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The Microbiology Department at Oxford University Hospitals has very close links with the research departments of the University of Oxford. Listed here is a selection of the many publications that departmental staff has been involved in over recent years.


Oral versus Intravenous Antibiotics for Bone and Joint Infection.
Li HK, Rombach I, Zambellas R, Walker AS, McNally MA, Atkins BL, Lipsky BA, Hughes HC, Bose D, Kümin M, Scarborough C, Matthews PC, Brent AJ, Lomas J, Gundle R, Rogers M, Taylor A, Angus B, Byren I, Berendt AR, Warren S, Fitzgerald FE, Mack DJF, Hopkins S, Folb J, Reynolds HE, Moore E, Marshall J, Jenkins N, Moran CE, Woodhouse AF, Stafford S, Seaton RA, Vallance C, Hemsley CJ, Bisnauthsing K, Sandoe JAT, Aggarwal I, Ellis SC, Bunn DJ, Sutherland RK, Barlow G, Cooper C, Geue C, McMeekin N, Briggs AH, Sendi P, Khatamzas E, Wangrangsimakul T, Wong THN, Barrett LK, Alvand A, Old CF, Bostock J, Paul J, Cooke G, Thwaites GE, Bejon P, Scarborough M; OVIVA Trial Collaborators.
N Engl J Med. 2019 Jan 31;380(5):425-436. doi: 10.1056/NEJMoa1710926


Sonication versus Tissue Sampling for Diagnosis of Prosthetic Joint and Other Orthopedic Device-Related Infections.
Dudareva M, Barrett L, Figtree M, Scarborough M, Watanabe M, Newnham R, Wallis R, Oakley S, Kendrick B, Stubbs D, McNally MA, Bejon P, Atkins BA, Taylor A, Brent AJ.
J Clin Microbiol. 2018 Nov 27;56(12). pii: e00688-18. doi: 10.1128/JCM.00688-18. Print 2018 Dec

A Candida auris Outbreak and Its Control in an Intensive Care Setting.
Eyre DW, Sheppard AE, Madder H, Moir I, Moroney R, Quan TP, Griffiths D, George S, Butcher L, Morgan M, 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.
N Engl J Med. 2018 Oct 4;379(14):1322-1331. doi: 10.1056/NEJMoa1714373.

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices.
Sanderson ND, Street TL, Foster D, Swann J, Atkins BL, Brent AJ, McNally MA, Oakley S, Taylor A, Peto TEA, Crook DW, Eyre DW.
BMC Genomics. 2018 Sep 27;19(1):714. doi: 10.1186/s12864-018-5094-y

Hepatitis virus (HCV) diagnosis and access to treatment in a UK cohort.
Adland E, Jesuthasan G, Downs L, Wharton V, Wilde G, McNaughton AL, Collier J, Barnes E, Klenerman P, Andersson M, Jeffery K, Matthews PC.
BMC Infect Dis. 2018 Sep 14;18(1):461. doi: 10.1186/s12879-018-3367-3.

Gonorrhoea treatment failure caused by a Neisseria gonorrhoeae strain with combined ceftriaxone and high-level azithromycin resistance, England, February 2018.
Eyre DW, Sanderson ND, Lord E, Regisford-Reimmer N, Chau K, Barker L, Morgan M, Newnham R, Golparian D, Unemo M, Crook DW, Peto TE, Hughes G, Cole MJ, Fifer H, Edwards A, Andersson MI.
Euro Surveill. 2018 Jul;23(27). doi: 10.2807/1560-7917.ES.2018.23.27.1800323.

DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing.
Anson LW, Chau K, Sanderson N, Hoosdally S, Bradley P, Iqbal Z, Phan H, Foster D, Oakley S, Morgan M, Peto TEA, Modernizing Medical Microbiology Informatics Group Mmmig, Crook DW, Pankhurst LJ.
J Med Microbiol. 2018 Mar;67(3):347-357. doi: 10.1099/jmm.0.000664. Epub 2018 Jan 10

Oxford Screening CSF and Respiratory samples ('OSCAR'): results of a pilot study to screen clinical samples from a diagnostic microbiology laboratory for viruses using Illumina next generation sequencing.
Sharp C, Golubchik T, Gregory WF, McNaughton AL, Gow N, Selvaratnam M, Mirea A, Foster D, Andersson M, Klenerman P, Jeffery K, Matthews PC.
BMC Res Notes. 2018 Feb 9;11(1):120. doi: 10.1186/s13104-018-3234-8.


Metalware-associated orthopaedic infections caused by Staphylococcus lugdunensis: An emerging pathogen.
Li A, Gow N, Atkins BL, Taylor A, Peto T, mcnally MA, Matthews PC.
J Infect. 2017 Oct;75(4):368-370. Doi: 10.1016/j.jinf.2017.05.013. Epub 2017 May 25. No abstract available.

Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: Risk factors for colonization and carriage, and genetic overlap with regional C. Difficile infection strains.
Stoesser N, Eyre DW, Quan TP, Godwin H, Pill G, 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; Modernising Medical Microbiology Informatics Group (MMMIG).
Plos One. 2017 Aug 16;12(8):e0182307. Doi: 10.1371/journal.pone.0182307. Ecollection 2017.

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing.
Street TL, Sanderson ND, Atkins BL, Brent AJ, Cole K, Foster D, mcnally MA, Oakley S, Peto L, Taylor A, Peto TEA, Crook DW, Eyre DW.
J Clin Microbiol. 2017 Aug;55(8):2334-2347. Doi: 10.1128/JCM.00462-17. Epub 2017 May 10.

A spinal infection with Staphylococcus pseudintermedius.
Darlow CA, Paidakakos N, Sikander M, Atkins B.
BMJ Case Rep. 2017 Aug 7;2017. Pii: bcr-2017-221260. Doi: 10.1136/bcr-2017-221260.


Screening, characterisation and prevention of Hepatitis B virus (HBV) co-infection in HIV-positive children in South Africa.
Jooste P, van Zyl A, Adland E, Daniels S, Hattingh L, Brits A, Wareing S, Goedhals D, Jeffery K, Andersson M, Goulder P, Matthews PC.
J Clin Virol. 2016 Dec;85:71-74. Doi: 10.1016/j.jcv.2016.10.017. Epub 2016 Oct 31.

Mycobacterium tuberculosis and prosthetic joint infection.
Sendi P, Brent A.
Lancet Infect Dis. 2016 Aug;16(8):893-4. Doi: 10.1016/S1473-3099(16)30142-6. No abstract available.

Outbreak or illusion: consequences of 'improved' diagnostics for gonorrhoea.
Bennett A, Jeffery K, O'Neill E, Sherrard J.
Int J STD AIDS. 2016 Jul 12. pii: 0956462416660928. [Epub ahead of print].

Detecting asymptomatic Trichomonas vaginalis in females using the BD ProbeTec™ Trichomonas vaginalis Qx nucleic acid amplification test.
Lord E, Newnham T, Dorrell L, Jesuthasan G, Clarke L, Jeffery K, Sherrard J.
Int J STD AIDS. 2016 May 5. pii: 0956462416649888. [Epub ahead of print].

Increasing burden of community-acquired pneumonia leading to hospitalisation, 1998-2014.
Quan TP, Fawcett NJ, Wrightson JM, Finney J, Wyllie D, Jeffery K, Jones N, Shine B, Clarke L, Crook D, Walker AS, Peto TE; Infections in Oxfordshire Research Database (IORD).
Thorax. 2016 Jun;71(6):535-42. doi: 10.1136/thoraxjnl-2015-207688. Epub 2016 Feb 17.

Infection and low back pain: seeking evidence or fear of exploring new indications for antibiotics?
Artus M, Fairbank J, Scarborough M, Foster N.
Eur Spine J. 2016 Mar 14. [Epub ahead of print] No abstract available.


Oral versus intravenous antibiotic treatment for bone and joint infections (OVIVA): study protocol for a randomised controlled trial.
Li HK, Scarborough M, Zambellas R, Cooper C, Rombach I, Walker AS, Lipsky BA, Briggs A, Seaton A, Atkins B, Woodhouse A, Berendt A, Byren I, Angus B, Pandit H, Stubbs D, McNally M, Thwaites G, Bejon P.
Trials. 2015 Dec 21;16:583. doi: 10.1186/s13063-015-1098-y.

HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults.
Matthews PC, Carlson JM, Beloukas A, Malik A, Jooste P, Ogwu A, Shapiro R, Riddell L, Chen F, Luzzi G, Jesuthasan G, Jeffery K, Jojic N, Ndung'u T, Carrington M, Goulder PJ, Geretti AM, Klenerman P.
J Infect Dis. 2016 Apr 15;213(8):1248-52. doi: 10.1093/infdis/jiv592. Epub 2015 Dec 9.

Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana.
Matthews PC, Beloukas A, Malik A, Carlson JM, Jooste P, Ogwu A, Shapiro R, Riddell L, Chen F, Luzzi G, Jaggernath M, Jesuthasan G, Jeffery K, Ndung'u T, Goulder PJ, Geretti AM, Klenerman P.
PLoS One. 2015 Jul 28;10(7):e0134037. doi: 10.1371/journal.pone.0134037. eCollection 2015.

Mycobacterial DNA Extraction for Whole-Genome Sequencing from Early Positive Liquid (MGIT) Cultures. Votintseva AA, Pankhurst LJ, Anson LW, Morgan MR, Gascoyne-Binzi D, Walker TM, Quan TP, Wyllie DH, Del Ojo Elias C, Wilcox M, Walker AS, Peto TE, Crook DW. J Clin Microbiol. 2015 Apr;53(4):1137-43.

Hepatitis C. Webster DP, Klenerman P, Dusheiko GM. Lancet. 2015 Mar 21;385(9973):1124-35.
Screening and treatment for hepatitis C: a balanced perspective. Matthews PC, Jeffery K, Klenerman P, Barnes E, Cooke G. BMJ. 2015 Feb 24;350:h644.


Microbiology and visual outcomes of culture-positive bacterial endophthalmitis in Oxford, UK. Gupta A, Orlans HO, Hornby SJ, Bowler IC. Graefes Arch Clin Exp Ophthalmol. 2014 Nov;252(11):1825-30.

Genomic pneumococcal load and CSF cytokines are not related to outcome in Malawian adults with meningitis. Wall EC, Gritzfeld JF, Scarborough M, Ajdukiewicz KM, Mukaka M, Corless C, Lalloo DG, Gordon SB. J Infect. 2014 Nov;69(5):440-6.

Multidrug-resistant Escherichia coli soft tissue infection investigated with bacterial whole genome sequencing. Buchanan R, Stoesser N, Crook D, Bowler IC. BMJ Case Rep. 2014 Oct 19;2014.

The clinical presentation of prosthetic joint infection. Barrett L, Atkins B. J Antimicrob Chemother. 2014 Sep;69 Suppl 1:i25-7.

Epidemiology and impact of HIV coinfection with hepatitis B and hepatitis C viruses in Sub-Saharan Africa. Matthews PC, Geretti AM, Goulder PJ, Klenerman P. J Clin Virol. 2014 Sep;61(1):20-33.

Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study. Pankhurst L, Macfarlane-Smith L, Buchanan J, Anson L, Davies K, O'Connor L, Ashwin H, Pike G, Dingle KE, Peto TE, Wordsworth S, Walker AS, Wilcox MH, Crook DW. Health Technol Assess. 2014 Aug;18(53):1-167.

Use of an automated blood culture system (BD BACTEC™) for diagnosis of prosthetic joint infections: easy and fast. Minassian AM, Newnham R, Kalimeris E, Bejon P, Atkins BL, Bowler IC. BMC Infect Dis. 2014 May 4;14:233.
Skin and soft tissue infections caused by nontuberculous mycobacteria. Atkins BL, Gottlieb T. Curr Opin Infect Dis. 2014 Apr;27(2):137-45.

Increased teicoplanin doses are associated with improved serum levels but not drug toxicity. Matthews PC, Chue AL, Wyllie D, Barnett A, Isinkaye T, Jefferies L, Lovering A, Scarborough M. J Infect. 2014 Jan;68(1):43-9.


One hundred and twelve infected arthroplasties treated with 'DAIR' (debridement, antibiotics and implant retention): antibiotic duration and outcome. Byren I, Bejon P, Atkins BL, Angus B, Masters S, McLardy-Smith P, Gundle R, Berendt A. J Antimicrob Chemother. 2009 Jun;63(6):1264-71. Erratum in: J Antimicrob Chemother. 2013 Dec;68(12):2964-5. J Antimicrob Chemother. 2011 May;66(5):1203.

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo Elias C, Johnson JR, Walker AS, Peto TE, Crook DW. J Antimicrob Chemother. 2013 Oct;68(10):2234-44.

Relationship between bacterial strain type, host biomarkers, and mortality in Clostridium difficile infection. 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 TE; Infections in Oxfordshire Research Database. Clin Infect Dis. 2013 Jun;56(11):1589-600.

Cost savings and clinical acceptability of an intravascular line tip culture triage policy. Colston J, Batchelor B, Bowler IC. J Hosp Infect. 2013 May;84(1):77-80.

High-dose daptomycin monotherapy cures Staphylococcus epidermidis 'endotipsitis' after failure of conventional therapy. Colston JM, Scarborough M, Collier J, Bowler IC. BMJ Case Rep. 2013 Apr 16;2013.
Endovascular stent-associated infection with Staphylococcus lugdunensis. Morris TC, Davies O, Bradlow WM, Jeffery K, Bowler IC. BMJ Case Rep. 2013 Feb 18;2013.


Surveillance of infection severity: a registry study of laboratory diagnosed Clostridium difficile. Schlackow I, Walker AS, Dingle K, Griffiths D, Oakley S, Finney J, Vaughan A, Gill MJ, Crook DW, Peto TE, Wyllie DH. PLoS Med. 2012;9(7):e1001279.
Clostridium septicum sepsis and its implications. Khalid M, Lazarus R, Bowler IC, Darby C. BMJ Case Rep. 2012 Sep 7;2012.


Performance of the MGIT TBc identification test and meta-analysis of MPT64 assays for identification of the Mycobacterium tuberculosis complex in liquid culture. Brent AJ, Mugo D, Musyimi R, Mutiso A, Morpeth S, Levin M, Scott JA.

J Clin Microbiol. 2011 Dec;49(12):4343-6. doi: 10.1128/JCM.05995-11. Epub 2011 Oct 12.

Microbiological diagnosis of prosthetic joint infections: a prospective evaluation of four bacterial culture media in the routine laboratory. Hughes HC, Newnham R, Athanasou N, Atkins BL, Bejon P, Bowler IC. Clin Microbiol Infect. 2011 Oct;17(10):1528-30.

Impact of a clonal outbreak of extended-spectrum ß-lactamase-producing Klebsiella pneumoniae in the development and evolution of bloodstream infections by K. pneumoniae and Escherichia coli: an 11 year experience in Oxfordshire, UK. Webster DP, Young BC, Morton R, Collyer D, Batchelor B, Turton JF, Maharjan S, Livermore DM, Bejon P, Cookson BD, Bowler IC. J Antimicrob Chemother. 2011 Sep;66(9):2126-35.

Acute necrotizing sinusitis caused by Staphylococcus lugdunensis. Matthews PC, Lazarus R, Protheroe A, Milford C, Bowler IC. J Clin Microbiol. 2011 Jul;49(7):2740-2.

Serial measurement of the C-reactive protein is a poor predictor of treatment outcome in prosthetic joint infection. Bejon P, Byren I, Atkins BL, Scarborough M, Woodhouse A, McLardy-Smith P, Gundle R, Berendt AR. J Antimicrob Chemother. 2011 Jul;66(7):1590-3.

In vitro antibiotic susceptibility patterns of bacterial keratitis isolates in Oxford, UK: a 10-year review. Orlans HO, Hornby SJ, Bowler IC. Eye (Lond). 2011 Apr;25(4):489-93.

Two-stage revision for prosthetic joint infection: predictors of outcome and the role of reimplantation microbiology. Bejon P, Berendt A, Atkins BL, Green N, Parry H, Masters S, McLardy-Smith P, Gundle R, Byren I. J Antimicrob Chemother. 2010 Mar;65(3):569-75. Erratum in: J Antimicrob Chemother. 2011 May;66(5):1204.

Risk score to stratify children with suspected serious bacterial infection: observational cohort study. Brent AJ, Lakhanpaul M, Thompson M, Collier J, Ray S, Ninis N, Levin M, MacFaul R. Arch Dis Child. 2011 Apr;96(4):361-7. doi: 10.1136/adc.2010.183111. Epub 2011 Jan 24.