Walker TM*, Ip CLC*, Harrell RH*, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TEA. Whole-genome sequencing to delineate M. tuberculosis outbreaks: a retrospective observational study. Lancet Inf Dis 2013; 13(2):137-46. doi: 10.1016/S1473-3099(12)70277-3. [PMID: 23158499; PMCID: PMC3556524]

Price JR, Didelot X, Crook DW, Llewelyn MJ, Paul J. Whole genome sequencing in the prevention and control of Staphylococcus aureus infection. J Hosp Infect 2013; 83(1):14-21. [PMID: 23164609]

Dingle KE, Didelot X, Ansari MA, Eyre DW, Vaughan A, Griffiths D, Ip CLC, Batty EM, Golubchik T, Bowden R, Jolley KA, Hood DW, Fawley WN, Walker AS, Peto TEA, Wilcox MH, Crook DW. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large scale whole genome sequencing. J Infect Dis 2013; 207(4):675-86. [PMID: 23204167]

Ammerlaan H, Harbarth S, Rohner P, Herwaldt L, Pottinger J, Hanberger H, Lingaas E, Kuchenbecker R, Pires dos Santos R, Ziesing S, Kola A, Gastmeier P, Fitzpatrick F, Morris-Downes M, Seifert H, Kluytmans J, van Keulen P, Buiting A, Meessen N, Crook DW, Walker AS, Bonten M. Secular trends in nosocomial bloodstream infections: antibiotic-resistant bacteria increase the total burden of infection. Clin Inf Dis 2013; 56(6):798-805. doi: 10.1093/cid/cis1006. [PMID:23223600]

Price JR, Gordon NC, Crook DW, Llewelyn MJ, Paul J. The usefulness of whole genome sequencing in Staphylococcus aureus infection. Clin Microbiol Infect 2013; 19(9) :784-9. [PMID: 23331482]

Dearlove B, Wilson DJ. Coalescent inference for infectious disease: meta-analysis of Hepatitis C. Phil Trans R Soc B 2013;368(1614):20120314. doi: 10.1098/rstb.2012.0314 [PMID: 23382432]

Walker AS, Eyre DW, Crook DW, Wilcox MH, Peto TE. Regarding “Clostridium difficile ribotype does not predict severe infection”. Clin Infect Dis 2013;56(12):1845-6. doi: 10.1093/cid/cit098. [PMID: 23420817]

Walker TM, Monk P, Smith EG, Peto TEA. Contact investigations for outbreaks of M. tuberculosis: advances through whole-genome sequencing. Clin Microbiol Infect 2013 Sep;19(9):796-802. doi: 10.1111/1469-0691.12183. [PMID: 23432709]

Stoesser NE, Martin J, Mawer D, Eyre DW, Walker AS, Peto TE, Crook DW, Wilcox MH. Risk factors for Clostridium difficile acquisition in infants: importance of study design. Clin Infect Dis 2013 Jun;56(11):1680-1. doi: 10.1093/cid/cit089. [PMID:23442761]

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 TEA* on behalf of the Infections in Oxfordshire Research Database (IORD). Relationship between bacterial strain type, host biomarkers and mortality in Clostridium difficile infection. Clin Infect Dis 2013;56(11):1589-600. doi: 10.1093/cid/cit127. [PMID: 23463640]

Eyre DW, Cule ML, Griffiths D, Crook DW, Peto TEA, Walker AS*, Wilson DJ*. Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. PLoS Comput Biol 2013 May;9(5):e1003059. doi: 10.1371/journal.pcbi.1003059. [PMID: 23658511; PMCID: PMC3642043]

Golubchik T, Batty EM, Miller RM, Farr H, Young BC, Larner-Svensson H, Fung R, Godwin H, Knox K, Votintseva A, Everitt RG, Street T, Cule ML, Ip CLC, Didelot X, Peto TEA, Harding RM, Wilson DJ, Crook DW, Bowden R. Within-host evolution of Staphylococcus aureus during asymptomatic carriage. PLoS ONE 2013 May 1;8(5):e61319. doi: 10.1371/journal.pone.0061319. [PMID: 23658690]

Eyre DW, Walker AS, Freeman J, Baines SD, Fawley WN, Chilton CH, Griffiths D, Vaughan A, Crook DW, Peto TEA, Wilcox MH. Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease. PLoS ONE 2013 May 15;8(5):e63540. doi: 10.1371/journal.pone.0063540. [PMID: 23691061]

Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T, Bentley SD, Parkhill J, Dingle KE, Bowler ICJ, Jolley KA, Maiden AM. Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Micro. 2013 Aug;51(8):2526-34. doi: 10.1128/JCM.00066-13. [PMID: 23698529 PMCID: PMC3719633]

Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo Elias C, Johnson JR, Walker AS, Peto TE, Crook DW. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemo 2013;68(10):2234-44. doi: 10.1093/jac/dkt180. [PMID: 23722448; PMCID: PMC3772739]

Batty EM, Wong THN, Trebes A, Argoud K, Attar M, Buck D, Ip CLC, Golubchik T, Cule M, Bowden R, Wilson DJ, Klenerman P, Barnes E, Walker AS, Wyllie DH, Dingle KE, Peto TEA, Crook DW, Piazza P. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS ONE 2013 Jun 10;8(6):e66129. doi: 10.1371/journal.pone. [PMID: 23762474]

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. Differences in outcome according to Clostridium difficile testing method: a prospective multicentre diagnostic validation study of C difficile infection. Lancet Inf Dis 2013 Nov;13(11):936-45. doi: 10.1016/S1473-3099(13)70200-7. [PMID:24007915]

Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O’Connor L, Ip CLC, Golubchik T, Batty EM, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH*, Peto TEA*, Walker AS*. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Eng J Med 2013;26;369(13):1195-205. doi: 10.1056/NEJMoa1216064. [PMID: 24066741; PMCID PMC3868928]

Eyre DW, Fawley WN, Best EL, Griffiths D, Stoesser NE, Crook DW, Peto TEA, Walker AS, Wilcox MH. Comparison of multilocus variable number tandem repeat analysis and whole genome sequencing for investigation of Clostridium difficile transmission. J Clin Micro 2013; 2013 Dec;51(12):4141-9. doi: 10.1128/JCM.01095-13. [PMID: 24108611]

Eyre DW, Walker AS. Clostridium difficile surveillance: harnessing new technologies to control transmission. Expert Rev Anti Infect Ther 2013;11(11):1193–1205. doi: 10.1586/14787210.2013.845987. [PMID: 24151834]

Wong THN, Dearlove BL, Hedge J, Giess PA, Piazza P, Trebes A, Paul J, Smit E, Smith EG, Sutton JK, Wilcox MH, Dingle KE, Peto TEA, Crook DW, Wyllie DH. Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England. Virology J 2013 Nov 13;10:335. doi: 10.1186/1743-422X-10-335.. [PMID: 24220146]

Eyre DW, Griffiths D, Vaughan A, Golubchik T, Acharya M, O’Connor L, Crook DW, Walker AS*, Peto TEA*. Asymptomatic Clostridium difficile colonisation and onward transmission. PLoS ONE 2013; 8(11): e78445. doi:10.1371/journal.pone.0078445. [PMID: 24265690]