Price JR, Cole K, Bexley A, Kostiou V, Eyre DW, Golubchik T, Wilson DJ, Crook DW, Walker AS, Peto TEA, Llewelyn MJ, Paul J. Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing. Lancet Infect Dis 2017; 2017 Feb;17(2):207-214.DOI: 10.1016/S1473-3099(16)30413-3 [PMID: 27863959 PMCID: PMC5266793]

Chand M, Lamagni T, Kranzer K, Hedge J, Moore G, Parks S, Collins S, Del Ojo Elias C, Admed N, Brown T, Smith EG, Hoffman P, Kirwan P, Mason B, Smith-Palmer A, Veal P, Lalor MK, Bennett A, Walker J, Yeap A, Isidro Carrion MA, Dolan G, Bhatt S, Skingsley A, Charlett A, Pearce D, Russell K, Kendall S, Klein AA, Robins S, Schelenz S, Newsholme W, Thomas S, Collyns T, Davies E, McMenamin J, Doherty L, Peto TE, Crook D, Zambon M, Phin N. 2016. Insidious risk of severe Mycobacterium chimaera infection in cardiac surgery patients. Clin Infect Dis 2017 Feb 1;64(3):335-34DOI: 10.1093/cid/ciw754 [PMID: 2797870, PMCID: PMC4879409]

Mathers AJ, Stoesser N, Chai W, Carroll J, Barry K, Cherunvanky A, Sebra R, Kasarskis A, Peto TE, Walker AS, Sifri CD, Crook DW, Sheppard AE. 2016. Chromosomal integration of blaKPC in Klebsiella species: elusive but not rare. Antimicro Agents Chemo. 2017 Feb 23;61(3). pii: e01823-16. doi: 10.1128/AAC.01823-16. Print 2017 Mar.. doi: 10.11. 28/AAC.01823-16 [PMID: 28031204]

Dingle KE*, Didelot X*, Quan P*, Eyre DW, Stoesser N, Golubchik T, Harding RM, Wilson DJ, Griffiths D, Vaughan A, Finney JM, Wyllie DH, Oakley SJ, Fawley WN, Freeman J, Morris K, Martin J, Howard P, Gorbach S, Goldstein EJ, Citron DM, Hopkins S, Hope R, Johnson AP, Wilcox MH**, Peto TE**, Walker AS**, Crook DW**. Effects of control interventions on Clostridium difficile infection in England: an observational study. Lancet Inf Dis 2017 DOI: http://dx.doi.org/10.1016/S1473-3099(16)30514-X [PMID: 28130063]

Ledda A, Price JR, Cole K, Llewelyn MJ, Kearns AM, Crook DW, Paul J, Didelot X. Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus. J Antimicrob Chemother 2017. [epub ahead of print] DOI: https://doi.org/10.1093/jac/dkw570 [PMID: 28108681]

Kizny Gordon A, Mathers AJ, Cheong EYL, Gottlieb T, Kotay S, Walker AS, Peto TEA, Crook DW, Stoesser N. The hospital water environment as a reservoir for carbapenem-resistant organisms causing hospital-acquired infections – A systematic review of the literature. Clin Infect Dis 2017. Feb 13. doi: 10.1093/cid/cix132. [Epub ahead of print] [PMID: 28200000]

Orlek A, Stoesser N, Anjum MF, Doumith M, Ellington MJ, Peto T, Crook D, Woodford N, Walker AS, Phan H, Sheppard A. Plasmid Classification in an era of whole-genome sequencing. Frontiers in Microbiology 2017 Feb 9;8:182. doi: 10.3389/fmicb.2017.00182. eCollection 2017 [PMID: 28232822 PMCID: PMC5299020]

Mawer DPC, Eyre DW, Griffiths D, Fawley WN, Martin JSH, Quan P, Peto TEA, Crook DW, Walker AS, Wilcox MH. Contribution of Clostridium difficile transmission of symptomatic patients with toxigenic strains who are fecal toxin negative. Clin Infect Dis 2017 doi: 10.1093/cid/cix079. [Epub ahead of print] [PMID: 28158441]

Harrison OB, Cole K, Peters J, Cresswell F, Dean G, Eyre DW, Paul J, Maiden MC. Genomic analysis of urogenital and rectal Neisseria meningitis isolates reveals encapsulated hyperinvasive meningococci and coincident multi-resistant gonococci. Sex Transm. Infect. 2017 Jan 30. pii: sextrans-2016-052781. doi: 10.1136/sextrans-2016-052781. [Epub ahead of print] [PMID: 28137933]

Ajileye A, Alvarez N, Marker M, Walker TM, Akter S, Brown K, Moradigaravand D, Schon T, Andres S, Schleusener V, Omar SV, Coll F, Huang H, Diel R, Ismail N, Parkhill J, de Jong BC, Peto TE, Crook DW, Niemann S, Robledo J, Smith EG, Peacock SJ, Koser CU. Some synonymous and non-synonymous gryA mutations in Mycobacterium tuberculosis lead to systematic false-positive fluoroquinolone resistance results with the Hain GenoType MTBDRsl assays. Antimicrobial Agents Chemother. 2017. pii: AAC.02169-16. doi: 10.1128/AAC.02169-16. [PMID: 2813812]

Young BC, Votintseva AA, Foster D, Godwin H, Miller RR, Anson LW, Walker AS, Peto TEA, Crook DW, Knox K. Mulit-site and nasal swabbing for carriage of Stapylococcus aureus: what does a single nasal swab predict? J Hosp Infect 2017 Jan 30. Pii: S0195-670(17)30059_2. doi: 10.1016/j.jhin.2017.01.015 [epub ahead of print] [PMID: 28246002]

De Maio N, Wilson D. The Bacterial Sequential Markov Coalescent. Genetics 2017 Mar 3. Pii: genetics116.198796. doi: 10/1534/genetics.116.198796 [epub ahead of print] [PMID: 28258183]

Orlek A, Phan H, Sheppard A, Doumith M, Ellington MJ, Peto T, Crook D, Walker AS, Woodford N, Anjum MF, A. Stoesser N. Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids. Plasmid. 2017 Mar 9;9:42-52. Doi: 10.1016/jplasmid.2017.03.002 [PMID: 28286183]

Votintseva AA*, Bradley P*, Pankhurst L*, del Ojo Elias C, Loose M, Nilgiriwala K, Chatterjee A, Smith EG, Sanderson N, Walker TM, Morgan MR, Wyllie DH, Walker AS, Peto TEA, Crook DW, Iqbal Z. Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples J Clin Micro. 2017 pii.JCM.02483-16. Doi: 10.1128/JCM.02483-16. [PMID: 28275074]

Cheruvanky A, Stoesser N, Sheppard AE, Crook DC, Hoffman PS, Weddle E, Carroll J, Sifri CD, Chai W, Barry K, Ramakrishnan G, Mathers AJ. Enhanced Klebsiella penumoniae carbapenemase (KPC) expression from a novel Tn4401 deletion. Antimicrob. Agents Chemother. 2017 Apr 3. Pii: ACC.00025-17. Doi: 10.1128/AAC.00025-17[PMID: 28373185]

Eyre DW, De Silva D, Cole K, Peters J, Cole MJ, Grad YH, Demczuk W, Martin I, Mulvey MR, Crook DW, Walker AS, Peto TEA, Paul J. Whole genome sequencing to predict antibiotic minimum inhibitory concentrations for Neiserria gonorrhoeae. J. Antimicro. Chemo. 2017 Mar 10. doi: 10.1093/jac/dkx067. [epub ahead of print] [PMID: 28333355]

Donker T, Henderson KL, Hopkins KL, Dodgson AR, Thomas S, Crook DW, Peto TEA, Johnson AP, Woodford N, Walker SA, Robotham. The relative importance of large problems far away versus small problems closer to home: insights into limiting the spread of antimicrobial resistance in England. BMC Medicine. 2017 15:86. Doi: 10.1186/s12916-017-08442 [PMID: 28446169; PMCID: PMC5406888]

Walker AS, Mason A, Quan P, Fawcett N, Watkinson P, Llewelyn MD, Stoesser N, Finney J, Davies J, Wyllie DH, Crook DW, Peto TEA. Mortality risks associated with emergency admissions during weekends and public holidays: electronic health records study. Lancet Published online May 9, 2017 http://dx.doi.org/10.1016/S0140-6736(17)30782-1

Gordon N, Pichon B, Golubchik T, Wilson D, Paul J, Blanc D, Cole K, Collins J, Cortes N, Cubbon M, Gould F, Jenks P, Llewellyn M, Nash J, Orendi J, Paranthaman K, Price J, Senn L, Thomas, Wyllie S, Crook D, Peto T, Walker S, Kearns A. Whole genome sequencing reveals the contribution of long-term carriers in Staphylococcus aureus outbreak investigation. J Clin Micro Posted Online 3 May 2017
J. Clin. Microbiol. doi:10.1128/JCM.00363-17

George S, Pankhurst L, Hubbard A, Votintseva A, Stoesser N, Sheppard AE, Mathers A, Norris R, Navickaite I, Eaton C, Iqbal Z, Crook DW, Phan HRR. Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches. Microbial Genomics (in press)

Teresa L. Street, Nicholas D. Sanderson, Bridget L. Atkins, Andrew J. Brent, Kevin Cole, Dona Foster, Martin A. McNally, Sarah Oakley, Leon Peto, Adrian Taylor, Tim E. A. Peto, Derrick W. Crook, David W. Eyre. Molecular diagnosis of orthopaedic device infection direct from sonication fluid by metagenomic sequencing. J Clin Microbiol. 2017 May 10. pii: JCM.00462-17. doi: 10.1128/JCM.00462-17. [Epub ahead of print]

Walker TM, Merker M, Kohl TA, Crook DW, Niemann S, Peto TEA. Whole genome sequencing for M/DR tuberculosis surveillance and for resistance testing. Clin Micro Infect 2017 Mar;23(3):161-166. doi: 10.1016/j.cmi.2016.10.014.

Eyre DW, Fawley WN, Rajgopal A, Settle C, Mortimer K, Goldeberg SD, Dawson S, Crook DW, Peto TEA, Walker AS, Wilcox, MH.Comparison of Control of Clostridium difficile infection in six English using whole-genome sequencing.  Clin Infect Dis. 2017 29 May

Orlek A, Phan H, Sheppard AEA, Doumith M, Ellington M, Peto T, Crook D, Walker AS, Woodford N, Anjum MF, Stoesser  A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database. N. Data Brief 2017 Apr 23; 12:423-426. doi: 10.1016/jib.2017.04.024

Llewelyn MJ, Fitzpatrick JM, Darwin E, Tonkin-Crine S, Gorton C, Paul J, Peto TEA, Yardley L, Hopkins S, Walker AS. The antibiotic course has had its day. BMJ 2017;358:j3418 doi: 10.1136/bmj.j3418

Stoesser N, Eyre DW, Quan TP, Godwin H, Pill H, Mbuvi E, Vaughan A, Griffiths D, Martin J, Fawley W, Dingle KE, Oakley S, Wanelik K, Finney JM, Kachrimanidou M, Moore CE, Gorbach S, Riley TV, Crook DW, Peto TEA, Wilcox MH, Walker AS and MMMIG. Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: risk factors for colonization and carriage, and genetic overlap with regional C . difficile strains. PlosOne 2017 Aug 16;12(8):e0182307 doi: 10.1371/journal.pone.0182307

Stoesser N, Sheppard AE, Peirano G, Anson LW, Pankhurst L, Sebra R, Phan HTT, Kasarskis A, Mathers AJ, Peto TEA, Bradford P, Motyl M, Walker AS, Crook DW, Pitout. Genomic epidemiology of global Klebsiella pneumonia carbarpenemase (KPC) producing E coli. Nat Sci Rep 2017 Jul 19;7(1):5917. Doi: 10.1038/s41598-0117-06256-2

Donker T, Smieszek T, Henderson KL, Johnson AP, Walker AS, Robotham JV. Measuring Distance through Dense Weighted Networks: the Case of Hospital- Associated Pathogens. PLoS Computational Biology 2017 Aug 3;13(8):e1005622 doi: 10.1371/journal.pcbi.1005622