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Method: Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Anna K. Pöntinen,
- Sergio Arredondo-Alonso,
- Stephen D. Bentley,
- and Jukka Corander
Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
...does not always have an impact on a microbe's fitness, it can lead to critical phenotypic changes such as the acquisition of antimicrobial resistance, virulence factors, and vaccine escape (Croucher et al. 2013; Wyres et al. 2019).A common approach to analyzing horizontal exchange in microbial genomics...
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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
...associated with urinary tract infections and bacteremia has been intensively investigated, including recent work focusing on the virulent, globally disseminated, multidrug-resistant lineage ST131. To contextualize ST131 within the broader E. coli population associated with disease, we used genomics...
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Research: Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting
- Steven Y.C. Tong,
- Matthew T.G. Holden,
- Emma K. Nickerson,
- Ben S. Cooper,
- Claudio U. Köser,
- Anne Cori,
- Thibaut Jombart,
- Simon Cauchemez,
- Christophe Fraser,
- Vanaporn Wuthiekanun,
- Janjira Thaipadungpanit,
- Maliwan Hongsuwan,
- Nicholas P. Day,
- Direk Limmathurotsakul,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. January 2015 25: 111-118; Published in Advance December 9, 2014, doi:10.1101/gr.174730.114
...option. 25:111–118 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/15; www..org Genome Research 111 www..org MRSA (HA-MRSA) belong to a restricted number of successful lineages worldwide (Enright et al. 2002), so that in a given setting most HA-MRSA isolates will have the same genotype...
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Research: A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland
- Kathy E. Raven,
- Sandra Reuter,
- Rosy Reynolds,
- Hayley J. Brodrick,
- Julie E. Russell,
- M. Estée Török,
- Julian Parkhill,
- and Sharon J. Peacock
Genome Res. October 2016 26: 1388-1396; Published in Advance August 15, 2016, doi:10.1101/gr.204024.116
...-adapted Enterococcus faecalis lineages. Nat Microbiol 1: 15033. Reuter S, TörökME, HoldenMTG, Reynolds R, Raven KE, Blane B, Donker T, Bentley SD, Aanensen DM, Grundmann H, et al. 2016. Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland. Genome Res 26: 263...
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Research: Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
- Sophia David,
- Christophe Rusniok,
- Massimo Mentasti,
- Laura Gomez-Valero,
- Simon R. Harris,
- Pierre Lechat,
- John Lees,
- Christophe Ginevra,
- Philippe Glaser,
- Laurence Ma,
- Christiane Bouchier,
- Anthony Underwood,
- Sophie Jarraud,
- Timothy G. Harrison,
- Julian Parkhill,
- and Carmen Buchrieser
Genome Res. November 2016 26: 1555-1564; Published in Advance September 23, 2016, doi:10.1101/gr.209536.116
...et al. 2014 Streptococcus pneumoniae (13 different clades) 1.45 × 10−6–4.81 × 10−6 Chewapreecha et al. 2014 aThe units provided are those given in the original publications. L. pneumophila disease clones emerged recently Genome Research 1559 www..org which is strongly induced in the virulent...
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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
...Infect 45: 42–46. Holt KE,WertheimH, Zadoks RN, Baker S,Whitehouse CA,DanceD, Jenney A, Connor TR, Hsu LY, Severin J, et al. 2015. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci...
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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
...to regulate virulence factors, including capsule, in S. pyogenes (Grahamet al. 2002). Both isolates shared a second SNP in csrS, which is predicted to result in a Leu257Phe amino acid substitution in addition to one nonsense mutation and a further 40 nonsynonymous mutations elsewhere in the (Supplemental...
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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
...isolate from patient 1 differed from that of patient 29 by 355 genomic variants and harbored 11 additional virulence factors. These genomic data unambiguously demonstrate independent sources of infection, rather than nosocomial transmission. Nevertheless, a strain genomically identical to the ST131-H30...
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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
.... Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from...
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Letter: Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance
- Jie Feng,
- Andréanne Lupien,
- Hélène Gingras,
- Jessica Wasserscheid,
- Ken Dewar,
- Danielle Légaré,
- and Marc Ouellette
Genome Res. July 2009 19: 1214-1223; Published in Advance April 6, 2009, doi:10.1101/gr.089342.108
...Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance Jie Feng 1 , 2 , Andréanne Lupien 1 , 2 , Hélène Gingras 1 , 2 , Jessica Wasserscheid 3 , Ken Dewar 3 , Danielle...

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