IORD peer-reviewed journal articles (* indicates equal contribution)
2024
Tan CCS, Kelly G, Cregan J, Wilson I, James TJ, Chand M, Hopkins S, Swets M, Baillie K, Jeffery K, Walker AS, Eyre DW, Stoesser N, Matthews PC. Temporal trends and clinical characteristics of acute hepatitis with unknown aetiology and human adenovirus infections in Oxfordshire from 2016 to 2022. BMC Public Health (in press).
https://www.medrxiv.org/content/10.1101/2023.06.19.23291626v1
Wei J, Uppal A, Nganjimi C, Warr H, Ibrahim Y, Gu Q, Yuan H, Rahman NM, Jones N, Walker AS, Eyre D. No evidence of difference in mortality with amoxicillin versus co-amoxiclav for hospital treatment of community-acquired pneumonia. J Infect 2024 Jun; 88(6):106161. https://www.journalofinfection.com/article/S0163-4453(24)00095-1/fulltext
Alkhmees MW, Van den Bruel A, Hayward G, Blanker MH, Walker AS, Holtman GA. Trends in C reactive protein testing: A retrospective cohort study in paediatric ambulatory care settings. BMJ Open. 2024 Jun 10; 14(6):e081658.
https://bmjopen.bmj.com/content/14/6/e081658
Gu Q, Wei J, Yoon CH, Yuan K, Jones N, Brent A, Llewelyn M, Peto TEA, Pouwels KB, Eyre DW*, Walker AS*. Distinct patterns of vital sign and inflammatory marker responses in adults with suspected bloodstream infection. J Infection 2024 May; 88(5):106156.
https://www.journalofinfection.com/article/S0163-4453(24)00090-2/fulltext
Lipworth S, Matlock W, Shaw L, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto TEA, Crook D, Walker AS, Stoesser N. The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies. Nat Comms 2024 Feb 22; 15(1):1612.
https://www.nature.com/articles/s41467-024-45761-7
Cross ELA, Quan TP, Hayward GN, Walker AS, Llewelyn MJ. Development and validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score. J Infect 2024 Feb; 88(2):103–11.
https://www.journalofinfection.com/article/S0163-4453(23)00593-5/fulltext
Vasqez-Montes MDLA, Fanshawe TR, Stoesser N, Walker AS, Butler CC, Hayward G. Epidemiology and microbiology of recurrent UTI in women in Oxfordshire, UK. JAC AMR 2024; 6(1);dlad 156.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10781434/
Yang J, El-Bouri R, O’Donoghue O, Lachapelle AS, Soltan AA, Clifton DA. Deep reinforcement learning for multi-class imbalanced training. Mach Learn 2024; 113(5):2655-2674.
https://link.springer.com/article/10.1007/s10994-023-06481-z
2023
Shah RA, Mentzer AJ, James T, Cox S, Paddon K, Bowen J, Fullerton JN. A novel near-patient host-protein score predicts COVID-19 deterioration at presentation to secondary care. J Infect. 2023 May; 86(5): 534–536. doi: 10.1016/j.jinf.2023.01.017.
https://www.journalofinfection.com/article/S0163-4453(23)00022-1/fulltext
Jackson N, Woods J, Watkinson P, Brent A, Peto TEA, Walker AS, Eyre DW. The quality of vital signs measurements and value preferences in electronic medical records varies by hospital, specialty, and patient demographics. Sci Rep. 2023 Mar 8;13(1):3858. doi: 10.1038/s41598-023-30691-z. https://www.nature.com/articles/s41598-023-30691-z
Yang J, Soltan AA, Eyre DW, Yang Y, Clifton DA. An adversarial training framework for mitigating algorithmic biases in clinical machine learning. NPJ Digit Med. 2023 Mar 29;6(1):55. doi: 10.1038/s41746-023-00805-y.
https://www.nature.com/articles/s41746-023-00805-y
Thakur A, Armstrong J, Youseff A, Eyre D, Clifton D. Self-Aware SGD: reliable incremental adaptation framework for clinical AI models. IEEE J Biomed Health Inform. 2023 Feb 6;PP. doi: 10.1109/JBHI.2023.3237592.
https://ieeexplore.ieee.org/document/10036945
2022
Lipworth S, Vihta KD, Davies T, Wright S, Tabirao M, Chau K, Vaughan A, Kavanagh J, Barker L, George S, Segal S, Paulus S, Barrett L, Oakley S, Jeffery K, Butcher L, Peto T, Crook D, Walker AS, Kadambari S, Stoesser N. Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria in Oxfordshire, UK. Commun Med. 2022 Aug 11;2:101. doi: 10.1038/s43856-022-00161-0. https://www.nature.com/articles/s43856-022-00161-0
Ward V, Wei J, Gordon W, Barnes E, Dunachie S, Jeffery K, Eyre DW, O’Donnell AM. SARS-CoV-2 antibody responses post-vaccination in UK healthcare workers with pre-existing medical conditions: a cohort study. BMJ open 2022 Dec 1;12(12):e066766. doi: 10.1136/bmjopen-2022-066766.
https://bmjopen.bmj.com/content/12/12/e066766.long
Jamshidi E, Asgary A, Tavakoli N, Zali A, Setareh S, Esmaily H, Jamaldini SH, Daaee A, Babajani A, Kashi MHS, Jamshidi M, Rahi SJ, Mansouri N. Using machine learning to predict mortality for COVID-19 Patients on day 0 in the ICU. Front Digit Health. 2022 Jan 13;3:681608. doi: 10.3389/fdgth.2021.681608.
https://www.frontiersin.org/articles/10.3389/fdgth.2021.681608/full
Zhuang X, Wang W, Borrmann H, Balfe P, Matthews PC, Eyre DW, Klerman E, McKeating JA. Time-of-day variation in SARS-CoV-2 RNA levels during the second wave of COVID-19 infection. Viruses. 2022 Aug 5;14(8):1728. doi: 10.3390/v14081728.
https://www.mdpi.com/1999-4915/14/8/1728
Gu Q, Jones N, Drennan P, Peto TEA, Walker AS, Eyre DW. Assessment of an institutional guideline for vancomycin dosing and identification of predictive factors associated with dose and drug trough levels. J Infect. 2022. Jul 12;S0163-4453(22)00403-0. doi: 10.1016/j.jinf.2022.06.029. PMID: 35840011. https://www.journalofinfection.com/article/S0163-4453(22)00403-0/fulltext
Yoon CH, Bartlett S, Stoesser N, Pouwels KB, Jones N, Crook DW, Peto TEA, Walker AS, Eyre DW. Mortality risks associated with empirical antibiotic activity in Escherichia coli bacteraemia: an analysis of electronic health records. J Antimicrob Chemother. 2022 Jun 20;dkac189. doi: 10.1093/jac/dkac189. PMID: 35723965. https://academic.oup.com/jac/advance-article/doi/10.1093/jac/dkac189/6611841?login=false
Lumley SF, Richens N, Lees E, Cregan J, Kalimeris E, Oakley S, Morgan M, Segal S, Dawson M, Walker AS, Eyre DW, Crook DW, Beer S, Novak A, Stoesser NE, Matthews PC. Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic. J Infect. 2022 Jan;84(1):40-47. doi: 10.1016/j.jinf.2021.10.022. https://linkinghub.elsevier.com/retrieve/pii/S0163-4453(21)00540-5
Mentzer AJ, James T, Yongya M, Cox S, Paddon K, Shine B, Bowen J, Novak A, Knight JC, Fullerton JN. Serum calprotectin is not an independent predictor of severe COVID-19 in ambulatory adult patients. J Infect. 2022 Feb; 84(2), e27–e29. doi: 10.1016/j.jinf.2021.11.017. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626154/
Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022 Feb 12;399(10325):629-655. doi: 10.1016/S0140-6736(21)02724-0. PMID: 35065702. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)02724-0/fulltext
Wang W, Balfe P, Eyre DW, Lumley SF, O’Donnell D, Warren F, Crook DW, Jeffery K, Matthews PC, Klerman EB, McKeating JA. Time of day of vaccination affects SARS-CoV-2 antibody responses in an observational study of healthcare workers. J Biol Rhythms. 2022 Feb;37(1):124-129. doi: 10.1177/07487304211059315. https://journals.sagepub.com/doi/10.1177/07487304211059315
Soltan AAS, Yang J, Pattanshetty R, Novak A, Yang Y, Rohanian O, Beer S, Soltan MA, Thickett DR, Fairhead R, Zhu T, Eyre DW, Clifton DA; CURIAL Translational Collaborative. Real-world evaluation of rapid and laboratory-free COVID-19 triage for emergency care: external validation and pilot deployment of artificial intelligence driven screening. Lancet Digit Health. 2022 Apr;4(4):e266-e278. doi: 10.1016/S2589-7500(21)00272-7. PMID: 35279399. https://www.thelancet.com/journals/landig/article/PIIS2589-7500(21)00272-7/fulltext
Yang J, Soltan AA, Clifton DA. Machine learning generalizability across healthcare settings: insights from multi-site COVID-19 screening. NPJ Digit Med. 2022 Jun 7;5(1):69. doi: 10.1038/s41746-022-00614-9. PMID: 35672368. https://www.nature.com/articles/s41746-022-00614-9
2021
Ordóñez-Mena JM, Fanshawe TR, Foster D, Andersson M, Oakley S, Stoesser N, Walker AS, Hayward G. Frequencies and patterns of microbiology test requests from primary care in Oxfordshire, UK, 2008–2018: a retrospective cohort study of electronic health records to inform point-of-care testing. BMJ Open. 2021 Nov 23;11(11):e048527. doi: 10.1136/bmjopen-2020-048527. PMID: 34815274. https://bmjopen.bmj.com/content/11/11/e048527.long
Vihta KD, Gordon NC, Stoesser N, Quan TP, Tyrrell C, Vongsouvath M, Ashley EA, Chansamouth V, Turner P, Ling C, Eyre D, White NJ, Crook D, Peto T, Walker AS. Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections. Scientific Reports. 2021 Dec 3;11(1):23359. doi: 10.1038/s41598-021-02755-5. PMID: 34862445. https://www.nature.com/articles/s41598-021-02755-5
Bishop J*, Javed HA*, El-Bouri R, Zhu T, Taylor T, Peto T, Watkinson P, Eyre DW, Clifton DA. Improving patient flow during infectious disease outbreaks using machine learning for real-time prediction of patient readiness for discharge. PLoS One. 2021 Nov 23;16(11):e0260476. doi: 10.1371/journal.pone.0260476. PMID: 34813632. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0260476
El-Bouri R, Eyre DW, Watkinson P, Zhu T*, Clifton DA*. Hospital admission location prediction via deep interpretable networks for the year-round improvement of emergency patient care. IEEE Journal of Biomedical and Health Informatics. 2021 Jan;25(1):289-300. doi: 10.1109/JBHI.2020.2990309. PMID: 32750898. https://ieeexplore.ieee.org/document/9103941
Mo Y, Eyre DW, Lumley SF, Walker TM, Shaw RH, O’Donnell D, Butcher L, Jeffery K, Donnelly CA; Oxford COVID infection review team, Cooper BS. Transmission of community- and hospital-acquired SARS-CoV-2 in hospital settings in the UK: A cohort study. PLoS Med. 2021 Oct 12;18(10):e1003816. doi: 10.1371/journal.pmed.1003816. PMID: 34637439. https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003816
Young BC, Eyre DW, Jeffery K. Use of lateral flow devices allows rapid triage of patients with SARS-CoV-2 on admission to hospital. J Infect. 2021 Jun;82(6):276-316. doi: 10.1016/j.jinf.2021.02.025. J Infect 82:276-316. PMID: 33662408. https://www.journalofinfection.com/article/S0163-4453(21)00096-7/fulltext
Eyre DW, Lumley SF, Wei J, Cox S, James T, Justice A, Jesuthasan G, O’Donnell D, Howarth A, Hatch SB, Marsden BD, Jones EY, Stuart DI, Ebner D, Hoosdally S, Crook DW, Peto TEA, Walker TM, Stoesser NE, Matthews PC, Pouwels KB, Walker AS, Jeffery K. Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status. Clin Microbiol Infect. 2021 Oct;27(10):1516.e7-1516.e14. doi: 10.1016/j.cmi.2021.05.041. PMID: 34111577. https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(21)00289-5/fulltext
Lumley SF, Constantinides B, Sanderson N, Rodger G, Street TL, Swann J, Chau KK, O’Donnell D, Warren F, Hoosdally S; OUH Microbiology laboratory; OUH Infection Prevention and Control team, O’Donnell AM, Walker TM, Stoesser NE, Butcher L, Peto TE, Crook DW, Jeffery K, Matthews PC, Eyre DW. Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals. J Infect. 2021 Oct;83(4):473-482. doi: 10.1016/j.jinf.2021.07.034. PMID: 34332019. https://www.journalofinfection.com/article/S0163-4453(21)00377-7/fulltext
Laager M, Cooper BS, Eyre DW. Probabilistic modelling of effects of antibiotics and calendar time on transmission of healthcare-associated infection. Sci Rep. 2021 Nov 1;11(1):21417. doi: 10.1038/s41598-021-00748-y. PMID: 34725404. https://www.nature.com/articles/s41598-021-00748-y
Lipworth S, Vihta KD, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Genome Med. 2021 Sep 3;13(1):144. doi: 10.1186/s13073-021-00947-2. PMID: 34479643 https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00947-2
Youssef A, Kouchaki S, Shamout F, Armstrong J, El-Bouri R, Taylor T, Birrenkott D, Vasey B, Soltan A, Zhu T, Clifton DA, Eyre DW. Development and validation of early warning score systems for COVID-19 patients. Health Technol Lett. 2021 May 27:10.1049/htl2.12009. doi: 10.1049/htl2.12009. PMID: 34221413. https://ietresearch.onlinelibrary.wiley.com/doi/10.1049/htl2.12009
Soltan A, Kouchaki S, Zhu T, Kiyasseh D, Taylor T, Hussain ZB, Peto T, Brent AJ, Eyre DW. Rapid triage for COVID-19 using routine clinical data for patients attending hospital: development and prospective validation of an artificial intelligence screening test. Lancet Digit Health. 2021 Feb;3(2):e78-e87. doi: 10.1016/S2589-7500(20)30274-0. https://www.thelancet.com/journals/landig/article/PIIS2589-7500(20)30274-0/fulltext
Eyre TA, Peters L, Andersson MI, Peniket A, Eyre DW. Reduction in incidence of non-COVID-19 respiratory virus infection amongst haematology inpatients following UK social distancing measures. Br J Haematol. 2021 Jun 7:10.1111/bjh.17651. doi: 10.1111/bjh.17651. PMID: 34097303. https://onlinelibrary.wiley.com/doi/10.1111/bjh.17651
Lumley SF, Rodger G, Constantinides B, Sanderson N, Chau KK, Street TL, O’Donnell D, Howarth A, Hatch SB, Marsden BD, Cox S, James T, Warren F, Peck LJ, Ritter TG, de Toledo Z, Warren L, Axten D, Cornall RJ, Jones EY, Stuart DI, Screaton G, Ebner D, Hoosdally S, Chand M, Crook DW, O’Donnell AM, Conlon CP, Pouwels KB, Walker AS, Peto TEA, Hopkins S, Walker TM, Stoesser NE, Matthews PC, Jeffery K, Eyre DW. An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status. Clin Infect Dis. 2021 Jul 3:ciab608. doi: 10.1093/cid/ciab608. PMID: 34216472. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab608/6314286
Lumley SF, Wei J, O’Donnell D, Stoesser NE, Matthews PC, Howarth A, Hatch SB, Marsden BD, Cox S, James T, Peck LJ, Ritter TG, de Toledo Z, Cornall RJ, Jones EY, Stuart DI, Screaton G, Ebner D, Hoosdally S, Crook DW, Conlon CP, Pouwels KB, Walker AS, Peto TEA, Walker TM, Jeffery K, Eyre DW; Oxford University Hospitals Staff Testing Group. The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers. Clin Infect Dis. 2021 Jan 6:ciab004. doi: 10.1093/cid/ciab004. PMID: 33400782. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab004/6064824
Eyre DW, Lumley SF, O’Donnell D, Stoesser NE, Matthews PC, Howarth A, Hatch SB, Marsden BD, Cox S, James T, Cornall RJ, Stuart DI, Screaton G, Ebner D, Crook DW, Conlon CP, Jeffery K, Walker TM, Peto TEA. Stringent thresholds in SARS-CoV-2 IgG assays lead to under-detection of mild infections. BMC Infect Dis. 2021 Feb 18;21(1):187. doi: 10.1186/s12879-021-05878-2. PMID: 33602152. https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-021-05878-2
Downs LO, Eyre DW, O’Donnell D, Jeffery K. Home-based SARS-CoV-2 lateral flow antigen testing in hospital workers .J Infect. 2021 Feb;82(2):282-327. doi: 10.1016/j.jinf.2021.01.008. PMID: 33573777. https://www.journalofinfection.com/article/S0163-4453(21)00033-5/fulltext
Howarth A, Hatch SB, Marsden BD, Jones EY, Stuart DI, Ebner D, Hoosdally S, Crook DW, Peto TEA, Walker TM, Stoesser NE, Matthews PC, Pouwels KB, Walker AS, Jeffery K. Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status. Clin Micro Inf 2021. https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(21)00289-5/fulltext
Eyre DW, Laager M, Walker AS, Cooper BS, Wilson DJ; CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare). Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission. PLoS Comput Biol. 2021 Jan 14;17(1):e1008417. doi: 10.1371/journal.pcbi.1008417. PMID: 33444378. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008417
Pritchard E, Fawcett N, Quan TP, Crook DW, Peto TEA, Walker AS. Combining Charlson and Elixhauser scores with varying lookback predicted mortality better than using individual scores. J Clin Epidem 2021; 130:32-41. https://linkinghub.elsevier.com/retrieve/pii/S0895-4356(20)31106-9
Lipworth S, Vihta K-D, Chau KK, Kavanagh J, Davies T, George S, Barker L, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections. Clin Infect Dis 2021. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab006/6067638
2020
Eyre DW, Lumley SF, O’Donnell D, Campbell M, Sims E, Lawson E, Warren F, James TJ, Cox S, Howarth A, Doherty G, Hatch SB, Kavanagh J, Chau KK, Fowler PW, Swann J, Volk D, Yang-Turner F, Stoesser HE, Matthews PC, Dudareva M, Davies T, Shaw RH, Peto L, Downs LO, Vogt A, Amini A, Young BC, Drennan P, Mentzer AJ, Skelly D, Karpe F, Neville MJ, Andersson M, Brent AJ, Jones N, Ferreira LM, Christott T, Marsden B, Hoosdally S, Cornall R, Crook DW, Stuart D, Screaton G, Oxford University Hospitals Staff Testing Group, Peto TEA, Holthof B, O’Donnell AM, Ebner D, Conlon CP, Jeffery K, Walker TM. Differential occupational risks to healthcare workers from SARS-CoV-2: A prospective observational study. Elife. 2020 Aug 21;9:e60675. doi: 10.7554/eLife.60675. PMID: 32820721. https://elifesciences.org/articles/60675
Lumley SF, O’Donnell D, Stoesser NE, Matthews PC, Howarth A, Hatch SB, Marsden BD, Cox S, James T, Warren F, Peck LJ, Ritter TG, de Toledo Z, Warren L, Axten D, Cornall RJ, Jones EY, Stuart DI, Screaton G, Ebner D, Hoosdally S, Chand M, Oxford University Hospitals Staff Testing Group, Crook DW, O’Donnell AM, Conlon CP, Pouwels KB, Walker AS, Peto TEA, Hopkins S, Walker TM, Jeffery K, Eyre DW. Antibody status and incidence of SARS-CoV-2 infection in health care workers. N Eng J Med 2020; NEJMoa2034545. https://www.nejm.org/doi/pdf/10.1056/NEJMoa2034545?articleTools=true
Constantinides B, Chau KK, Quan TP, Rodger G, Andersson MI, Jeffery K, Lipworth S, Gweon HS, Peniket A, Pike G, Millo J, Byukusenge M, Holdaway M, Gibbons C, Mathers AJ, Crook DW, Peto TEA, Walker AS, Stoesser. Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Microb Genom 2020;10.1099/mgen.0.000391. [https://www.microbiologyresearch.org/docserver/fulltext/mgen/10.1099/mgen.0.000391/mgen000391.pdf?expires=1595679763&id=id&accname=guest&checksum=FBF58D4A9E3F917997DD9974B5B5B067]
2019
Fawcett N, Young B, Peto L, Quan TP, Gillott R, Wu J, Middlemass C, Weston S, Crook DW, Peto TEA, Johnson A, Muller-Pebody B, Walker AS*, Sandoe JAT*. ‘Caveat emptor’: the cautionary tale of endocarditis and the potential pitfalls of clinical coding data: an electronic health records study. BMC Medicine 2019;17(1):169.
[https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-019-1390-x]
2018
Eyre DW, Sheppard A, Madder H, Moir I, Moroney R, Quan TP, Griffiths D, George S, Butcher L, Newnham R, Sunderland M, Clarke T, Foster D, Hoffman P, Borman AM, Johnson EM, Moore G, Brown CS, Walker AS, Peto TEA, Crook DW, Jeffery KJM. A Candida auris outbreak and its control in an intensive care setting. N Eng J Med 2018; 379:1322-1331.
[https://www.nejm.org/doi/10.1056/NEJMoa1714373]
Vihta KD, Stoesser N, Llewelyn M, Quan TP, Davies T, Fawcett NJ, Dunn L, Jeffrey K, Butler C, Hayward G, Andersson M, Morgan M, Oakley S, Mason A, Wyllie DH, Crook DW, Wilcox MH, Johnson AP, Peto TEA*, Walker AS*. Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: a cohort study. Lancet Inf Dis 2018;18(10):1138-1149. doi: 10.1016/S1473-3099(18)30353-0. [https://www.sciencedirect.com/science/article/pii/S1473309918303530?via%3Dihub]
2017
Cule M, Donnelly P. Stochastic modelling and inference in electronic hospital databases for the spread of infections: Clostridium difficile transmission in Oxfordshire hospitals 2007–2010. Annals of Applied Statistics 2017;11(2):655-679. doi: 10.1214/16-aoas1011 [https://projecteuclid.org/download/pdfview_1/euclid.aoas/1500537718]
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 2017;390(10089):62-72. Doi: 10.1016/S0140-6736(17)30782-1. [http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(17)30782-1/fulltext]
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;17(5):478-479. doi: 10.1016/S1473-3099(17)30185-8. [https://www.sciencedirect.com/science/article/pii/S147330991630514X?via%3Dihub]
[https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(16)30514-X/fulltext]
2016
Fawcett NJ, Jones N, Quan P, Mistry V, Peto TEA, 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:e010969 doi:10.1136/bmjopen-2015-010969. [http://bmjopen.bmj.com/content/6/8/e010969.full]
Quan TP, Fawcett NJ, Wrightson JM, Finney J, Wyllie D, Jones N, Jeffery K, 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. [http://thorax.bmj.com/content/early/2016/02/17/thoraxjnl-2015-207688.full.pdf+html]
2013
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. [http://cid.oxfordjournals.org/content/56/11/1589.full.pdf+html]
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. [http://cid.oxfordjournals.org/content/56/6/798.full.pdf+html]
2012
Schlackow I, Walker AS, Crook DW, Peto TEA, Wyllie DH. Surveillance of infection severity: A registry study of laboratory diagnosed Clostridium difficile. PLoS Med 2012 9(7): e1001279. doi:10.1371/journal.pmed.1001279. [http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1001279]
Schlackow I, Stoesser N, Walker AS, Crook DW, Peto TEA, Wyllie DH. Increasing incidence of E. coli bacteraemia is driven by an increase in antibiotic-resistant isolates: Electronic database study in Oxfordshire 1999-2011. J Antimicrob Chemo 2012; 67(6):1514-24. [http://jac.oxfordjournals.org/content/67/6/1514.full.pdf+html]
Eyre DW, Walker AS, Wyllie D, Dingle KE, Griffiths D, Finney J, O’Connor L, Vaughan A, Crook DW, Wilcox MH, Peto TEA on behalf of the Infections in Oxfordshire Research Database (IORD). Predictors of recurrent C. difficile infection: implications for initial management. Clin Inf Dis2012;55:S77-S87. [http://cid.oxfordjournals.org/content/55/suppl_2/S77.full]
Walker AS*, Eyre DW*, WyllieDH, Dingle KE, Harding RM, O’ConnorL, Griffiths D, Vaughan A, FinneyJ, Wilcox MH, Crook DW, Peto TEA on behalf of the Infections in Oxfordshire Research Database (IORD). Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing. Plos Med 2012; 9(2): e1001172. doi:10.1371/journal.pmed.1001172. [http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1001172]
2011
Wyllie DH, Walker AS, Miller R, Williamson SR, Schlackow I, Finney JM, O’Connor L, Peto TEA, Crook DW. Decline of meticillin resistant S. aureus in Oxfordshire hospitals is strain specific and preceded infection control intensification. BMJ Open 2011;doi:10.1136/bmjopen-2011-000160. [http://bmjopen.bmj.com/content/1/1/e000160.full]
Finney JM, Walker AS, Peto TE and Wyllie DH. An efficient record linkage scheme using graphical analysis for identifier error detection. BMC Medical Informatics and Decision Making 2011; 11:7doi:10.1186/1472-6947-11-7. [http://link.springer.com/article/10.1186%2F1472-6947-11-7#]