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Items: 48

1.

Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper.

Bénard AHM, Guenou E, Fookes M, Ateudjieu J, Kasambara W, Siever M, Rebaudet S, Boncy J, Adrien P, Piarroux R, Sack DA, Thomson N, Debes AK.

PLoS Negl Trop Dis. 2019 May 30;13(5):e0007330. doi: 10.1371/journal.pntd.0007330. eCollection 2019 May.

2.

Functional analysis of Salmonella Typhi adaptation to survival in water.

Kingsley RA, Langridge G, Smith SE, Makendi C, Fookes M, Wileman TM, El Ghany MA, Keith Turner A, Dyson ZA, Sridhar S, Pickard D, Kay S, Feasey N, Wong V, Barquist L, Dougan G.

Environ Microbiol. 2018 Nov;20(11):4079-4090. doi: 10.1111/1462-2920.14458.

3.

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR.

Sci Rep. 2018 Jun 29;8(1):9868. doi: 10.1038/s41598-018-28199-y.

4.

Dynamics of cholera epidemics from Benin to Mauritania.

Moore S, Dongdem AZ, Opare D, Cottavoz P, Fookes M, Sadji AY, Dzotsi E, Dogbe M, Jeddi F, Bidjada B, Piarroux M, Valentin OT, Glèlè CK, Rebaudet S, Sow AG, Constantin de Magny G, Koivogui L, Dunoyer J, Bellet F, Garnotel E, Thomson N, Piarroux R.

PLoS Negl Trop Dis. 2018 Apr 9;12(4):e0006379. doi: 10.1371/journal.pntd.0006379. eCollection 2018 Apr.

5.

Direct Whole-Genome Sequencing of Cutaneous Strains of Haemophilus ducreyi.

Marks M, Fookes M, Wagner J, Ghinai R, Sokana O, Sarkodie YA, Solomon AW, Mabey DCW, Thomson NR.

Emerg Infect Dis. 2018 Apr;24(4):786-789. doi: 10.3201/eid2404.171726.

6.

Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure.

Fookes MC, Hadfield J, Harris S, Parmar S, Unemo M, Jensen JS, Thomson NR.

BMC Genomics. 2017 Dec 28;18(1):993. doi: 10.1186/s12864-017-4399-6.

7.

Diagnostics for Yaws Eradication: Insights From Direct Next-Generation Sequencing of Cutaneous Strains of Treponema pallidum.

Marks M, Fookes M, Wagner J, Butcher R, Ghinai R, Sokana O, Sarkodie YA, Lukehart SA, Solomon AW, Mabey DCW, Thomson N.

Clin Infect Dis. 2018 Mar 5;66(6):818-824. doi: 10.1093/cid/cix892.

8.

Rare disease registries: a call to action.

Lacaze P, Millis N, Fookes M, Zurynski Y, Jaffe A, Bellgard M, Winship I, McNeil J, Bittles AH.

Intern Med J. 2017 Sep;47(9):1075-1079. doi: 10.1111/imj.13528.

PMID:
28891182
9.

Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice.

Oshota O, Conway M, Fookes M, Schreiber F, Chaudhuri RR, Yu L, Morgan FJE, Clare S, Choudhary J, Thomson NR, Lio P, Maskell DJ, Mastroeni P, Grant AJ.

PLoS One. 2017 Aug 10;12(8):e0181365. doi: 10.1371/journal.pone.0181365. eCollection 2017.

10.

Erratum: Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, Harris SR, Mather AE, Fookes M, Aslett M, Msefula C, Kariuki S, Maclennan CA, Onsare RS, Weill FX, Le Hello S, Smith AM, McClelland M, Desai P, Parry CM, Cheesbrough J, French N, Campos J, Chabalgoity JA, Betancor L, Hopkins KL, Nair S, Humphrey TJ, Lunguya O, Cogan TA, Tapia MD, Sow SO, Tennant SM, Bornstein K, Levine MM, Lacharme-Lora L, Everett DB, Kingsley RA, Parkhill J, Heyderman RS, Dougan G, Gordon MA, Thomson NR.

Nat Genet. 2017 Mar 30;49(4):651. doi: 10.1038/ng0417-651c. No abstract available.

PMID:
28358127
11.

The secondary resistome of multidrug-resistant Klebsiella pneumoniae.

Jana B, Cain AK, Doerrler WT, Boinett CJ, Fookes MC, Parkhill J, Guardabassi L.

Sci Rep. 2017 Feb 15;7:42483. doi: 10.1038/srep42483.

12.

The Type III Secretion System Effector SeoC of Salmonella enterica subsp. salamae and S. enterica subsp. arizonae ADP-Ribosylates Src and Inhibits Opsonophagocytosis.

Pollard DJ, Young JC, Covarelli V, Herrera-León S, Connor TR, Fookes M, Walker D, Echeita A, Thomson NR, Berger CN, Frankel G.

Infect Immun. 2016 Nov 18;84(12):3618-3628. Print 2016 Dec.

13.

What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.

Connor TR, Owen SV, Langridge G, Connell S, Nair S, Reuter S, Dallman TJ, Corander J, Tabing KC, Le Hello S, Fookes M, Doublet B, Zhou Z, Feltwell T, Ellington MJ, Herrera S, Gilmour M, Cloeckaert A, Achtman M, Parkhill J, Wain J, De Pinna E, Weill FX, Peters T, Thomson N.

MBio. 2016 Aug 23;7(4). pii: e00527-16. doi: 10.1128/mBio.00527-16.

14.

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, Harris SR, Mather AE, Fookes M, Aslett M, Msefula C, Kariuki S, Maclennan CA, Onsare RS, Weill FX, Le Hello S, Smith AM, McClelland M, Desai P, Parry CM, Cheesbrough J, French N, Campos J, Chabalgoity JA, Betancor L, Hopkins KL, Nair S, Humphrey TJ, Lunguya O, Cogan TA, Tapia MD, Sow SO, Tennant SM, Bornstein K, Levine MM, Lacharme-Lora L, Everett DB, Kingsley RA, Parkhill J, Heyderman RS, Dougan G, Gordon MA, Thomson NR.

Nat Genet. 2016 Oct;48(10):1211-1217. doi: 10.1038/ng.3644. Epub 2016 Aug 22. Erratum in: Nat Genet. 2017 Mar 30;49(4):651.

15.

Salmonella Enteritidis Isolate Harboring Multiple Efflux Pumps and Pathogenicity Factors, Shows Absence of O Antigen Polymerase Gene.

Jones-Dias D, Clemente L, Egas C, Froufe H, Sampaio DA, Vieira L, Fookes M, Thomson NR, Manageiro V, Caniça M.

Front Microbiol. 2016 Aug 3;7:1130. doi: 10.3389/fmicb.2016.01130. eCollection 2016. No abstract available.

16.

Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities.

Baker KS, Dallman TJ, Behar A, Weill FX, Gouali M, Sobel J, Fookes M, Valinsky L, Gal-Mor O, Connor TR, Nissan I, Bertrand S, Parkhill J, Jenkins C, Cohen D, Thomson NR.

Emerg Infect Dis. 2016 Sep;22(9):1545-53. doi: 10.3201/eid2209.151953.

17.

Correction: Elucidation of the RamA Regulon in Klebsiella pneumoniae Reveals a Role in LPS Regulation.

De Majumdar S, Yu J, Fookes M, McAteer SP, Llobet E, Spence SF, Monaghan A, Kissenpfennig A, Ingram RJ, Bengoechea J, Gally DL, Fanning S, Elborn JS, Schneiders T.

PLoS Pathog. 2016 May 11;12(5):e1005649. doi: 10.1371/journal.ppat.1005649. eCollection 2016 May.

18.

Survey of healthcare experiences of Australian adults living with rare diseases.

Molster C, Urwin D, Di Pietro L, Fookes M, Petrie D, van der Laan S, Dawkins H.

Orphanet J Rare Dis. 2016 Mar 24;11:30. doi: 10.1186/s13023-016-0409-z.

19.

Roary: rapid large-scale prokaryote pan genome analysis.

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J.

Bioinformatics. 2015 Nov 15;31(22):3691-3. doi: 10.1093/bioinformatics/btv421. Epub 2015 Jul 20.

20.

Whole genome analysis to detect potential vaccine-induced changes on Shigella sonnei genome.

Behar A, Fookes MC, Goren S, Thomson NR, Cohen D.

Vaccine. 2015 Jun 12;33(26):2978-83. doi: 10.1016/j.vaccine.2015.04.074. Epub 2015 Apr 30.

PMID:
25936664
21.

Elucidation of the RamA regulon in Klebsiella pneumoniae reveals a role in LPS regulation.

De Majumdar S, Yu J, Fookes M, McAteer SP, Llobet E, Finn S, Spence S, Monahan A, Monaghan A, Kissenpfennig A, Ingram RJ, Bengoechea J, Gally DL, Fanning S, Elborn JS, Schneiders T.

PLoS Pathog. 2015 Jan 29;11(1):e1004627. doi: 10.1371/journal.ppat.1004627. eCollection 2015 Jan. Erratum in: PLoS Pathog. 2015 Mar;11(3):e1004766. Monaghan, Avril [corrected to Monahan, Avril]. PLoS Pathog. 2016 May;12(5):e1005649.

22.

Patterns of genome evolution that have accompanied host adaptation in Salmonella.

Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HM, Barquist L, Stedman A, Humphrey T, Wigley P, Peters SE, Maskell DJ, Corander J, Chabalgoity JA, Barrow P, Parkhill J, Dougan G, Thomson NR.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):863-8. doi: 10.1073/pnas.1416707112. Epub 2014 Dec 22.

23.

RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri.

Vergara-Irigaray M, Fookes MC, Thomson NR, Tang CM.

BMC Genomics. 2014 Jun 6;15:438. doi: 10.1186/1471-2164-15-438.

24.

Parallel independent evolution of pathogenicity within the genus Yersinia.

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcão JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A, Thomson NR.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6768-73. doi: 10.1073/pnas.1317161111. Epub 2014 Apr 21.

25.

Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi.

Bronowski C, Fookes MC, Gilderthorp R, Ashelford KE, Harris SR, Phiri A, Hall N, Gordon MA, Wain J, Hart CA, Wigley P, Thomson NR, Winstanley C.

PLoS Negl Trop Dis. 2013 Nov 14;7(11):e2557. doi: 10.1371/journal.pntd.0002557. eCollection 2013 Nov.

26.

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection.

Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ, Browall S, Zemlickova H, Parkhill J, Normark S, Henriques-Normark B, Hinds J, Mitchell TJ, Bentley SD.

PLoS Genet. 2013;9(10):e1003868. doi: 10.1371/journal.pgen.1003868. Epub 2013 Oct 10.

27.

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor TR, Suchard MA, Lemey P, Mellor DJ, Haydon DT, Thomson NR.

Science. 2013 Sep 27;341(6153):1514-7. doi: 10.1126/science.1240578. Epub 2013 Sep 12.

28.

Clinically relevant mutant DNA gyrase alters supercoiling, changes the transcriptome, and confers multidrug resistance.

Webber MA, Ricci V, Whitehead R, Patel M, Fookes M, Ivens A, Piddock LJ.

MBio. 2013 Jul 23;4(4). pii: e00273-13. doi: 10.1128/mBio.00273-13.

29.

Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation.

Fookes M, Yu J, De Majumdar S, Thomson N, Schneiders T.

Genome Announc. 2013 Jan;1(1). pii: e00027-12. doi: 10.1128/genomeA.00027-12. Epub 2013 Jan 31.

30.

Genomic Comparison of the Closely Related Salmonella enterica Serovars Enteritidis and Dublin.

Betancor L, Yim L, Martínez A, Fookes M, Sasias S, Schelotto F, Thomson N, Maskell D, Chabalgoity JA.

Open Microbiol J. 2012;6:5-13. doi: 10.2174/1874285801206010005. Epub 2012 Feb 10.

31.

Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae.

Seth-Smith HM, Fookes MC, Okoro CK, Baker S, Harris SR, Scott P, Pickard D, Quail MA, Churcher C, Sanders M, Harmse J, Dougan G, Parkhill J, Thomson NR.

J Bacteriol. 2012 Mar;194(6):1494-504. doi: 10.1128/JB.06403-11. Epub 2012 Jan 13.

32.

The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella.

Ricci V, Loman N, Pallen M, Ivens A, Fookes M, Langridge GC, Wain J, Piddock LJ.

J Antimicrob Chemother. 2012 Mar;67(3):589-99. doi: 10.1093/jac/dkr515. Epub 2011 Dec 20.

33.

Salmonella bongori provides insights into the evolution of the Salmonellae.

Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, Connor TR, Seth-Smith H, Vernikos GS, Robinson KS, Sanders M, Petty NK, Kingsley RA, Bäumler AJ, Nuccio SP, Contreras I, Santiviago CA, Maskell D, Barrow P, Humphrey T, Nastasi A, Roberts M, Frankel G, Parkhill J, Dougan G, Thomson NR.

PLoS Pathog. 2011 Aug;7(8):e1002191. doi: 10.1371/journal.ppat.1002191. Epub 2011 Aug 18.

34.

Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

Petty NK, Feltwell T, Pickard D, Clare S, Toribio AL, Fookes M, Roberts K, Monson R, Nair S, Kingsley RA, Bulgin R, Wiles S, Goulding D, Keane T, Corton C, Lennard N, Harris D, Willey D, Rance R, Yu L, Choudhary JS, Churcher C, Quail MA, Parkhill J, Frankel G, Dougan G, Salmond GP, Thomson NR.

PLoS Pathog. 2011 Apr;7(4):e1002018. doi: 10.1371/journal.ppat.1002018. Epub 2011 Apr 7.

35.

Salmonella Typhi sense host neuroendocrine stress hormones and release the toxin haemolysin E.

Karavolos MH, Bulmer DM, Spencer H, Rampioni G, Schmalen I, Baker S, Pickard D, Gray J, Fookes M, Winzer K, Ivens A, Dougan G, Williams P, Khan CM.

EMBO Rep. 2011 Mar;12(3):252-8. doi: 10.1038/embor.2011.4. Epub 2011 Feb 18.

36.

Prevalence of Salmonella enterica in poultry and eggs in Uruguay during an epidemic due to Salmonella enterica serovar Enteritidis.

Betancor L, Pereira M, Martinez A, Giossa G, Fookes M, Flores K, Barrios P, Repiso V, Vignoli R, Cordeiro N, Algorta G, Thomson N, Maskell D, Schelotto F, Chabalgoity JA.

J Clin Microbiol. 2010 Jul;48(7):2413-23. doi: 10.1128/JCM.02137-09. Epub 2010 May 19.

37.

Epidemic multidrug-resistant (MDR-AmpC) Salmonella enterica serovar Newport strains contain three phage regions and a MDR resistance plasmid.

Wu G, Abuoun M, Hackl E, La Ragione RM, Fookes M, Fenner J, Pan Z, Wenzl P, Anjum MF, Woodward MJ.

Environ Microbiol Rep. 2010 Apr;2(2):228-35. doi: 10.1111/j.1758-2229.2009.00095.x. Epub 2009 Nov 24.

PMID:
23766073
38.

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

Betancor L, Yim L, Fookes M, Martinez A, Thomson NR, Ivens A, Peters S, Bryant C, Algorta G, Kariuki S, Schelotto F, Maskell D, Dougan G, Chabalgoity JA.

BMC Microbiol. 2009 Nov 18;9:237. doi: 10.1186/1471-2180-9-237.

39.

A simple method for directional transcriptome sequencing using Illumina technology.

Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB, Keane T, Quail MA, He M, Assefa S, Bähler J, Kingsley RA, Parkhill J, Bentley SD, Dougan G, Thomson NR.

Nucleic Acids Res. 2009 Dec;37(22):e148. doi: 10.1093/nar/gkp811.

40.

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, Maskell DJ, Parkhill J, Choudhary J, Thomson NR, Dougan G.

PLoS Genet. 2009 Jul;5(7):e1000569. doi: 10.1371/journal.pgen.1000569. Epub 2009 Jul 17.

41.

Identification of genetic and phenotypic differences associated with prevalent and non-prevalent Salmonella Enteritidis phage types: analysis of variation in amino acid transport.

Pan Z, Carter B, Núñez-García J, Abuoun M, Fookes M, Ivens A, Woodward MJ, Anjum MF.

Microbiology. 2009 Oct;155(Pt 10):3200-13. doi: 10.1099/mic.0.029405-0. Epub 2009 Jul 2.

PMID:
19574306
42.

Characterization of the genomes of a diverse collection of Salmonella enterica serovar Typhimurium definitive phage type 104.

Cooke FJ, Brown DJ, Fookes M, Pickard D, Ivens A, Wain J, Roberts M, Kingsley RA, Thomson NR, Dougan G.

J Bacteriol. 2008 Dec;190(24):8155-62. doi: 10.1128/JB.00636-08. Epub 2008 Oct 10.

43.

Prophage sequences defining hot spots of genome variation in Salmonella enterica serovar Typhimurium can be used to discriminate between field isolates.

Cooke FJ, Wain J, Fookes M, Ivens A, Thomson N, Brown DJ, Threlfall EJ, Gunn G, Foster G, Dougan G.

J Clin Microbiol. 2007 Aug;45(8):2590-8. Epub 2007 May 23.

44.

An H-NS-like stealth protein aids horizontal DNA transmission in bacteria.

Doyle M, Fookes M, Ivens A, Mangan MW, Wain J, Dorman CJ.

Science. 2007 Jan 12;315(5809):251-2.

45.

Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray.

Anjum MF, Marooney C, Fookes M, Baker S, Dougan G, Ivens A, Woodward MJ.

Infect Immun. 2005 Dec;73(12):7894-905.

46.

Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX).

Bishop AL, Baker S, Jenks S, Fookes M, Gaora PO, Pickard D, Anjum M, Farrar J, Hien TT, Ivens A, Dougan G.

J Bacteriol. 2005 Apr;187(7):2469-82.

47.

The role of prophage-like elements in the diversity of Salmonella enterica serovars.

Thomson N, Baker S, Pickard D, Fookes M, Anjum M, Hamlin N, Wain J, House D, Bhutta Z, Chan K, Falkow S, Parkhill J, Woodward M, Ivens A, Dougan G.

J Mol Biol. 2004 May 28;339(2):279-300.

PMID:
15136033
48.

Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7.

Pickard D, Wain J, Baker S, Line A, Chohan S, Fookes M, Barron A, Gaora PO, Chabalgoity JA, Thanky N, Scholes C, Thomson N, Quail M, Parkhill J, Dougan G.

J Bacteriol. 2003 Sep;185(17):5055-65.

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