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An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome.

Gomez-Gonzalez PJ, Andreu N, Phelan JE, de Sessions PF, Glynn JR, Crampin AC, Campino S, Butcher PD, Hibberd ML, Clark TG.

Sci Rep. 2019 Mar 26;9(1):5204. doi: 10.1038/s41598-019-41692-2.


Diagnostic accuracy of a prototype rapid chlamydia and gonorrhoea recombinase polymerase amplification assay: a multicentre cross-sectional preclinical evaluation.

Harding-Esch EM, Fuller SS, Chow SC, Nori AV, Harrison MA, Parker M, Piepenburg O, Forrest MS, Brooks DG, Patel R, Hay PE, Fearnley N, Pond MJ, Dunbar JK, Butcher PD, Planche T, Lowndes CM, Sadiq ST.

Clin Microbiol Infect. 2019 Mar;25(3):380.e1-380.e7. doi: 10.1016/j.cmi.2018.06.003. Epub 2018 Jun 12.


Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial.

Witney AA, Bateson AL, Jindani A, Phillips PP, Coleman D, Stoker NG, Butcher PD, McHugh TD; RIFAQUIN Study Team.

BMC Med. 2017 Mar 29;15(1):71. doi: 10.1186/s12916-017-0834-4.


Drug resistant TB: UK multicentre study (DRUMS): Treatment, management and outcomes in London and West Midlands 2008-2014.

Arnold A, Cooke GS, Kon OM, Dedicoat M, Lipman M, Loyse A, Butcher PD, Ster IC, Harrison TS.

J Infect. 2017 Mar;74(3):260-271. doi: 10.1016/j.jinf.2016.12.005. Epub 2016 Dec 18.


XDR-TB transmission in London: Case management and contact tracing investigation assisted by early whole genome sequencing.

Arnold A, Witney AA, Vergnano S, Roche A, Cosgrove CA, Houston A, Gould KA, Hinds J, Riley P, Macallan D, Butcher PD, Harrison TS.

J Infect. 2016 Sep;73(3):210-8. doi: 10.1016/j.jinf.2016.04.037. Epub 2016 Jun 14.


Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy.

Honeyborne I, McHugh TD, Kuittinen I, Cichonska A, Evangelopoulos D, Ronacher K, van Helden PD, Gillespie SH, Fernandez-Reyes D, Walzl G, Rousu J, Butcher PD, Waddell SJ.

BMC Med. 2016 Apr 7;14:68. doi: 10.1186/s12916-016-0609-3.


Clinical use of whole genome sequencing for Mycobacterium tuberculosis.

Witney AA, Cosgrove CA, Arnold A, Hinds J, Stoker NG, Butcher PD.

BMC Med. 2016 Mar 23;14:46. doi: 10.1186/s12916-016-0598-2. Review.


Accurate detection of Neisseria gonorrhoeae ciprofloxacin susceptibility directly from genital and extragenital clinical samples: towards genotype-guided antimicrobial therapy.

Pond MJ, Hall CL, Miari VF, Cole M, Laing KG, Jagatia H, Harding-Esch E, Monahan IM, Planche T, Hinds J, Ison CA, Chisholm S, Butcher PD, Sadiq ST.

J Antimicrob Chemother. 2016 Apr;71(4):897-902. doi: 10.1093/jac/dkv432. Epub 2016 Jan 26.


Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases.

Witney AA, Gould KA, Arnold A, Coleman D, Delgado R, Dhillon J, Pond MJ, Pope CF, Planche TD, Stoker NG, Cosgrove CA, Butcher PD, Harrison TS, Hinds J.

J Clin Microbiol. 2015 May;53(5):1473-83. doi: 10.1128/JCM.02993-14. Epub 2015 Feb 11.


Performance evaluation of automated urine microscopy as a rapid, non-invasive approach for the diagnosis of non-gonococcal urethritis.

Pond MJ, Nori AV, Patel S, Laing K, Ajayi M, Copas AJ, Butcher PD, Hay P, Sadiq ST.

Sex Transm Infect. 2015 May;91(3):165-70. doi: 10.1136/sextrans-2014-051761. Epub 2015 Jan 22.


High-dose rifapentine with moxifloxacin for pulmonary tuberculosis.

Jindani A, Harrison TS, Nunn AJ, Phillips PP, Churchyard GJ, Charalambous S, Hatherill M, Geldenhuys H, McIlleron HM, Zvada SP, Mungofa S, Shah NA, Zizhou S, Magweta L, Shepherd J, Nyirenda S, van Dijk JH, Clouting HE, Coleman D, Bateson AL, McHugh TD, Butcher PD, Mitchison DA; RIFAQUIN Trial Team.

N Engl J Med. 2014 Oct 23;371(17):1599-608. doi: 10.1056/NEJMoa1314210.


Potassium availability triggers Mycobacterium tuberculosis transition to, and resuscitation from, non-culturable (dormant) states.

Salina EG, Waddell SJ, Hoffmann N, Rosenkrands I, Butcher PD, Kaprelyants AS.

Open Biol. 2014 Oct;4(10). pii: 140106. doi: 10.1098/rsob.140106.


Oleoyl coenzyme A regulates interaction of transcriptional regulator RaaS (Rv1219c) with DNA in mycobacteria.

Turapov O, Waddell SJ, Burke B, Glenn S, Sarybaeva AA, Tudo G, Labesse G, Young DI, Young M, Andrew PW, Butcher PD, Cohen-Gonsaud M, Mukamolova GV.

J Biol Chem. 2014 Sep 5;289(36):25241-9. doi: 10.1074/jbc.M114.577338. Epub 2014 Jul 10.


Antimicrobial treatment improves mycobacterial survival in nonpermissive growth conditions.

Turapov O, Waddell SJ, Burke B, Glenn S, Sarybaeva AA, Tudo G, Labesse G, Young DI, Young M, Andrew PW, Butcher PD, Cohen-Gonsaud M, Mukamolova GV.

Antimicrob Agents Chemother. 2014 May;58(5):2798-806. doi: 10.1128/AAC.02774-13. Epub 2014 Mar 3.


Evidence for a role for interleukin-17, Th17 cells and iron homeostasis in protective immunity against tuberculosis in cynomolgus macaques.

Wareham AS, Tree JA, Marsh PD, Butcher PD, Dennis M, Sharpe SA.

PLoS One. 2014 Feb 4;9(2):e88149. doi: 10.1371/journal.pone.0088149. eCollection 2014.


Genome sequencing and characterization of an extensively drug-resistant sequence type 111 serotype O12 hospital outbreak strain of Pseudomonas aeruginosa.

Witney AA, Gould KA, Pope CF, Bolt F, Stoker NG, Cubbon MD, Bradley CR, Fraise A, Breathnach AS, Butcher PD, Planche TD, Hinds J.

Clin Microbiol Infect. 2014 Oct;20(10):O609-18. doi: 10.1111/1469-0691.12528. Epub 2014 Feb 8.


High prevalence of antibiotic-resistant Mycoplasma genitalium in nongonococcal urethritis: the need for routine testing and the inadequacy of current treatment options.

Pond MJ, Nori AV, Witney AA, Lopeman RC, Butcher PD, Sadiq ST.

Clin Infect Dis. 2014 Mar;58(5):631-7. doi: 10.1093/cid/cit752. Epub 2013 Nov 26.


BμG@Sbase--a microbial gene expression and comparative genomic database.

Witney AA, Waldron DE, Brooks LA, Tyler RH, Withers M, Stoker NG, Wren BW, Butcher PD, Hinds J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D605-9. doi: 10.1093/nar/gkr796. Epub 2011 Sep 24.


Mycobacterial p(1)-type ATPases mediate resistance to zinc poisoning in human macrophages.

Botella H, Peyron P, Levillain F, Poincloux R, Poquet Y, Brandli I, Wang C, Tailleux L, Tilleul S, Charrière GM, Waddell SJ, Foti M, Lugo-Villarino G, Gao Q, Maridonneau-Parini I, Butcher PD, Castagnoli PR, Gicquel B, de Chastellier C, Neyrolles O.

Cell Host Microbe. 2011 Sep 15;10(3):248-59. doi: 10.1016/j.chom.2011.08.006.


Examining the basis of isoniazid tolerance in nonreplicating Mycobacterium tuberculosis using transcriptional profiling.

Tudó G, Laing K, Mitchison DA, Butcher PD, Waddell SJ.

Future Med Chem. 2010 Aug;2(8):1371-83. doi: 10.4155/fmc.10.219.


Moxifloxacin and pyrazinamide susceptibility testing in a complex case of multidrug-resistant tuberculosis.

Feasey NA, Pond M, Coleman D, Solomon AW, Cosgrove CA, Delgado R, Butcher PD, Mitchison DA, Harrison T.

Int J Tuberc Lung Dis. 2011 Mar;15(3):417-20.


Point-of-care antibiotic susceptibility testing for gonorrhoea: improving therapeutic options and sparing the use of cephalosporins.

Sadiq ST, Dave J, Butcher PD.

Sex Transm Infect. 2010 Nov;86(6):445-6. doi: 10.1136/sti.2010.044230. No abstract available.


Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages.

Li AH, Waddell SJ, Hinds J, Malloff CA, Bains M, Hancock RE, Lam WL, Butcher PD, Stokes RW.

PLoS One. 2010 Jun 10;5(6):e11066. doi: 10.1371/journal.pone.0011066.


Use of DNA arrays to study transcriptional responses to antimycobacterial compounds.

Waddell SJ, Butcher PD.

Methods Mol Biol. 2010;642:75-91. doi: 10.1007/978-1-60327-279-7_6.


Professor D A Mitchison: 60 years of contributions to the chemotherapy of tuberculosis.

Butcher PD, Jindani A.

Tuberculosis (Edinb). 2010 May;90(3):160-1. doi: 10.1016/ Epub 2010 Apr 9. No abstract available.


Prevalence and clinical correlations of genetic subtypes of Giardia lamblia in an urban setting.

Breathnach AS, McHugh TD, Butcher PD.

Epidemiol Infect. 2010 Oct;138(10):1459-67. doi: 10.1017/S0950268810000208. Epub 2010 Feb 10.


Whole genome analysis using microarrays.

Waddell SJ, Hinds J, Butcher PD.

Methods Mol Biol. 2009;465:83-93. doi: 10.1007/978-1-59745-207-6_6.


Mycobacterium tuberculosis DNA repair in response to subinhibitory concentrations of ciprofloxacin.

O'Sullivan DM, Hinds J, Butcher PD, Gillespie SH, McHugh TD.

J Antimicrob Chemother. 2008 Dec;62(6):1199-202. doi: 10.1093/jac/dkn387. Epub 2008 Sep 16.


Microarrays for Microbes: the BmuG@S Approach.

Hinds J, Laing KG, Mangan JA, Butcher PD.

Comp Funct Genomics. 2002;3(4):333-7. doi: 10.1002/cfg.187. No abstract available.


The heat shock response of Mycobacterium tuberculosis: linking gene expression, immunology and pathogenesis.

Stewart GR, Wernisch L, Stabler R, Mangan JA, Hinds J, Laing KG, Butcher PD, Young DB.

Comp Funct Genomics. 2002;3(4):348-51. doi: 10.1002/cfg.183.


Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar.

Stavrum R, Valvatne H, Bø TH, Jonassen I, Hinds J, Butcher PD, Grewal HM.

PLoS One. 2008 Apr 9;3(4):e1973. doi: 10.1371/journal.pone.0001973.


Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum.

Garton NJ, Waddell SJ, Sherratt AL, Lee SM, Smith RJ, Senner C, Hinds J, Rajakumar K, Adegbola RA, Besra GS, Butcher PD, Barer MR.

PLoS Med. 2008 Apr 1;5(4):e75. doi: 10.1371/journal.pmed.0050075.


Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies.

Waddell SJ, Laing K, Senner C, Butcher PD.

BMC Genomics. 2008 Feb 25;9:94. doi: 10.1186/1471-2164-9-94.


Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages.

Tailleux L, Waddell SJ, Pelizzola M, Mortellaro A, Withers M, Tanne A, Castagnoli PR, Gicquel B, Stoker NG, Butcher PD, Foti M, Neyrolles O.

PLoS One. 2008 Jan 2;3(1):e1403. doi: 10.1371/journal.pone.0001403.


RNA profiling in host-pathogen interactions.

Waddell SJ, Butcher PD, Stoker NG.

Curr Opin Microbiol. 2007 Jun;10(3):297-302. Epub 2007 Jun 15. Review.


Microarray analysis of whole genome expression of intracellular Mycobacterium tuberculosis.

Waddell SJ, Butcher PD.

Curr Mol Med. 2007 May;7(3):287-96. Review.


Lipid composition and transcriptional response of Mycobacterium tuberculosis grown under iron-limitation in continuous culture: identification of a novel wax ester.

Bacon J, Dover LG, Hatch KA, Zhang Y, Gomes JM, Kendall S, Wernisch L, Stoker NG, Butcher PD, Besra GS, Marsh PD.

Microbiology. 2007 May;153(Pt 5):1435-1444. doi: 10.1099/mic.0.2006/004317-0.


Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes.

Lindsay JA, Moore CE, Day NP, Peacock SJ, Witney AA, Stabler RA, Husain SE, Butcher PD, Hinds J.

J Bacteriol. 2006 Jan;188(2):669-76.


Dissection of ESAT-6 system 1 of Mycobacterium tuberculosis and impact on immunogenicity and virulence.

Brodin P, Majlessi L, Marsollier L, de Jonge MI, Bottai D, Demangel C, Hinds J, Neyrolles O, Butcher PD, Leclerc C, Cole ST, Brosch R.

Infect Immun. 2006 Jan;74(1):88-98.


Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics.

Witney AA, Marsden GL, Holden MT, Stabler RA, Husain SE, Vass JK, Butcher PD, Hinds J, Lindsay JA.

Appl Environ Microbiol. 2005 Nov;71(11):7504-14.


Inactivation of polyketide synthase and related genes results in the loss of complex lipids in Mycobacterium tuberculosis H37Rv.

Waddell SJ, Chung GA, Gibson KJ, Everett MJ, Minnikin DE, Besra GS, Butcher PD.

Lett Appl Microbiol. 2005;40(3):201-6.


DNA microarrays for virus detection in cases of central nervous system infection.

Boriskin YS, Rice PS, Stabler RA, Hinds J, Al-Ghusein H, Vass K, Butcher PD.

J Clin Microbiol. 2004 Dec;42(12):5811-8.


Stationary phase gene expression of Mycobacterium tuberculosis following a progressive nutrient depletion: a model for persistent organisms?

Hampshire T, Soneji S, Bacon J, James BW, Hinds J, Laing K, Stabler RA, Marsh PD, Butcher PD.

Tuberculosis (Edinb). 2004;84(3-4):228-38.


The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis.

Bacon J, James BW, Wernisch L, Williams A, Morley KA, Hatch GJ, Mangan JA, Hinds J, Stoker NG, Butcher PD, Marsh PD.

Tuberculosis (Edinb). 2004;84(3-4):205-17.


Microarrays for Mycobacterium tuberculosis.

Butcher PD.

Tuberculosis (Edinb). 2004;84(3-4):131-7. Review.


Use of genome level-informed PCR as a new investigational approach for analysis of outbreak-associated Mycobacterium tuberculosis isolates.

Rajakumar K, Shafi J, Smith RJ, Stabler RA, Andrew PW, Modha D, Bryant G, Monk P, Hinds J, Butcher PD, Barer MR.

J Clin Microbiol. 2004 May;42(5):1890-6.


Increased transcription of a potential sigma factor regulatory gene Rv1364c in Mycobacterium bovis BCG while residing in macrophages indicates use of alternative promoters.

Li MS, Waddell SJ, Monahan IM, Mangan JA, Martin SL, Everett MJ, Butcher PD.

FEMS Microbiol Lett. 2004 Apr 15;233(2):333-9.


Genetic composition of Mycobacterium bovis BCG substrain Sofia.

Stefanova T, Chouchkova M, Hinds J, Butcher PD, Inwald J, Dale J, Palmer S, Hewinson RG, Gordon SV.

J Clin Microbiol. 2003 Nov;41(11):5349. No abstract available.

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