Dearlove BL, Cody AJ, Pascoe B, Méric G, Wilson DJ, Sheppard SK. Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. ISME Journal 2016;10(3):721-9. doi:10.1038/ismej.2015.149. [PMID: 26305157]

Earle, SG, Wu, C-H, Charlesworth J, Stroesser N, Gordon, NC, Walker TM, Spencer CCA, Iqbal Z, Clifton DA, Smith EG, Ismail N, Llewelyn MJ, Peto TE, Crook DW, McVean G, Walker AS, Wilson DJ. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nature Microbiology 2016; ;1:16041. doi: 10.1038/nmicrobiol.2016.41. [PMID: 27572646 PMCID: PMC5049680]

Pankhurst LJ, DelOjo Elias C, Votintseva AA, Walker TM, Cole K, Davies J, Fermont JM, Gascoyne-Binzi DM, Kohl TA, Kong C, Lemaitre N, Niemann S, Paul J, Rogers TR, Roycroft E, Smith EG, Supply P, Tang P, Wilcox MH, Wordsworth S, Wyllie D, Xu L, Crook DW, COMPASS-TB Study Group. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study. Lancet Respir Med 2016 4(1):49-58. [PMID: 26669893 PMCID: PMC4698465]

Senn L, Clerc O, Zanetti G, Basset P, Prodham G, Sheppard AE, Crook DW, James R, Thorpe HA, Feil EJ, Blanc DS. The stealthy superbug: The role of asymptomatic enteric carriage in maintaining a long-term hospital outbreak of ST228 methicillin resistant Staphylococcus aureus. Mbio 2016 19;7 (1):e02039-15. [PMID: 26787833 PMCID: PMC4725017]

Quan TP, Fawcett NJ, Wrightson JM, Finney J, Wyllie D, Jeffery K, Jones N, Shine B, Clarke L, Crook D, Walker AS*, Peto TEA* on behalf of the Infections in Oxfordshire Research Database (IORD). Increasing burden of community-acquired pneumonia leading to hospitalisation, 1998-2014. Thorax 2016; 71(6):535-42. doi: 10.1136/thoraxjnl-2015-207688. [PMID: 26888780]

Sheppard AE, Stoesser N, Sebra R, Kasarskis A, Deikus G, Anson L, Walker AS, Peto TE, Crook DW, Mathers AJ. 2016. Complete genome sequence of KPC-producing Klebsiella pneumoniae strain CAV1193. Genome Announc 2016 4(1):e01649-15. doi:10.1128/genomeA.01649-15.[PMID: 26823590 PMCID: PMC4732343]

Sheppard AE, Vaughan A, Jones N, Turner P, Turner C, Efstratiou A, Patel D, the Modernising Medical Microbiology (MMM) Informatics Group, Walker AS, Berkley JA, Crook DC, Seale AC. Capsular typing method for Streptococcus agalactiae using whole genome sequence data. J Clin Micro 2016; 54(5):1388-90. doi: 10.1128/JCM.03142-15. [PMID: 26962081]

Stoesser N, Sheppard A, Pankhurst L, de Maio N, Moore CE, Sebra R, Turner P, Anson LW, Kasarskis A, Batty EM, Kos V, Wilson DJ, Phetsouvanh R, Wyllie D, Sokurenko E, Manges AR, Johnson TJ, Price LB, Peto TEA, Johnson JR, Didelot X, Walker AS, Crook DC, Modernising Medical Microbiology Informatics Group. Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131. MBio 2016;7(2):e02162. doi: 10.1128/mBio.02162-15. [PMID: 27006459 PMCID: PMC4807372]

Didelot X, Walker AS, Peto TEA, Crook DW, Wilson DJ. Within-host evolution of bacterial pathogens. Nat Rev Microbiol 2016;14(3):150-62. doi: 10.1038/nrmicro.2015.13. [PMID: 26806595]

Leekitcharoenphon P, Hendriksen RS, Le Hello S, Weill F-X, Baggesen DL, Jun S-R, Ussery DW, Lund O, Crook DW, Wilson DJ, Aarestrup FM. Global genomic epidemiology of Salmonella enterica serovar Typhimurium DT104. Appl Environ Microbiol 2016;82(8):2516-26. doi: 10.1128/AEM.03821-15. [PMID: 26944846, PMCID: PMC4959494]

Stoesser N, Mathers AJ, Moore CE, Day NP Crook DW. Colistin resistance gene mcr-1 and pHNSHP45 plasmid in human isolates of Escherichia coli and Klebsiella pneumoniae. Lancet Infect Dis 2016;16(3):285-6. doi: 10.1016/S1473-3099(16)00010-4. (Correspondence) [PMID: 26774239]

Stoesser N, Sheppard AE, Perirano G, Sebra R, Lynch T, Anson L, Kasarskis A, Motyp MR, Crook DW, Pitout JD. First report of blaIMP-14 on a plasmid harbouring multiple drug resistance genes in Escherichia coli ST131. Antimicrob Agents Chemother 2016; 60(8):5068-71. doi: 10.1128/AAC.00840-16. [PMID: 27246777]

Guo Q, Tomich AD, McElheny CL, Cooper VS, Stoesser N, Wang M, Sluis-Cremer N, Doi Y. Glutathione-S-transferase FosA6 of Klebsiella pneumoniae origin conferring fosfomycin resistance in ESBL-producing Escherichia coli. J Antimicrobiol Chemother 2016;71(9):2460-5. doi: 10.1093/jac/dkw177. [PMID: 27261267]

De Silva D, Peters J, Cole K, Cole MJ, Cresswell F, Dean G, Dave J, Thomas DR, Foster K, Waldram A, Wilson D, Didecot X, Grad YH, Crook DW, Peto TEA, Walker AS, Paul J, Eyre E. Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study. Lancet Infect Dis 2016; 16(11): 1295-1303. doi: 10.1016/S1473-3099(16)30157-8 [PMID: 27427203]

Fizpatrick JM, Biswas JS, Edgeworth JD, Islam J, Jenkins N, Judge R, Lavery AJ, Melzer M, Morris-Jones S, Nsutebu EF, Peters J, Pillay DG, Pink F, Price JR, Scarborough M, Thwaites GE, Tiley R, Walker AS, Llewelyn MJ, United Kingdom Clinical Infection Research Group. Gram-negative bacteraemia: a multi-center prospective evaluation of empiric antibiotic therapy and outcome in English acute hospitals. Clin Microbiol Infect 2016;22(3):244-51. DOI: 10.1016/j.cmi.2015.10.034 [PMID: 26577143]

Fawcett NK, Jones N, Quan TP, Mistry V, Crook D, Peto T, Walker AS. Antibiotic use and clinical outcomes in the acute setting under management by an infectious diseases acute physician versus other clinical teams: a cohort study. BMJ Open 2016;6(8):e010969. DOI:10.1136/bmjopen-2015-010969 [PMID: 27554101]

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 2016 pii: S1198-743X(16)30484-0. doi: 10.1016/j.cmi.2016.10.014. [Epub ahead of print] [PMID: 27789379]

Stoesser N, Sheppard AE, Peirano G, Sebra R, Lynch T, Anson L, Kasarskis A, Motyl MR, Crook DW, Pitout JD. Complete sequencing of plasmids containing blaOXA-163 and blaOXA-48 in Escherichia coli sequence type 131. Antimicro Agents Chemother 2016;60:6948–6951. doi:10.1128/AAC.01130-16. [PMID: 27600043 PMCID: PMC5075115]

Seale AC, Koech AC, Sheppard AE, Barsosio HC, Langat J, Anyango E, Mwakio S, Mwarumba S, Morpeth SC, Anampiu K, Vaughan A, Geiss A, Mogeni P, Walusuna L, Mwangudzah H, Mwanzui D, Salim M, Kemp B, Jones C, Nturi N, Tsofa B, Mumbo E, Mulewa D, Bandika V, Soita M, Owiti M, Onzere N, Walker AS, Schrag SJ, Kennedy SH, Fegan G, Crook DW, Berkley JA. Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya. Nat Microbiol 2016;1(7):16067. doi: 10.1038/nmicrobiol.2016.67 [PMID: 27572968]

Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A, Anson LW, Geiss L, Pankhurst LJ, Vaughan A, Grim CJ, Cox HL, Yeh AJ, MMM Informatics Group, Sifri CD, Walker AS, Peto TE, Crook DW, Mathers AJ. 2016. Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of Carbapenem Resistance Gene blaKPC. Antimicro Agents Chemother 2016; 60(6): 3767-3778. doi: 10.1128/ACC.00464-16 [PMID: 27067320 PMCID: PMC4879409]

Walker TM, Crook DW, Peto TEA, Conlon CP. 2016. Whole-genome sequencing identifies nosocomial transmission of extra-pulmonary M. tuberculosis. QJM 2016;10(12):819-820. DOI: http://dx.doi.org/10.1093/qjmed/hcw202. [PMID: 28011853]

Das S, Lindermann C, Young B, Muller J, Osterreich B, Ternette N, Winkler AC, Paprotka K, Reinhardt R, Forstner KU, Allen E, Flaxman A, Yamaguchi Y, Rollier CS, van Dieman P, Blattner S, Remmele CW, Selle M, Dittrich M, Muller T, Vogel J, Ohlsen K, Crook DW, Massey R, Wilson DJ, Rudel T, Wyllie DH, Fraunholz MJ. 2016. Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation. PNAS 2016; 113(22):E3101-3110 doi: 10.107/pnas.1520255113 [PMID: 27185949, PMCID: PMC4896717]

De Maio N, Wu CH, Wilson DJ. SCOTTI: Efficient reconstruction of Transmission within outbreaks with the structured coalescent. Plos Comput Biol. 2016: Sep 28;12(9): e1005130 doi: 10.1371/journal.pcbi1005130 [PMID: 27681228, PMCID: PMC5040440]

Brown T, Didelot X, Wilson DJ, De Maio N. SimBAc: simulation of whole bacterial genomes with homologous recombination. Micro Genom. 2016 Jan 19; 2(1) doi: 1099/mgen.0.000044 [PMID: 27713837, PMCID: PMC5049688]