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Items: 1 to 50 of 60

1.

The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid.

Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M, Hinton JCD.

PLoS Pathog. 2019 Sep 27;15(9):e1007948. doi: 10.1371/journal.ppat.1007948. eCollection 2019 Sep.

2.

Draft Whole-Genome Sequences of 10 Aeromonas Strains from Clinical and Environmental Sources.

Gray K, Green LR, Chaudhuri RR, Shaw JG.

Microbiol Resour Announc. 2019 Jul 25;8(30). pii: e00170-19. doi: 10.1128/MRA.00170-19.

3.

Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli.

Pattrick CA, Webb JP, Green J, Chaudhuri RR, Collins MO, Kelly DJ.

mSystems. 2019 Jun 11;4(4). pii: e00163-19. doi: 10.1128/mSystems.00163-19.

4.

Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580.

Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J, Monack DM, Kingsley RA, Brownridge P, Chaudhuri RR, Rowe WPM, Predeus AV, Hokamp K, Gordon MA, Hinton JCD.

PLoS Biol. 2019 Jan 15;17(1):e3000059. doi: 10.1371/journal.pbio.3000059. eCollection 2019 Jan.

5.

Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle.

Vohra P, Chaudhuri RR, Mayho M, Vrettou C, Chintoan-Uta C, Thomson NR, Hope JC, Hopkins J, Stevens MP.

BMC Genomics. 2019 Jan 8;20(1):20. doi: 10.1186/s12864-018-5319-0.

6.

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.

7.

Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain.

Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF, Squire D, Cunningham AF, Cole JA, Loman N, Henderson IR.

Microb Genom. 2017 Mar 23;3(3):mgen000106. doi: 10.1099/mgen.0.000106. eCollection 2017 Mar.

8.

"Pathotyping" Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence.

Howell KJ, Weinert LA, Peters SE, Wang J, Hernandez-Garcia J, Chaudhuri RR, Luan SL, Angen Ø, Aragon V, Williamson SM, Langford PR, Rycroft AN, Wren BW, Maskell DJ, Tucker AW.

J Clin Microbiol. 2017 Sep;55(9):2617-2628. doi: 10.1128/JCM.02464-16. Epub 2017 Jun 14.

9.

Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae.

Bossé JT, Li Y, Rogers J, Fernandez Crespo R, Li Y, Chaudhuri RR, Holden MT, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR.

Front Microbiol. 2017 Mar 6;8:311. doi: 10.3389/fmicb.2017.00311. eCollection 2017.

10.

Draft Genome Sequences of Three Clinical Isolates of Tannerella forsythia Isolated from Subgingival Plaque from Periodontitis Patients in the United States.

Stafford GP, Chaudhuri RR, Haraszthy V, Friedrich V, Schäffer C, Ruscitto A, Honma K, Sharma A.

Genome Announc. 2016 Dec 1;4(6). pii: e01286-16. doi: 10.1128/genomeA.01286-16.

11.

ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae.

Bossé JT, Li Y, Fernandez Crespo R, Chaudhuri RR, Rogers J, Holden MT, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR; the BRaDP1T Consortium.

Front Microbiol. 2016 Jun 15;7:810. doi: 10.3389/fmicb.2016.00810. eCollection 2016.

12.

A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus.

Wielgoss S, Didelot X, Chaudhuri RR, Liu X, Weedall GD, Velicer GJ, Vos M.

ISME J. 2016 Oct;10(10):2468-77. doi: 10.1038/ismej.2016.34. Epub 2016 Apr 5.

13.

Two Unrelated 8-Vinyl Reductases Ensure Production of Mature Chlorophylls in Acaryochloris marina.

Chen GE, Hitchcock A, Jackson PJ, Chaudhuri RR, Dickman MJ, Hunter CN, Canniffe DP.

J Bacteriol. 2016 Apr 14;198(9):1393-400. doi: 10.1128/JB.00925-15. Print 2016 May.

14.

Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae.

Bossé JT, Chaudhuri RR, Li Y, Leanse LG, Fernandez Crespo R, Coupland P, Holden MT, Bazzolli DM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR.

Genome Announc. 2016 Jan 28;4(1). pii: e01667-15. doi: 10.1128/genomeA.01667-15.

15.

Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficient gp91-/- phox Mice.

Grant AJ, Oshota O, Chaudhuri RR, Mayho M, Peters SE, Clare S, Maskell DJ, Mastroeni P.

Infect Immun. 2016 Mar 24;84(4):989-997. doi: 10.1128/IAI.01423-15. Print 2016 Apr.

16.

Supramolecular structure in the membrane of Staphylococcus aureus.

García-Lara J, Weihs F, Ma X, Walker L, Chaudhuri RR, Kasturiarachchi J, Crossley H, Golestanian R, Foster SJ.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):15725-30. doi: 10.1073/pnas.1509557112. Epub 2015 Dec 7.

17.

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.

Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MT, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ.

Front Microbiol. 2015 Nov 4;6:1191. doi: 10.3389/fmicb.2015.01191. eCollection 2015.

18.

Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis.

Howell KJ, Peters SE, Wang J, Hernandez-Garcia J, Weinert LA, Luan SL, Chaudhuri RR, Angen Ø, Aragon V, Williamson SM, Parkhill J, Langford PR, Rycroft AN, Wren BW, Maskell DJ, Tucker AW; BRaDP1T Consortium.

J Clin Microbiol. 2015 Dec;53(12):3812-21. doi: 10.1128/JCM.01991-15. Epub 2015 Sep 30.

19.

Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae.

Bossé JT, Li Y, Atherton TG, Walker S, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Holden MT, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR; BRaDP1T consortium.

Vet Microbiol. 2015 Aug 5;178(3-4):279-82. doi: 10.1016/j.vetmic.2015.05.020. Epub 2015 May 28. Erratum in: Vet Microbiol. 2015 Sep 30;179(3-4):341. BRaDP1T consortium [added].

20.

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N, Harris D, Chieu TT, Chau NV, Campbell J, Schultsz C, Parkhill J, Bentley SD, Langford PR, Rycroft AN, Wren BW, Farrar J, Baker S, Hoa NT, Holden MT, Tucker AW, Maskell DJ; BRaDP1T Consortium.

Nat Commun. 2015 May 12;6:7272. doi: 10.1038/ncomms8272. No abstract available.

21.

Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae.

Bossé JT, Li Y, Walker S, Atherton T, Fernandez Crespo R, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Oshota O, Holden MT, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR; BRaDP1T Consortium.

J Antimicrob Chemother. 2015 Aug;70(8):2217-22. doi: 10.1093/jac/dkv121. Epub 2015 May 8.

22.

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N, Harris D, Chieu TT, Van Vinh Chau N, Campbell J, Schultsz C, Parkhill J, Bentley SD, Langford PR, Rycroft AN, Wren BW, Farrar J, Baker S, Hoa NT, Holden MT, Tucker AW, Maskell DJ; BRaDP1T Consortium.

Nat Commun. 2015 Mar 31;6:6740. doi: 10.1038/ncomms7740. Erratum in: Nat Commun. 2015;6:7272.

23.

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis.

Howell KJ, Weinert LA, Chaudhuri RR, Luan SL, Peters SE, Corander J, Harris D, Angen Ø, Aragon V, Bensaid A, Williamson SM, Parkhill J, Langford PR, Rycroft AN, Wren BW, Holden MT, Tucker AW, Maskell DJ; BRADP1T Consortium.

BMC Genomics. 2014 Dec 24;15:1179. doi: 10.1186/1471-2164-15-1179.

24.

Genome-wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus).

Smith G, Smith C, Kenny JG, Chaudhuri RR, Ritchie MG.

Mol Biol Evol. 2015 Apr;32(4):888-95. doi: 10.1093/molbev/msu344. Epub 2014 Dec 21.

PMID:
25534027
25.

Phylogenomics of the killer whale indicates ecotype divergence in sympatry.

Moura AE, Kenny JG, Chaudhuri RR, Hughes MA, Reisinger RR, de Bruyn PJ, Dahlheim ME, Hall N, Hoelzel AR.

Heredity (Edinb). 2015 Jan;114(1):48-55. doi: 10.1038/hdy.2014.67. Epub 2014 Jul 23.

26.

Single-step selection of bivalent aptamers validated by comparison with SELEX using high-throughput sequencing.

Wilson R, Bourne C, Chaudhuri RR, Gregory R, Kenny J, Cossins A.

PLoS One. 2014 Jun 25;9(6):e100572. doi: 10.1371/journal.pone.0100572. eCollection 2014.

27.

Multiplex PCR assay for unequivocal differentiation of Actinobacillus pleuropneumoniae serovars 1 to 3, 5 to 8, 10, and 12.

Bossé JT, Li Y, Angen Ø, Weinert LA, Chaudhuri RR, Holden MT, Williamson SM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR; BRaDP1T consortium.

J Clin Microbiol. 2014 Jul;52(7):2380-5. doi: 10.1128/JCM.00685-14. Epub 2014 Apr 23.

28.

Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival.

Christiansen MT, Kaas RS, Chaudhuri RR, Holmes MA, Hasman H, Aarestrup FM.

PLoS One. 2014 Feb 12;9(2):e89018. doi: 10.1371/journal.pone.0089018. eCollection 2014.

29.

Generation of a Tn5 transposon library in Haemophilus parasuis and analysis by transposon-directed insertion-site sequencing (TraDIS).

Luan SL, Chaudhuri RR, Peters SE, Mayho M, Weinert LA, Crowther SA, Wang J, Langford PR, Rycroft A, Wren BW, Tucker AW, Maskell DJ; BRaDP1T Consortium.

Vet Microbiol. 2013 Oct 25;166(3-4):558-66. doi: 10.1016/j.vetmic.2013.07.008. Epub 2013 Jul 20.

PMID:
23928120
30.

Gene content and diversity of the loci encoding biosynthesis of capsular polysaccharides of the 15 serovar reference strains of Haemophilus parasuis.

Howell KJ, Weinert LA, Luan SL, Peters SE, Chaudhuri RR, Harris D, Angen O, Aragon V, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ; BRaDP1T Consortium.

J Bacteriol. 2013 Sep;195(18):4264-73. doi: 10.1128/JB.00471-13. Epub 2013 Jul 19.

31.

Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals.

Chaudhuri RR, Morgan E, Peters SE, Pleasance SJ, Hudson DL, Davies HM, Wang J, van Diemen PM, Buckley AM, Bowen AJ, Pullinger GD, Turner DJ, Langridge GC, Turner AK, Parkhill J, Charles IG, Maskell DJ, Stevens MP.

PLoS Genet. 2013 Apr;9(4):e1003456. doi: 10.1371/journal.pgen.1003456. Epub 2013 Apr 18.

32.

Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms.

Dziva F, Hauser H, Connor TR, van Diemen PM, Prescott G, Langridge GC, Eckert S, Chaudhuri RR, Ewers C, Mellata M, Mukhopadhyay S, Curtiss R 3rd, Dougan G, Wieler LH, Thomson NR, Pickard DJ, Stevens MP.

Infect Immun. 2013 Mar;81(3):838-49. doi: 10.1128/IAI.00585-12. Epub 2012 Dec 28.

33.

The evolution of the Escherichia coli phylogeny.

Chaudhuri RR, Henderson IR.

Infect Genet Evol. 2012 Mar;12(2):214-26. doi: 10.1016/j.meegid.2012.01.005. Epub 2012 Jan 14. Review.

PMID:
22266241
34.

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome.

Chaudhuri RR, Yu L, Kanji A, Perkins TT, Gardner PP, Choudhary J, Maskell DJ, Grant AJ.

Microbiology. 2011 Oct;157(Pt 10):2922-32. doi: 10.1099/mic.0.050278-0. Epub 2011 Aug 4.

35.

Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605.

Clarke DJ, Chaudhuri RR, Martin HM, Campbell BJ, Rhodes JM, Constantinidou C, Pallen MJ, Loman NJ, Cunningham AF, Browning DF, Henderson IR.

J Bacteriol. 2011 Sep;193(17):4540. doi: 10.1128/JB.05374-11. Epub 2011 Jun 24.

36.

Retrospective application of transposon-directed insertion site sequencing to a library of signature-tagged mini-Tn5Km2 mutants of Escherichia coli O157:H7 screened in cattle.

Eckert SE, Dziva F, Chaudhuri RR, Langridge GC, Turner DJ, Pickard DJ, Maskell DJ, Thomson NR, Stevens MP.

J Bacteriol. 2011 Apr;193(7):1771-6. doi: 10.1128/JB.01292-10. Epub 2011 Jan 28.

37.

Structure and function of BamE within the outer membrane and the β-barrel assembly machine.

Knowles TJ, Browning DF, Jeeves M, Maderbocus R, Rajesh S, Sridhar P, Manoli E, Emery D, Sommer U, Spencer A, Leyton DL, Squire D, Chaudhuri RR, Viant MR, Cunningham AF, Henderson IR, Overduin M.

EMBO Rep. 2011 Feb;12(2):123-8. doi: 10.1038/embor.2010.202. Epub 2011 Jan 7.

38.

A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.

Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL, Savarino SJ, Turner SM, Pallen MJ, Penn CW, Parkhill J, Turner AK, Johnson TJ, Thomson NR, Smith SG, Henderson IR.

J Bacteriol. 2010 Nov;192(21):5822-31. doi: 10.1128/JB.00710-10. Epub 2010 Aug 27.

39.

Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.

Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM, Frankel G, Tang CM, Dudley EG, Roberts IS, Rasko DA, Pallen MJ, Parkhill J, Nataro JP, Thomson NR, Henderson IR.

PLoS One. 2010 Jan 20;5(1):e8801. doi: 10.1371/journal.pone.0008801.

40.

Characterization of ISBth4, a functional new IS231 variant from Bacillus thuringiensis MEX312.

Wang J, Chaudhuri RR, Ellar DJ.

Plasmid. 2010 Jan;63(1):46-52. doi: 10.1016/j.plasmid.2009.10.002. Epub 2009 Oct 29.

PMID:
19879290
41.

Comprehensive identification of Salmonella enterica serovar typhimurium genes required for infection of BALB/c mice.

Chaudhuri RR, Peters SE, Pleasance SJ, Northen H, Willers C, Paterson GK, Cone DB, Allen AG, Owen PJ, Shalom G, Stekel DJ, Charles IG, Maskell DJ.

PLoS Pathog. 2009 Jul;5(7):e1000529. doi: 10.1371/journal.ppat.1000529. Epub 2009 Jul 31.

42.

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).

Chaudhuri RR, Allen AG, Owen PJ, Shalom G, Stone K, Harrison M, Burgis TA, Lockyer M, Garcia-Lara J, Foster SJ, Pleasance SJ, Peters SE, Maskell DJ, Charles IG.

BMC Genomics. 2009 Jul 1;10:291. doi: 10.1186/1471-2164-10-291.

43.

MycoDB: an online database for comparative genomics of the mycobacteria and related organisms.

Chaudhuri RR.

Methods Mol Biol. 2009;465:419-31. doi: 10.1007/978-1-59745-207-6_27.

PMID:
20560061
44.

xBASE2: a comprehensive resource for comparative bacterial genomics.

Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D543-6. Epub 2007 Nov 5.

45.

Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4.

Chaudhuri RR, Ren CP, Desmond L, Vincent GA, Silman NJ, Brehm JK, Elmore MJ, Hudson MJ, Forsman M, Isherwood KE, Gurycová D, Minton NP, Titball RW, Pallen MJ, Vipond R.

PLoS One. 2007 Apr 4;2(4):e352.

46.

Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages.

Turner SM, Chaudhuri RR, Jiang ZD, DuPont H, Gyles C, Penn CW, Pallen MJ, Henderson IR.

J Clin Microbiol. 2006 Dec;44(12):4528-36. Epub 2006 Oct 18.

47.

A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria.

Ou HY, Chen LL, Lonnen J, Chaudhuri RR, Thani AB, Smith R, Garton NJ, Hinton J, Pallen M, Barer MR, Rajakumar K.

Nucleic Acids Res. 2006 Jan 9;34(1):e3.

48.

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.

Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL.

Nucleic Acids Res. 2006 Jan 5;34(1):1-9. Print 2006.

49.

xBASE, a collection of online databases for bacterial comparative genomics.

Chaudhuri RR, Pallen MJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D335-7.

50.

A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis.

Ideses D, Gophna U, Paitan Y, Chaudhuri RR, Pallen MJ, Ron EZ.

J Bacteriol. 2005 Dec;187(23):8164-71.

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