2015

Llewelyn M, Hand K, Hopkins S, Walker AS. Antibiotic policies in acute English NHS Trusts; implementation of Start Smart then Focus and relationship with Clostridium difficile infection rates. J Antimicrob Chemo 2015;70(4):1230-5. doi: 10.1093/jac/dku515. [PMID: 25538165]

Stoesser N, Sheppard AE, Shakya M, Sthapit B, Thorson S, Giess A, Kelly D, Pollard AJ, Peto TEA, Walker AS, Crook DW. Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: Insights using wider sampling frames and next generation sequencing. J Antimicrob Chemo 2015; 70(4):1008-15. doi: 10.1093/jac/dku521. [PMID: 25558071]

Mathers AJ*, Stoesser N*, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, Didelot X, Turner SD, Sebra R, Kasarskis A, Peto T, Crook D, Sifri CD. Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing. Antimicrob Agents Chemother 2015;59(3):1656-63. doi: 10.1128/AAC.04292-14. [PMID: 25561339]

Stoesser N, Xayaheuang S, Vongsouvath M, Phommasone K, Elliott I, Del Ojo Elias C, Crook DW, Newton PN, Buisson Y, Lee SJ, Dance DA. Colonization with Enterobacteriaceae producing ESBLs in children attending pre-school childcare facilities in the Lao People’s Democratic Republic. J Antimicrob Chemother 2015; 2015;70(6):1893-7. [PMID: 25681128]

Buchanan R, Stoesser N, Crook D, Bowler IC. Multidrug-resistant Escherichia coli soft tissue infection investigated with bacterial whole genome sequencing. BMJ Case Rep 2014; pii: bcr2014207200. doi: 10.1136/bcr-2014-207200. [PMID: 25331151]

Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comp Biol 2015 11: e1004041. doi: 10.1371/journal.pcbi.1004041. [PMID: 25675341]

Eyre DW*, Tracey L*, Elliott B, Slimings C, Huntington P, Kotsanas D, Stuart R, Korman T, Kotsiou G, McCann R, Griffiths D, Fawley WN, Armstrong P, Dingle KE, Walker AS, Peto TEA, Crook DW, Wilcox MH, Riley TV. Emergence and spread of predominantly community-onset Clostridium difficile PCR ribotype 244 infection in Australia, 2010 to 2012. Eurosurveillance 2015;20(10):pii=21059. [PMID: 25788254]

Wyllie D, Davies J. Role of data warehousing in healthcare epidemiology. J Hosp Infect 2015; doi 10.1016/j.jhin.2015.01.005. [PMID: 25737091]

Votintseva A, Pankhurst L, Anson L, Morgan M, Walker T, Gascoyne-Binzi D, Quan T, Wyllie D, Wilcox MH, Walker AS, Peto TEA, Crook DW. Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) culture. J Clin Micro 2015; 53(4):1137-43. doi: 10.1128/JCM.03073-14. [PMID: 25631807]

Buchanan J, Wordsworth S, O’Connor L, Pike G, Walker AS, Wilcox MH, Crook DW. Management of patients with suspected infectious diarrhoea in hospitals in England. J Hosp Inf 2015;90(3):199-207. doi: 10.1016/j.jhin.2014.12.021. [PMID: 25997802]

Tonkin-Crine S, Walker AS, Butler C. Contribution of behavioural science to antimicrobial stewardship. BMJ 2015;350:h3413. doi: 10.1136/bmj.h3413. [PMID: 26111947]

Stoesser N, Sheppard A, Moore C, Golubchik T, Parry C, Nget P, Saroeun M, Day N, Giess A, Johnson J, Peto T, Crook D, Walker AS and Modernising Medical Microbiology (MMM) Informatics Group. Extensive within-host diversity in fecally carried extended-spectrum beta-lactamase-producing Escherichia coli: implications for transmission analyses. J Clin Micro 2015; 2015;53(7):2122-31. doi: 10.1128/JCM.00378-15. [PMID: 25903575]

Knox K. Women should be able to get antibiotics for urinary tract infection without a prescription. BMJ 2015;351:h3441. doi: 10.1136/bmj.h3441. [PMID: 26173946]

Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ, Clifton DA, Kapatai G, Ip CL, Bowden R, Drobniewski FA, Allix-Béguec C, Gaudin C, Parkhill J, Diel R, Supply P, Crook DW, Smith EG, Walker AS, Ismail N, Niemann S, Peto TE; Modernizing Medical Microbiology (MMM) Informatics Group. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. Lancet Infect Dis 2015. pii: S1473-3099(15)00062-6. doi: 10.1016/S1473-3099(15)00062-6. [PMID: 26116186]

Wrightson JM, Wray JA, Street TL, Chapman SJ, Gleeson FV, Maskell NA, Peto TE, Rahman NW, Crook DW. Absence of Atypical Pathogens in Pleural Infection Chest 2015;148(3):e102-3. doi: 10.1378/chest.15-1130. (correspondance) [PMID: 26324137]

Laabei M, Uhlemann AC, Lowy FD, Austin ED, Yokoyama M, Ouadi K, Feil E, Thorpe HA, Williams B, Perkins M, Peacock SJ, Clarke SR, Dordel J, Holden M, Votintseva AA, Bowden R, Crook DW, Young BC, Wilson DJ*, Recker M*, Massey RC*. Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus. PLoS Biol 2015;13(9):e1002229. doi: 10.1371/journal.pbio.1002229.[PMID: 26331877 PMCID:PMC4558032]

De Maio N, Wu CH, O’Reilly KM, Wilson D.New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation. PLoS Genet 2015;11(8):e1005421. doi: 10.1371/journal.pgen.1005421.[PMID: 26267488 PMCID: PMC4534465]

Bradley P, Gordon C, Walker T, Dunn L, Earle S, Heys S, Huang B, Pankhurst L, Anson L, deCesare M, Votintseva A, Wilson D, Wyllie D, Niemann S, Feuerriegel S, Kohl T, Ismail N, Valley Omar S, Smith EG, Buck D, McVean G, Walker AS, Peto TEA, Crook D, Iqbal Z. Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis. Nature Communications, 2015: 6: 10063; doi: 10.1038/ncomms10063 [PMID: 26686880]

Cody AJ, McCathy ND, Bray JE, Wimalarathna HM, Colles FM, Jansen van Rensburg MJ, Dingle KE, Waldenstrom J, Maiden MC. Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom. Environ. Microbiolo Rep. 2015 Oct 7;(5):782-8. doi: 10.1111/1758-2229.12314. Epub 2015 Sep 8. [PMID: 26109474, PMCID: PMC4755149]