April 2013 – March 2014

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study. Walker TM, Lalor MK, Broda A, Ortega LS, Morgan M, Parker L, Churchill S, Bennett K, Golubchik T, Giess AP, Del Ojo Elias C, Jeffery KJ, Bowler IC, Laurenson IF, Barrett A, Drobniewski F, McCarthy ND, Anderson LF, Abubakar I, Thomas HL, Monk P, Smith EG, Walker AS, Crook DW, Peto TE, Conlon CP. The lancet. Respiratory medicine. [2014 Apr;2(4):285-92]

Asymptomatic Clostridium difficile colonisation and onward transmission. Eyre DW, Griffiths D, Vaughan A, Golubchik T, Acharya M, O'Connor L, Crook DW, Walker AS, Peto TE. PloS one. [2013;8(11):e78445]

Coalescent inference for infectious disease: meta-analysis of hepatitis C. Dearlove B, Wilson DJ [2013 Feb 4;368(1614):20120314]

The usefulness of whole genome sequencing in Staphylococcus aureus infection. Price JR, Gordon NC, Crook DW, Llewelyn MJ, Paul J [2013 Sep;19(9):784-9]

Clostridium difficile surveillance: harnessing new technologies to control transmission. Eyre DW, Walker AS [2013 Nov;11(11):1193-205]

Inference of the properties of the recombination process from whole bacterial genomes. Ansari MA, Didelot X [2014 Jan;196(1):253-65]

Prevalence of Staphylococcus aureus protein A (spa) mutants in the community and hospitals in Oxfordshire. Votintseva AA, Fung R, Miller RR, Knox K, Godwin H, Wyllie DH, Bowden R, Crook DW, Walker AS. BMC microbiology. [2014 Mar 12;14:63]

Multiple-strain colonization in nasal carriers of Staphylococcus aureus. Votintseva AA, Miller RR, Fung R, Knox K, Godwin H, Peto TE, Crook DW, Bowden R, Walker AS. Journal of clinical microbiology. [2014 Apr;52(4):1192-200]

Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. Gordon NC, Price JR, Cole K, Everitt R, Morgan M, Finney J, Kearns AM, Pichon B, Young B, Wilson DJ, Llewelyn MJ, Paul J, Peto TE, Crook DW, Walker AS, Golubchik T. Journal of clinical microbiology. [2014 Apr;52(4):1182-91]

Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone. Miller RM, Price JR, Batty EM, Didelot X, Wyllie D, Golubchik T, Crook DW, Paul J, Peto TE, Wilson DJ, Cule M, Ip CL, Day NP, Moore CE, Bowden R, Llewelyn MJ. The Journal of hospital infection. [2014 Feb;86(2):83-9]

Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit. Price JR, Golubchik T, Cole K, Wilson DJ, Crook DW, Thwaites GE, Bowden R, Walker AS, Peto TE, Paul J, Llewelyn MJ. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. [2014 Mar;58(5):609-18]

Evolutionary history of the Clostridium difficile pathogenicity locus. Dingle KE, Elliott B, Robinson E, Griffiths D, Eyre DW, Stoesser N, Vaughan A, Golubchik T, Fawley WN, Wilcox MH, Peto TE, Walker AS, Riley TV, Crook DW, Didelot X. Genome biology and evolution. [2014 Jan;6(1):36-52]

Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England. Wong TH, Dearlove BL, Hedge J, Giess AP, Piazza P, Trebes A, Paul J, Smit E, Smith EG, Sutton JK, Wilcox MH, Dingle KE, Peto TE, Crook DW, Wilson DJ, Wyllie DH. Virology journal. [2013 Nov 13;10:335]

Whole-genome sequencing demonstrates that fidaxomicin is superior to vancomycin for preventing reinfection and relapse of infection with Clostridium difficile. Eyre DW, Babakhani F, Griffiths D, Seddon J, Del Ojo Elias C, Gorbach SL, Peto TE, Crook DW, Walker AS. The Journal of infectious diseases. [2014 May 1;209(9):1446-51]

Comparison of multilocus variable-number tandem-repeat analysis and whole-genome sequencing for investigation of Clostridium difficile transmission. Eyre DW, Fawley WN, Best EL, Griffiths D, Stoesser NE, Crook DW, Peto TE, Walker AS, Wilcox MH. Journal of clinical microbiology. [2013 Dec;51(12):4141-9]

Diverse sources of C. difficile infection identified on whole-genome sequencing. Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O'Connor L, Ip CL, Golubchik T, Batty EM, Finney JM, Wyllie DH, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH, Peto TE, Walker AS. The New England journal of medicine. [2013 Sep 26;369(13):1195-205]

Differences in outcome according to Clostridium difficile testing method: a prospective multicentre diagnostic validation study of C difficile infection. Planche TD, Davies KA, Coen PG, Finney JM, Monahan IM, Morris KA, O'Connor L, Oakley SJ, Pope CF, Wren MW, Shetty NP, Crook DW, Wilcox MH. The Lancet infectious diseases. [2013 Nov;13(11):936-45]

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo Elias C, Johnson JR, Walker AS, Peto TE, Crook DW. The Journal of antimicrobial chemotherapy. [2013 Oct;68(10):2234-44]

Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. Eyre DW, Cule ML, Griffiths D, Crook DW, Peto TE, Walker AS, Wilson DJ. PLoS computational biology. [2013;9(5):e1003059]

Relationship between bacterial strain type, host biomarkers, and mortality in Clostridium difficile infection. Walker AS, Eyre DW, Wyllie DH, Dingle KE, Griffiths D, Shine B, Oakley S, O'Connor L, Finney J, Vaughan A, Crook DW, Wilcox MH, Peto TE, Infections in Oxfordshire Research Database. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. [2013 Jun;56(11):1589-600]

Risk factors for Clostridium difficile acquisition in infants: importance of study design. Stoesser NE, Martin J, Mawer D, Eyre DW, Walker AS, Peto TE, Crook DW, Wilcox MH. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. [2013 Jun;56(11):1680-1]

Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. Walker TM, Monk P, Smith EG, Peto TE. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. [2013 Sep;19(9):796-802]

Regarding "Clostridium difficile ribotype does not predict severe infection". Walker AS, Eyre DW, Crook DW, Wilcox MH, Peto TE. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. [2013 Jun;56(12):1845-6]