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Dr Mark Holmes MA, VetMB, PhD, MRCVS

Dr Mark Holmes, MA, VetMB, PhD, MRCVS

Reader in Microbial Genomics and Veterinary Science

Director of the Cambridge Clinical Research Outreach Programme


Bacterial genomics

Veterinary epidemiology

Evidence-based veterinary medicine

Clinical research

Mark Holmes is accepting applications for PhD students.

Mark Holmes is available for consultancy.

Office Phone: 01223 337636


Ph.D. in Veterinary Immunology. University of Cambridge. 1989

M.A. University of Cambridge 1986

Vet.MB. University of Cambridge 1985

B.A. Medical Sciences (Pt I) and Computer Science (Pt I). University of Cambridge 1982


2014 to date. Reader in Microbial Genomics and Veterinary Science, University of Cambridge.

1999 - 2014. Senior Lecturer in Preventive Veterinary Medicine, University of Cambridge.

1990 – 1999 Lecturer in Preventive Veterinary Medicine, University of Cambridge

Responsible for teaching production animal medicine, cattle medicine, epidemiology, veterinary immunology, statistics, and clinical research methodology.

Director of the Cambridge Infectious Disease Consortium Outreach Program.

Supervision of 8 successful PhD students

2001 TVI during FMD outbreak based in Bury St Edmunds and Exeter

1989-1990: Post doctoral research assistant working on a project entitled “COPD- The role of the immune system and treatment by immunotherapy”

1986-1989: Wellcome Trust Veterinary Research Training Scholar University of Cambridge

1985-1986:  Mixed veterinary practice in Lancashire.

Subject groups/Research projects

Infection and Immunity:

Microbial Genomics and Antimicrobial Resistance

Clinical Research/Evidence-based medicine

Mathematical Biology:

Departments and Institutes

Cambridge Infectious Diseases:

Research Interests

Mark Holmes leads a research group whose current focus of research follows their discovery of a new livestock-associated MRSA harboring a mecA homologue (now named mecC). The new MRSA was discovered during an epidemiological project looking at the transmission of S. aureus in dairy cows by one of our PhD students, Laura Garcia Alvarez. The original isolate was whole genome sequenced and analysed in collaboration with the Wellcome Trust Sanger Institute by Matt Holden and colleagues. We subsequently obtained funding from Defra and the MRC to investigate the discovery further. We are now undertaking studies to establish the prevalence and diversity of the new MRSA using whole genome sequencing and other techniques. In collaboration with Prof Alexander Tomasz’s lab at Rockefeller University we have recently published the results of a study into the function of the PBP2a produced by the mecC gene.

This work is funded by the BBSRC, Defra, and the MRC.

Mark Holmes also has interests in clinical research (including animal welfare) and evidence-based veterinary medicine and has published a number of papers and books in these areas.

Main collaborators

  • Sharon Peacock, Dept of Medicine, University of Cambridge
  • Julian Parkhill & Matt Holden, Wellcome Trust Sanger Institute
  • Ruth Zadoks, Moredun Institute
  • Giles Edwards, Scottish MRSA reference laboratory
  • Robert Skov & Anders Rhod Larsen, Serum Statens Institut, Copenhagen
  • Angela Kearns & Bruno Pichon, Health Protection Agency
  • Alexander Tomasz, Rockefeller University
  • Herminia de Lencastre, ITQB/UNL
  • Frederic Laurent, University of Lyon
  • Wolfgang Witte & Christiane Cuny, Robert Koch-Institutes
  • Katleen Hermans, Ghent University
  • Birgit Walther & Torsten Semmler, Freie Universität Berlin
  • Sara Hæggman, Swedish Institute for Communicable Disease Control


  • Immunology
  • Molecular epidemiology
  • Infection
  • Epidemiology
  • Bioinformatics
  • Bacteriology

Key Publications

Riggs J, Frazer Jennings JL, Friend EJ, Halfacree Z, Nelissen P, Holmes MA, Jackie Demetriou J. Full thickness skin grafting for distal limb defects in cats and dogs: factors affecting the outcome of 58 cases (2005-2012). JAVMA, Vol 247, No. 9, November 1, 2015

De Sousa R, Sutcliffe M, Rousset N, Holmes MA, Langley-Hobbs SJ. Treatment of cranial cruciate ligament rupture in the feline stifle: Biomechanical comparison of a standard fabella-tibial suture and lateral sutures placed between quasi-isometric points. Veterinary and Comparative Orthopaedics and Traumatology, September 18, 2015 doi:10.3415/VCOT-14-05-0078

Harrison EM, Ba X, Blane B, Ellington M, Loeffler A, Hill R, Holmes MA, Peacock SJ. PBP2a substitutions linked to ceftaroline resistance in MRSA isolates from the United Kingdom. J Antimicrob Chemother. 2015 Oct 12. pii: dkv317. [Epub ahead of print]

Ba X, Harrison EM, Lovering A, Gleadall N, Parkhill J, Zadoks RN, Peacock SJ, Holden MTG, Paterson GK, and Holmes MA. Old drugs to treat resistant bugs: methicillin-resistant Staphylococcus aureus isolates with mecC are susceptible to a combination of penicillin and clavulanic acid. 21 September 2015, Antimicrob. Agents Chemother. doi:10.1128/AAC.01469-15

Murray GG, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A, Welch JJ. The effect of genetic structure on molecular dating and tests for temporal signal. Methods in Ecology and Evolution 22 Sep 2015. DOI: 10.1111/2041-210X.12466

Hahn C, Harrison EM, Parkhill J, Holmes MA, Paterson GK. Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66. Genome Announc. May/June 2015 vol. 3 no. 3 e00697-15. doi: 10.1128/genomeA.00697-15

Hadjirin NF, Lay EM, Paterson GK, Harrison EM, Peacock SJ, Herrtage ME, Parkhill J, Holmes MA. Detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015. Euro Surveill. 2015 Jun 18;20(24)

Aiken MJ, Hughes TK, Abercromby RH, Holmes MA, Anderson AA. Prospective, Randomized Comparison of the Effect of Two Antimicrobial Regimes on Surgical Site Infection Rate in Dogs Undergoing Orthopedic Implant Surgery. Vet Surg. 2015 Jul;44(5):661-7. doi: 10.1111/vsu.12327. Epub 2015 Mar 17.

Paterson GK, Harrison EM, Murray GGR, Welch JJ, Warland JH, Holden MTG, Morgan FJE, Ba X, Koop G, Harris S, Maskell DJ, Peacock SJ, Herrtage ME, Parkhill J, Holmes MA. Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat. Commun. 6:6560 doi: 10.1038/ncomms7560 (2015).

Espinosa-Gongora C, Harrison, E, Moodley A, Guardabassi L, Holmes MA. Methicillin-resistant Staphylococcus aureus carrying mecC in captive mara. J Antimicrob Chemother 2015 Feb 25. doi:10.1093/jac/dkv024

Salgüero R, Johnson V, Williams D, Hartley C, Holmes MA, Dennis R, Herrtage ME. CT dimensions, volumes and densities of normal canine eyes. Veterinary Record 2015;176:386 doi:10.1136/vr.102940

Larsen A, Petersen A, Holmes MA; Kearns A, Hill R, Edwards G, Teale C, Skov R. Utility of a newly developed Muller Hinton E agar for the detection of MRSA carrying the novel mecA homologue mecC. J Antimicrob Chemother 2014 Dec 23 doi:10.1093/jac/dku512

McCarthy AJ, Harrison EM, Stanczak-Mrozek K, Leggett B, Waller A, Holmes MA, Lloyd DH, Lindsay JA, Loeffler A. Genomic insights into the rapid emergence and evolution of MDR in Staphylococcus pseudintermedius. J Antimicrob Chemother. 2015 Apr;70(4):997-1007. doi: 10.1093/jac/dku496. Epub 2014 Dec 18

Ives EJ, Doyle L, Holmes MA, Williams TL, Vanhaesebrouck AE. Association between the findings on MRI screening for syringomyelia in asymptomatic Cavalier King Charles spaniels and observation of clinical signs consistent with syringomyelia in later life. Vet J. 2015 Jan;203(1):129-30. doi: 10.1016/j.tvjl.2014.11.010. Epub 2014 Nov 20.

Kerschner H, Harrison EM, Hartl R, Holmes MA and Apfalter P. First report of mecC MRSA in human samples from Austria: molecular characteristics and clinical data. New Microbe and New Infect 2015; 3: 4–9

Porrero MC, Harrison EM, Fernández-Garayzabal JF, Paterson GK, Díez- Guerrier A, Holmes MA, Domínguez L Detection of mecC-river water: a potential role for water in the environmental dissemination. Environmental Microbiology Reports 2014 July 14 DOI:10.1111/1758-2229.12191

Prenafeta A, Sitjà M, Holmes MA, Paterson GK. Short communication: Biofilm production characterization of mecA and mecC methicillin-resistant Staphylococcus aureus isolated from bovine milk in Great Britain. J Dairy Sci. 2014 Aug;97(8):4838-41. doi: 10.3168/jds.2014-7986. Epub 2014 Jun 2. 70.

Harrison EM, Weinert LA, Holden MT, Welch JJ, Wilson K, Morgan FJ, Harris SR, Loeffler A, Boag AK, Peacock SJ, Paterson GK, Waller AS, Parkhill J, Holmes MA. A Shared Population of Epidemic Methicillin-Resistant Staphylococcus aureus 15 Circulates in Humans and Companion Animals. MBio. 2014 May 13;5(3). pii: e00985-13. doi: 10.1128/mBio.00985-13.

Gómez Selgas A, Bexfield N, Scase TJ, Holmes MA, Watson P. Total serum bilirubin as a negative prognostic factor in idiopathic canine chronic hepatitis. J Vet Diagn Invest. 2014 Mar 12. [Epub ahead of print]

Christiansen MT, Kaas RS, Chaudhuri RR, Holmes MA, Hasman H, et al. (2014) Genome-Wide High-Throughput Screening to Investigate Essential Genes Involved in Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Survival. PLoS ONE 9(2): e89018. doi:10.1371/journal.pone.0089018

Paterson GK, Harrison EM, Holmes MA. The emergence of mecC methicillin-resistant Staphylococcus aureus. Trends Microbiol. 2014 Jan;22(1):42-7. doi: 10.1016/j.tim.2013.11.003. Epub 2013 Dec 9.

Hadjirin NF, Harrison EM, Holmes MA, Paterson GK. Conjugative transfer frequencies of mef(A) containing Tn1207.3 to macrolide susceptible Streptococcus pyogenes belonging to different emm types. Lett Appl Microbiol. 2014 Jan 3. doi: 10.1111/lam.12213.

De Sousa RJ, Knudsen CS, Holmes MA, Langley-Hobbs SJ. Quasi-Isometric Points for the Technique of Lateral Suture Placement in the Feline Stifle Joint. Vet Surg. 2014 Jan 8. doi: 10.1111/j.1532-950X.2014.12090.x.

Little CJ, Ferasin L, Ferasin H, Holmes MA. Purring in cats during auscultation: how common is it, and can we stop it? J Small Anim Pract. 2014 Jan;55(1):33-8. doi: 10.1111/jsap.12159. Epub 2013 Dec 13.

Paterson GK, MorganFJE, Harrison EM, PeacockSJ, ParkhillJ, ZadoksRN and HolmesMA. Prevalence and properties of mecC methicillin-resistant Staphylococcus aureus (MRSA) in bulk tank milk in Great Britain. J Antimicrob Chemother. 2014 Mar;69(3):598-602. doi: 10.1093/jac/dkt417

Harrison EM, Paterson GK, Holden MTG, Ba X, Rolo J, Morgan FJE, Pichon B, Kearns A, Zadoks RN, Peacock SJ, Parkhill J, Holmes MA. A novel hybrid SCCmec-mecC region in Staphyloccus sciuriJ Antimicrob Chemother. 2013 Nov 11. [Epub ahead of print]

Paterson GK, Morgan FJ, Harrison EM, Cartwright EJ, Török ME, Zadoks RN, Parkhill J, Peacock SJ, Holmes MA. Prevalence and characterization of human mecC methicillin-resistant Staphylococcus aureus isolates in England. J Antimicrob Chemother. 2013 Nov 27. [Epub ahead of print]

Ba X, Harrison EM, Edwards GF, Holden MTG, Rhod Larsen A, Petersen A, Skov RL, Peacock SJ, Parkhill J, Paterson GK, Holmes MA. Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin-resistant on susceptibility testing but lack the mec gene. J Antimicrob Chemother 2014 Mar;69(3):594-7. doi: 10.1093/jac/dkt418

Hall JL, Holmes MA, Baines SJ. Prevalence and antimicrobial resistance of canine urinary tract pathogens. Vet Rec. 2013 Dec 7;173(22):549. doi: 10.1136/vr.101482. Epub 2013 Oct 24.

Skov R, Larsen AR, Kearns A, Holmes MA; Teale C, Hill R. Phenotypic detection of mecC-MRSA: Cefoxitin is more reliable than oxacillin. J Antimicrob Chemother. 2013 doi:10.1093/jac/dkt341 published online 12 Sep 13

Freeman PM, Holmes MA, Jeffery ND, Granger N. Time requirement and effect on owners of home-based management of dogs with severe chronic spinal cord injury. Journal of Veterinary Behavior: Clinical Applications and Research 2013, doi:10.1016/j.jveb.2013.06.001 published online 11 July 2013

Paterson GK, Harrison EM, Craven EF, Petersen A, Larsen AR, Ellington MJ, Török ME, Peacock SJ, Parkhill J, Zadoks RN, Holmes MA. Incidence and characterisation of methicillin-resistant Staphylococcus aureus (MRSA) from nasal colonisation in participants attending a cattle veterinary conference in the UK. PLoS ONE 8(7): e68463. doi:10.1371/journal.pone.0068463

Rousset N, Holmes MA, Caine A, Dobson J, Herrtage ME. Clinical and low-field MRI characteristics of injection site sarcoma in 19 cats. Vet Radiol Ultrasound. 2013 Jun 14. doi: 10.1111/vru.12067.

Cartwright EJ, Paterson GK, Raven KE, Harrison EM, Gouliouris T, Kearns A, Pichon B, Edwards G, Skov RL, Larsen AR, Holmes MA, Parkhill J, Peacock SJ, Török ME. Use of VITEK 2 antimicrobial susceptibility profile to identify mecC in methicillin-resistant Staphylococcus aureus. J Clin Microbiol. 2013 May 29.

Harrison EM, Paterson GK, Holden MT, Larsen J, Stegger M, Larsen AR, Petersen A, Skov RL, Christensen JM, Bak Zeuthen A, Heltberg O, Harris SR, Zadoks RN, Parkhill J, Peacock SJ, Holmes MA. Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC. EMBO Mol Med. 2013 Apr;5(4):509-15. doi: 10.1002/emmm.201202413.

Becker K, Larsen AR, Skov RL, Paterson GK, Holmes MA, Sabat AJ, Friedrich AW, Köck R, Peters G, Kriegeskorte A. Evaluation of a Modular Multiplex-PCR Methicillin-Resistant Staphylococcus aureus Detection Assay Adapted for mecC Detection. J Clin Microbiol. 2013 Jun;51(6):1917-9. doi: 10.1128/JCM.00075-13.

Harrison EM, Paterson GK, Holden MTG, Morgan FEJ, Rhod Larsen A, Leroy S, Zadoks RN, Peacock SJ, Parkhill J, Holmes MA. A Staphyloccocus xylosus isolate with a new mecC allotype provides insights into the evolutionary origins of the type XI SCCmec. Antimicrob Agents Chemother. 2013 Mar;57(3):1524-8. doi: 10.1128/AAC.01882-12.

Paterson GK, Larsen J, Harrison EM, Larsen AR, Morgan FJ, Peacock SJ, Parkhill J, Zadoks RN, Holmes MA. First detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in bulk tank milk in the United Kingdom, January to July 2012. Euro Surveill. 2012 Dec 13;17(50). doi:pii: 20337.

Kim C, Milheiriço C, Gardete D, Holmes MA, Holden MTG, de Lencastre H, and Tomasz A. Properties of a novel PBP2A protein homologue from Staphylococcus aureus strain LGA251 and its contribution to the β-lactam resistant phenotype. 2012 J. Biol. Chem [ePub ahead of print].

Paterson GK, Larsen AR, Robb A, Edwards GE, Pennycott TW, Foster G, Mot D, Hermans K, Baert K, Peacock SJ, Parkhill J, Zadoks RN, Holmes MA. The newly described mecA homologue, mecALGA251, is present in methicillin-resistant Staphylococcus aureus isolates from a diverse range of host species. J Antimicrob Chemother. 2012 Aug 31. [Epub ahead of print]

Pichon B, Hill R, Laurent F, Larsen AR, Skov RL, Holmes M, Edwards GF, Teale C, Kearns AM. Development of a real-time quadruplex PCR assay for simultaneous detection of nuc, Panton-Valentine leucocidin (PVL), mecA and homologue mecALGA251. J Antimicrob Chemother. 2012 Jun 11. [Epub ahead of print]

Stegger, M., Andersen, P. S., Kearns, A., Pichon, B., Holmes, M. A., Edwards, G., Laurent, F., Teale, C., Skov, R., Larsen, A. R. Rapid detection, differentiation and typing of methicillin-resistant Staphylococcus aureus harbouring either mecA or the new mecA homologue mecA(LGA251). Clin Microbiol Infect 2012 18:4 395-400

Holmes MA. Systematic reviews in small animal veterinary medicine: what are they and why do we need them? J Small Anim Pract. 2012 Apr;53(4):195-6.

Holmes, MA. MRSA found in dairy cows and people in Europe. Cattle Practice (peer reviewed paper) 2011 19:2 93-99

Holmes, M.A. & Zadoks, R.N. Methicillin resistant S. aureus in human and bovine mastitis. J Mammary Gland Biol Neoplasia. 2011 Dec;16(4):373-82.

García-Álvarez L, Holden MT, Lindsay H, Webb CR, Brown DF, Curran MD, et al. A descriptive study of MRSA harbouring a novel mecA homologue emerging in human and bovine populations in the United Kingdom and Denmark. Lancet Infect Dis. 2011 Aug;11(8):595-603

Alvarez LG, Webb CR, Holmes MA. A novel field-based approach to validate the use of network models for disease spread between dairy herds. Epidemiol Infect. 2011:Feb 1-12.

Lucianez A, Holmes MA, Tucker AW. Relationships between Processing Delay and Microbial Load of Broiler Neck Skin Samples. J Food Prot. 2010; 73(1): 26-31.

Holmes MA, Jeffcott L. Equitation science, rider effects, saddle and back problems in horses: can technology provide the answer? Vet J. 2010; 184(1): 5-6.

Belshaw Z, Constantino-Casas F, Brearley M, Dunning M, Holmes MA, Dobson J. COX-2 expression and outcome in canine nasal carcinomas treated with hypofractionated radiotherapy. Veterinary and Comparative Oncology. 2011. 9(2):141-8

Tatton B, Jeffery N, Holmes MA. Predicting recovery of urination control in cats after sacrocaudal injury: a prospective study. J Small Anim Pract. 2009; 50(11): 593-6.

Holmes MA. Philosophical foundations of evidence-based medicine for veterinary clinicians. J Am Vet Med Assoc. 2009; 235(9): 1035-9.

Carruthers H, Rusbridge C, Dube MP, Holmes MA, Jeffery N. Association between cervical and intracranial dimensions and syringomyelia in the cavalier King Charles spaniel. J Small Anim Pract. 2009; 50(8): 394-8.