Department of Molecular Biology and Biotechnology

Journal articles

• Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N , Harris D et al (2019) Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, 10(1).
• Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M & Hinton JCD (2019) The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid. PLoS Pathogens, 15(9), e1007948.
• Gray K, Green LR, Chaudhuri RR & Shaw JG (2019) Draft Whole-Genome Sequences of 10 Aeromonas Strains from Clinical and Environmental Sources. Microbiology Resource Announcements, 8(30). View this article in WRRO
• Pattrick CA, Webb JP, Green J, Chaudhuri RR, Collins MO & Kelly DJ (2019) Proteomic profiling, transcription factor modeling, and genomics of evolved tolerant strains elucidate mechanisms of vanillin toxicity in Escherichia coli.. mSystems, 4(4). View this article in WRRO
• Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J , Monack DM et al (2019) Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580. PLoS Biology, 17(1). View this article in WRRO
• Vohra P, Chaudhuri RR, Mayho M, Vrettou C, Chintoan-Uta C, Thomson NR, Hope JC, Hopkins J & Stevens MP (2019) Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle. BMC Genomics, 20. View this article in WRRO
• Brockmeier SL, Loving CL, Nicholson TL, Wang J, Peters SE, Weinert L, Chaudhuri R, Seilly DJ, Langford PR, Rycroft A , Wren BW et al (2018) Use of proteins identified through a functional genomic screen to develop a protein subunit vaccine that provides significant protection against virulent Streptococcus suis in pigs. Infection and Immunity, 86(3). View this article in WRRO
• Howell KJ, Weinert LA, Peters SE, Wang J, Hernandez-Garcia J, Chaudhuri RR, Luan S-L, Angen Ø, Aragon V, Williamson SM , Langford PR et al (2017) “Pathotyping” Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence. Journal of Clinical Microbiology, 55(9), 2617-2628. View this article in WRRO
• Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF, Squire D, Cunningham AF, Cole JA, Loman N & Henderson IR (2017) Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain. Microbial Genomics, 3. View this article in WRRO
• Bossé JT, Li Y, Rogers J, Fernandez Crespo R, Li Y, Chaudhuri RR, Holden MTG, Maskell DJ, Tucker AW, Wren BW , Rycroft AN et al (2017) Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae. Frontiers in Microbiology, 8. View this article in WRRO
• Stafford GP, Chaudhuri RR, Haraszthy V, Friedrich V, Schäffer C, Ruscitto A, Honma K & Sharma A (2016) Draft Genome Sequences of Three Clinical Isolates of Tannerella forsythia Isolated from Subgingival Plaque from Periodontitis Patients in the United States: TABLE 1. Genome Announcements, 4(6). View this article in WRRO
• Li Y, Bossé JT, Williamson SM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN & Langford PR (2016) Actinobacillus pleuropneumoniae serovar 8 predominates in England and Wales: TABLE 1:. Veterinary Record, 179, 276-276. View this article in WRRO
• Bossé JT, Li Y, Crespo RF, Chaudhuri RR, Rogers J, Holden MTG, Maskell DJ, Tucker AW, Wren BW, Rycroft AN , Langford PR et al (2016) ICEApl1, an integrative conjugative element related to ICEHin1056, identified in the pig pathogen Actinobacillus pleuropneumoniae. Frontiers in Microbiology, 7:810. View this article in WRRO
• Chen GE, Hitchcock A, Jackson PJ, Chaudhuri RR, Dickman MJ, Hunter CN & Canniffe DP (2016) Two Unrelated 8-Vinyl Reductases Ensure Production of Mature Chlorophylls in Acaryochloris marina. Journal of Bacteriology, 198(9), 1393-1400. View this article in WRRO
• Wielgoss S, Didelot X, Chaudhuri RR, Liu X, Weedall GD, Velicer GJ & Vos M (2016) A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. The ISME Journal, 10, 2468-2477. View this article in WRRO
• Grant AJ, Oshota O, Chaudhuri RR, Mayho M, Peters SE, Clare S, Maskell DJ & Mastroeni P (2016) Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficient gp91 −/− phox Mice. Infection and Immunity, 84(4), 989-997. View this article in WRRO
• Bossé JT, Chaudhuri RR, Li Y, Leanse LG, Fernandez Crespo R, Coupland P, Holden MTG, Bazzolli DM, Maskell DJ, Tucker AW , Wren BW et al (2016) Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae. Genome Announcements, 4(1), e01667-15-e01667-15. View this article in WRRO
• García-Lara J, Weihs F, Ma X, Walker L, Chaudhuri RR, Kasturiarachchi J, Crossley H, Golestanian R & Foster SJ (2015) Supramolecular structure in the membrane of Staphylococcus aureus. Proceedings of the National Academy of Sciences, 112(51), 15725-15730.
• Howell KJ, Peters SE, Wang J, Hernandez-Garcia J, Weinert LA, Luan S-L, Chaudhuri RR, Angen Ø, Aragon V, Williamson SM , Parkhill J et al (2015) Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis. Journal of Clinical Microbiology, 53(12), 3812-3821.
• Bossé JT, Li Y, Atherton TG, Walker S, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Holden MTG, Maskell DJ , Tucker AW et al (2015) Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae. Veterinary Microbiology, 178(3-4), 279-282.
• Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N , Harris D et al (2015) Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, 6(1).
• Bossé JT, Li Y, Walker S, Atherton T, Fernandez Crespo R, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Oshota O , Holden MTG et al (2015) Identification ofdfrA14in two distinct plasmids conferring trimethoprim resistance inActinobacillus pleuropneumoniae. Journal of Antimicrobial Chemotherapy, 70(8), 2217-2222.
• Bossé JT, Li Y, Atherton TG, Walker S, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Holden MTG, Maskell DJ , Tucker AW et al (2015) Corrigendum to ‘Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae’ [Veterinary Microbiology 178 (2015) 279–282]. Veterinary Microbiology, 179(3-4), 341-341.
• Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N , Harris D et al (2015) Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, 6(1). View this article in WRRO
• Smith G, Smith C, Kenny JG, Chaudhuri RR & Ritchie MG (2015) Genome-Wide DNA Methylation Patterns in Wild Samples of Two Morphotypes of Threespine Stickleback (Gasterosteus aculeatus). Molecular Biology and Evolution, 32(4), 888-895.
• Moura AE, Kenny JG, Chaudhuri RR, Hughes MA, Reisinger RR, de Bruyn PJN, Dahlheim ME, Hall N & Hoelzel AR (2015) Phylogenomics of the killer whale indicates ecotype divergence in sympatry. Heredity, 114(1), 48-55.
• Howell KJ, Weinert LA, Chaudhuri RR, Luan S-L, Peters SE, Corander J, Harris D, Angen Ø, Aragon V, Bensaid A , Williamson SM et al (2014) The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis. BMC Genomics, 15(1), 1179-1179. View this article in WRRO
• Moura AE, Kenny JG, Chaudhuri R, Hughes MA, J. Welch A, Reisinger RR, de Bruyn PJN, Dahlheim ME, Hall N & Hoelzel AR (2014) Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift. Molecular Ecology, 23(21), 5179-5192.
• Bosse JT, Li Y, Angen O, Weinert LA, Chaudhuri RR, Holden MT, Williamson SM, Maskell DJ, Tucker AW, Wren BW , Rycroft AN et al (2014) Multiplex PCR Assay for Unequivocal Differentiation of Actinobacillus pleuropneumoniae Serovars 1 to 3, 5 to 8, 10, and 12. Journal of Clinical Microbiology, 52(7), 2380-2385.
• Capeness MJ, Lambert C, Lovering AL, Till R, Uchida K, Chaudhuri R, Alderwick LJ, Lee DJ, Swarbreck D, Liddell S , Aizawa S-I et al (2013) Activity of Bdellovibrio Hit Locus Proteins, Bd0108 and Bd0109, Links Type IVa Pilus Extrusion/Retraction Status to Prey-Independent Growth Signalling. PLOS ONE, 8(11). View this article in WRRO
• Luan S-L, Chaudhuri RR, Peters SE, Mayho M, Weinert LA, Crowther SA, Wang J, Langford PR, Rycroft A, Wren BW , Tucker AW et al (2013) Generation of a Tn5 transposon library in Haemophilus parasuis and analysis by transposon-directed insertion-site sequencing (TraDIS).. Vet Microbiol, 166(3-4), 558-566.
• Howell KJ, Weinert LA, Luan S-L, Peters SE, Chaudhuri RR, Harris D, Angen O, Aragon V, Parkhill J, Langford PR , Rycroft AN et al (2013) Gene content and diversity of the loci encoding biosynthesis of capsular polysaccharides of the 15 serovar reference strains of Haemophilus parasuis.. J Bacteriol, 195(18), 4264-4273.
• Chaudhuri RR, Morgan E, Peters SE, Pleasance SJ, Hudson DL, Davies HM, Wang J, van Diemen PM, Buckley AM, Bowen AJ , Pullinger GD et al (2013) Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals.. PLoS Genet, 9(4), e1003456. View this article in WRRO
• Dziva F, Hauser H, Connor TR, van Diemen PM, Prescott G, Langridge GC, Eckert S, Chaudhuri RR, Ewers C, Mellata M , Mukhopadhyay S et al (2013) 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. Infection and Immunity, 81(3), 838-849.
• Maglennon GA, Cook BS, Matthews D, Deeney AS, Bossé JT, Langford PR, Maskell DJ, Tucker AW, Wren BW & Rycroft AN (2013) Development of a self-replicating plasmid system for Mycoplasma hyopneumoniae. Veterinary Research, 44(1), 63-63.
• Maglennon GA, Cook BS, Deeney AS, Bossé JT, Peters SE, Langford PR, Maskell DJ, Tucker AW, Wren BW & Rycroft AN (2013) Transposon mutagenesis in Mycoplasma hyopneumoniae using a novel mariner-based system for generating random mutations. Veterinary Research, 44(1), 124-124.
• Chaudhuri RR & Henderson IR (2012) The evolution of the Escherichia coli phylogeny.. Infect Genet Evol, 12(2), 214-226.
• Chaudhuri RR, Yu L, Kanji A, Perkins TT, Gardner PP, Choudhary J, Maskell DJ & Grant AJ (2011) Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome.. Microbiology, 157(Pt 10), 2922-2932.
• Clarke DJ, Chaudhuri RR, Martin HM, Campbell BJ, Rhodes JM, Constantinidou C, Pallen MJ, Loman NJ, Cunningham AF, Browning DF & Henderson IR (2011) Complete genome sequence of the crohn's disease-associated adherent-invasive Escherichia coli strain HM605. Journal of Bacteriology, 193(17), 4540-4540.
• Eckert SE, Dziva F, Chaudhuri RR, Langridge GC, Turner DJ, Pickard DJ, Maskell DJ, Thomson NR & Stevens MP (2011) 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. Journal of Bacteriology, 193(7), 1771-1776.
• Knowles TJ, Browning DF, Jeeves M, Maderbocus R, Rajesh S, Sridhar P, Manoli E, Emery D, Sommer U, Spencer A , Leyton DL et al (2011) Structure and function of BamE within the outer membrane and the β-barrel assembly machine.. EMBO Rep, 12(2), 123-128.
• Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL , Savarino SJ et al (2010) A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.. J Bacteriol, 192(21), 5822-5831.
• Wang J, Chaudhuri RR & Ellar DJ (2010) Characterization of ISBth4, a functional new IS231 variant from Bacillus thuringiensis MEX312.. Plasmid, 63(1), 46-52.
• Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM , Frankel G et al (2010) Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.. PLoS One, 5(1), e8801.
• Chaudhuri RR, Allen AG, Owen PJ, Shalom G, Stone K, Harrison M, Burgis TA, Lockyer M, Garcia-Lara J, Foster SJ , Pleasance SJ et al (2009) Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).. BMC Genomics, 10, 291. View this article in WRRO
• Chaudhuri RR, Peters SE, Pleasance SJ, Northen H, Willers C, Paterson GK, Cone DB, Allen AG, Owen PJ, Shalom G , Stekel DJ et al (2009) Comprehensive identification of Salmonella enterica serovar typhimurium genes required for infection of BALB/c mice. PLoS Pathogens, 5(7). View this article in WRRO
• Chaudhuri RR (2009) MycoDB: an online database for comparative genomics of the mycobacteria and related organisms.. Methods Mol Biol, 465, 419-431.
• Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R , Henderson IR et al (2008) The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology, 190(20), 6881-6893.
• Chaudhuri RR, Loman NJ, Snyder LAS, Bailey CM, Stekel DJ & Pallen MJ (2008) xBASE2: a comprehensive resource for comparative bacterial genomics.. Nucleic Acids Res, 36(Database issue), D543-D546.
• Chaudhuri RR, Ren C-P, Desmond L, Vincent GA, Silman NJ, Brehm JK, Elmore MJ, Hudson MJ, Forsman M, Isherwood KE , Gurycová D et al (2007) Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4.. PLoS One, 2(4), e352.
• Turner SM, Chaudhuri RR, Jiang Z-D, DuPont H, Gyles C, Penn CW, Pallen MJ & Henderson IR (2006) Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages.. J Clin Microbiol, 44(12), 4528-4536.
• Nagy G, Danino V, Dobrindt U, Pallen M, Chaudhuri R, Emödy L, Hinton JC & Hacker J (2006) Down-regulation of key virulence factors makes the Salmonella enterica serovar typhimurium rfaH mutant a promising live-attenuated vaccine candidate. Infection and Immunity, 74(10), 5914-5925.
• Ou HY, Chen LL, Lonnen J, Chaudhuri RR, Thani AB, Smith R, Garton NJ, Hinton J, Pallen M, Barer MR & Rajakumar K (2006) A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Research, 34(1).
• Riley M, Abe T, Arnaud MB, Berlyn MKB, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T , Mori H et al (2006) Escherichia coli K-12: A cooperatively developed annotation snapshot - 2005. Nucleic Acids Research, 34(1), 1-9.
• Chaudhuri RR & Pallen MJ (2006) xBASE, a collection of online databases for bacterial comparative genomics.. Nucleic Acids Res, 34(Database issue), D335-D337.
• Ideses D, Gophna U, Paitan Y, Chaudhuri RR, Pallen MJ & Ron EZ (2005) A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis. Journal of Bacteriology, 187(23), 8164-8171.
• Desvaux M, Khan A, Scott-Tucker A, Chaudhuri RR, Pallen MJ & Henderson IR (2005) Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824.. Biochim Biophys Acta, 1745(2), 223-253.
• Parham NJ, Pollard SJ, Chaudhuri RR, Beatson SA, Desvaux M, Russell MA, Ruiz J, Fivian A, Vila J & Henderson IR (2005) Prevalence of pathogenicity island IICFT073 genes among extraintestinal clinical isolates of Escherichia coli.. J Clin Microbiol, 43(5), 2425-2434.
• Pallen MJ, Penn CW & Chaudhuri RR (2005) Bacterial flagellar diversity in the post-genomic era.. Trends Microbiol, 13(4), 143-149.
• Ou HY, Smith R, Lucchini S, Hinton J, Chaudhuri RR, Pallen M, Barer MR & Rajakumar K (2005) ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes. NUCLEIC ACIDS RESEARCH, 33(1).
• Zhang L, Chaudhuri RR, Constantinidou C, Hobman JL, Patel MD, Jones AC, Sarti D, Roe AJ, Vlisidou I, Shaw RK , Falciani F et al (2004) Regulators encoded in the Escherichia coli type III secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic E. coli O157:H7.. Infect Immun, 72(12), 7282-7293.
• Betts HJ, Chaudhuri RR & Pallen MJ (2004) An analysis of type-III secretion gene clusters in Chromobacterium violaceum.. Trends Microbiol, 12(11), 476-482.
• Ren C-P, Chaudhuri RR, Fivian A, Bailey CM, Antonio M, Barnes WM & Pallen MJ (2004) The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition.. J Bacteriol, 186(11), 3547-3560.
• Chaudhuri RR (2004) coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Research, 32(90001), 296d-2299.
• Chaudhuri RR, Khan AM & Pallen MJ (2004) coliBASE: An online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Research, 32(DATABASE ISS.).
• Chaudhuri RR, Khan AM & Pallen MJ (2004) coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.. Nucleic Acids Res, 32(Database issue), D296-D299.
• Pallen MJ, Chaudhuri RR & Henderson IR (2003) Genomic analysis of secretion systems.. Curr Opin Microbiol, 6(5), 519-527.
• Pallen M, Chaudhuri R & Khan A (2002) Bacterial FHA domains: neglected players in the phospho-threonine signalling game?. Trends Microbiol, 10(12), 556-563.
• Sharp PM, Bailes E, Chaudhuri RR, Rodenburg CM, Santiago MO & Hahn BH (2001) The origins of acquired immune deficiency syndrome viruses: Where and when?. Philosophical Transactions of the Royal Society B: Biological Sciences, 356(1410), 867-876.
• Oshota O, Conway M, Fookes M, Schreiber F, Chaudhuri RR, Yu L, Morgan FJE, Clare S, Choudhary J, Thomson NR , Lio P et al () Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice. PLOS ONE, 12(8), e0181365-e0181365. View this article in WRRO
• Wilson R, Bourne C, Chaudhuri RR, Gregory R, Kenny J & Cossins A () Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing. PLoS ONE, 9(6), e100572-e100572. View this article in WRRO
• Christiansen MT, Kaas RS, Chaudhuri RR, Holmes MA, Hasman H & Aarestrup FM () Genome-Wide High-Throughput Screening to Investigate Essential Genes Involved in Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Survival. PLoS ONE, 9(2), e89018-e89018. View this article in WRRO
• Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MTG, Parkhill J, Langford PR, Rycroft AN , Wren BW et al () Whole genome investigation of a divergent clade of the pathogen Streptococcus suis. Frontiers in Microbiology, 6. View this article in WRRO

Chapters

• Bailes E, Chaudhuri RR, Santiago ML, Bibollet-Ruche F, Hahn BH & Sharp PM (2002) The Evolution of Primate Lentiviruses and the Origins of AIDS, The Molecular Epidemiology of Human Viruses (pp. 65-96). Springer US
• Chaudhuri RR & Thomas GH () Understanding the Model and the Menace: a Postgenomic View of Escherichia coli, Bacterial Pathogenomics (pp. 21-48). American Society of Microbiology