the temporal and spatial dynamics of transmission. Future applications of this approach to other bacterial strains may provide valuable epidemiological insights that may justify the cost of genome-wide typing.
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Published date: 26 November 2011
Keywords:
bayes theorem, communicable diseases, microbiology, evolution, molecular genome-wide association, study methods, humans likelihood functions, markov chains methicillin-resistant staphylococcus aureus, genetics isolation & purification models, genetic phylogeny phylogeography, staphylococcal infections
Organisations:
Geography & Environment, PHEW – P (Population Health)
Identifiers
Local EPrints ID: 344416
URI: http://eprints.soton.ac.uk/id/eprint/344416
PURE UUID: 214235a3-d8b9-4dc6-ab0e-50f9703b8a29
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Date deposited: 05 Nov 2012 15:24
Last modified: 15 Mar 2024 03:43
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Contributors
Author:
R.R. Gray
Author:
J.A. Johnson
Author:
A.V. Alekseyenko
Author:
O.G. Pybus
Author:
M.A. Suchard
Author:
M. Salemi
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