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Research: A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic
- Matthew T.G. Holden,
- Li-Yang Hsu,
- Kevin Kurt,
- Lucy A. Weinert,
- Alison E. Mather,
- Simon R. Harris,
- Birgit Strommenger,
- Franziska Layer,
- Wolfgang Witte,
- Herminia de Lencastre,
- Robert Skov,
- Henrik Westh,
- Helena Žemličková,
- Geoffrey Coombs,
- Angela M. Kearns,
- Robert L.R. Hill,
- Jonathan Edgeworth,
- Ian Gould,
- Vanya Gant,
- Jonathan Cooke,
- Giles F. Edwards,
- Paul R. McAdam,
- Kate E. Templeton,
- Angela McCann,
- Zhemin Zhou,
- Santiago Castillo-Ramírez,
- Edward J. Feil,
- Lyndsey O. Hudson,
- Mark C. Enright,
- Francois Balloux,
- David M. Aanensen,
- Brian G. Spratt,
- J. Ross Fitzgerald,
- Julian Parkhill,
- Mark Achtman,
- Stephen D. Bentley,
- and Ulrich Nübel
Genome Res. April 2013 23: 653-664; Published in Advance January 8, 2013, doi:10.1101/gr.147710.112
...A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic Matthew T.G. Holden 1 , 25 , Li-Yang Hsu 1 , 2 , Kevin Kurt 3 , Lucy A. Weinert 4 , 22 , Alison E. Mather 1...
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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
.... 2014. Dissecting vancomycin-intermediate resistance in Staphylococcus aureus using -wide association. Genome Biol Evol 6: 1174–1185. Alsterlund R, Axelsson C, Olsson-Liljequist B. 2012. Long-term carriage of extended-spectrum b-lactamase-producing Escherichia coli. Scand J Infect Dis 44: 51...
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Research: Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection
- Simon R. Harris,
- Carl Robinson,
- Karen F. Steward,
- Katy S. Webb,
- Romain Paillot,
- Julian Parkhill,
- Matthew T.G. Holden,
- and Andrew S. Waller
Genome Res. September 2015 25: 1360-1371; Published in Advance July 9, 2015, doi:10.1101/gr.189803.115
...of the sequenced isolates is shown in Figure 1A. Isolates are colored according to clusters defined using a tree-independent Bayesian method for subdividing populations based on sequence similarity (Corander et al. 2008). Clusters 1–3 correspond to the three major clades in the ML tree, with cluster 4 representing...
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PERSPECTIVE: Insights on biology and evolution from microbial genome sequencing
- Claire M. Fraser-Liggett
Genome Res. December 2005 15: 1603-1610; doi:10.1101/gr.3724205
....T., Ravel, J., Paulsen, I.T., Kolonay, J.F., Brinkac, L., Beanan, M., et al. 2005 . Insights on evolution of virulence and resistance from the complete analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J...
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Resource: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland
- Sandra Reuter,
- M. Estée Török,
- Matthew T.G. Holden,
- Rosy Reynolds,
- Kathy E. Raven,
- Beth Blane,
- Tjibbe Donker,
- Stephen D. Bentley,
- David M. Aanensen,
- Hajo Grundmann,
- Edward J. Feil,
- Brian G. Spratt,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. February 2016 26: 263-270; Published in Advance December 15, 2015, doi:10.1101/gr.196709.115
...applied to surveillance and outbreak investigation depends on accessible genomic databases to provide vital genetic context. Our aim was to construct and describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) s drawn from England, Northern Ireland...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...antibiotic use is more sporadic than in the hospital population. This is a strong contrast with the population structure of true nosocomial pathogens such as methicillin-resistant Staphylococcus aureus (MRSA), where specific drugresistant clones sequentially dominate the population within a niche where...
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Research: The effect of recombination on the evolution of a population of Neisseria meningitidis
- Neil MacAlasdair,
- Maiju Pesonen,
- Ola Brynildsrud,
- Vegard Eldholm,
- Paul A. Kristiansen,
- Jukka Corander,
- Dominique A. Caugant,
- and Stephen D. Bentley
Genome Res. July 2021 31: 1258-1268; Published in Advance June 9, 2021, doi:10.1101/gr.264465.120
..., Westh H, Boye K, Gulay Z, Bentley SD, Parkhill J, et al. 2012. Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus. Genome Biol 13: R126. doi:10.1186/gb-2012-13-12-r126 ↵Christensen H, May M, Bowen L, Hickman M, Trotter CL. 2010...
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Research: Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland
- Danesh Moradigaravand,
- Christine J. Boinett,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2016 26: 1101-1109; Published in Advance July 18, 2016, doi:10.1101/gr.205245.116
...of methicillin resistant Staphylococcus aureus (MRSA) (Reuter et al. 2016).Onequestion that is not answered by this study is whether antimicrobial-susceptible S.marcescens infections are also causedby recent clones, orwhether any representativeof thebroader species is capableof opportunistic infection.A global...
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Method: Microbial strain-level population structure and genetic diversity from metagenomes
- Duy Tin Truong,
- Adrian Tett,
- Edoardo Pasolli,
- Curtis Huttenhower,
- and Nicola Segata
Genome Res. April 2017 27: 626-638; Published in Advance February 6, 2017, doi:10.1101/gr.216242.116
...for isolate or human population genetics. Truong et al. 628 Genome Research www..org hard-limited sequence identity thresholds may be an oversimplification, because they are difficult to set universally and are both locus- and organism-specific. Phylogenetic modeling overcomes the need of defining hard...
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Perspective: On the origin of prokaryotic species
- W. Ford Doolittle and
- Olga Zhaxybayeva
Genome Res. May 2009 19: 744-756; doi:10.1101/gr.086645.108
...@dal.ca; fax (902) 494-1355. Article is online at http://www..org/cgi/doi/10.1101/gr.086645.108. 744 Genome Research www..org 19:744–756 2009 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/09; www..org that define them, then the word ‘‘species’’ itself has only a nominal significance, describing...

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