2014

Ansari MA, Didelot X. Inference of the properties of the recombination process from whole bacterial genomes. Genetics 2014 Jan;196(1):253-65. doi: 10.1534/genetics.113.157172. [PMID: 24172133]

Eyre DW, Babakhani F, Griffiths D, Seddon J, Peto TEA, Crook DW, Walker AS. Whole genome sequencing demonstrates fidaxomicin is superior to vancomycin for preventing reinfection and relapse of infection with Clostridium difficile. J Infect Dis 2014 May 1;209(9):1446-51. doi: 10.1093/infdis/jit598. [PMID: 24218500]

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. Evolutionary history of the Clostridium difficile pathogenicity locus. Genome biology and evolution 2014 Jan;6(1):36-52. doi: 10.1093/gbe/evt204. [PMID: 24336451]

Price JR, Golubchik T, Cole K, Wilson DJ, Crook DW, Bowden R, Walker AS, Peto TEA, Paul J, Llewelyn MJ. Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit. Clin Infect Dis 2014 Mar;58(5):609-18. [PMID: 24336829; PMCID: PMC3922217]

Miller R*, Walker AS*, Godwin H, Fung R, Votintseva A, Bowden R, Mant D, Peto TEA, Crook DW**, Knox K**. Dynamics of acquisition and loss of Staphylococcus aureus strains in the community: a cohort study. J Infect 2014 May;68(5):426-39. doi: 10.1016/j.jinf.2013.12.013. [PMID: 24393651]

Miller RM*, Price J*, Batty EM, Didelot X, Wyllie DH, Golubchik T, Crook DW, Paul J, Peto TEA, Wilson DJ, Cule M, Ip CLC, Day NPJ, Moore CE, Llewelyn MJ, Bowden R. Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone. J Hosp Infect 2014 Feb;86(2):83-9. doi: 10.1016/j.jhin.2013.11.007. [PMID: 24433924]

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. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Micro 2014 Apr;52(4):1182-91. doi: 10.1128/JCM.03117-13. [PMID: 24501024; PMCID: PMC3993491]

Votintseva AA, Miller RR, Fung R, Knox K, Godwin H, Peto TE, Crook DW, Bowden R, Walker AS. Multiple-strain colonization in nasal carriers of Staphylococcus aureus. J Clinical Micro 2014 Apr;52(4):1192-200. doi: 10.1128/JCM.03254-13. [PMID: 24501033]

Votintseva AA, Fung R, Miller RR, Knox K, Godwin H, Wyllie DH, Bowden R, Crook DW, Walker AS. Prevalence of Staphylococcus aureus protein A (spa) mutants in the community and hospitals in Oxfordshire. BMC Microbiology 2014 Mar 12;14:63. doi: 10.1186/1471-2180-14-63. [PMID: 24621342]

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. Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study. Lancet Respiratory Medicine 2014 Apr;2(4):285-92. doi: 10.1016/S2213-2600(14)70027-X. [PMID: 24717625]

Price JR, Golubchik T, Wilson DJ, Crook DW, Walker AS, Peto TE, Paul J, Llewelyn MJ. Reply to Mills and Linkin. Clin Infect Dis 2014 Sep 1;59(5):752-3. doi: 10.1093/cid/ciu370. [PMID: 24850802]

Everitt RG, Didelot X, Batty EM, Miller RR, Knox K, Young BC, Bowden R, Auton A, Votintseva A, Charlesworth J, Golubchik T, Ip CLC, Godwin H, Fung R, Peto TEA, Walker AS, Crook DW, Wilson DJ. Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus. Nature Communications 2014; 5:3956. doi: 10.1038/ncomms4956. [PMID: 24853639; PMCID: PMC4036114]

Stoesser N*, Giess A*, Batty EM, Sheppard AE, Walker AS, Wilson DJ, Didelot X, Bashir A, Sebra R, Kasarskis A, Sthapit B, Shakya M, Kelly D, Pollard AJ, Peto TEA, Crook DW, Donnelly P, Thorson S, Amatya P, Shrestha S. Genome sequencing of an extended series of NDM-Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting. Antimicro Agents Chemo 2014 Dec;58(12):7347-57. doi: 10.1128/AAC.03900-14. [PMID: 25267672; PMCID: PMC4249533]

Moore CE, Paul J, Foster D, Mahar S, Griffiths D, Knox K, Peto TEA, Walker AS*, Crook DW* on behalf of the Oxford Invasive Pneumococcal Surveillance Group. Reduction of invasive pneumococcal disease three years after the introduction of the 13 valent conjugate vaccine in the Oxfordshire region, England. J Infect Dis 2014;210:1001-11. doi: 10.1093/infdis/jiu213. [PMID: 24719477]

Pankhurst L, Macfarlane-Smith L, Buchanan J, Anson L, Davies K, O’Connor L, Ashwin H, Pike G, Dingle KE, Peto TEA, Wordsworth S, Walker AS*, Wilcox MH*, Crook DW*. Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study. Health Technol Assess 2014;18(53). doi: 10.3310/hta18530. [PMID: 25146932, PMCID: PMC4781491]

Hedge J, Wilson DJ. Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not. MBio 2014 Nov 25;5(6). pii: e02158-14. doi: 10.1128/mBio.02158-14. [PMID: 25425237, PMCID: PMC4251999]

Elliott B, Dingle KE, Didelot X, Crook DW, Riley TV. The complexity and diversity of the pathogenicity locus in Clostridium difficile clade 5. Genome Biol Evol 2014 Nov 8;6(12): 3159-70 doi: 10.1093/gbe/evu248 [PMID: 25381663, PMCID: PMC4986448]