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Mark Holmes

Antimicrobial resistance, Molecular Epidemiology, Clinical Veterinary Research, Evidence-based Veterinary Medicine

My group's  focus of research follows our discovery of a new livestock-associated MRSA harboring a mecC gene. mecC MRSA was discovered during an epidemiological project looking at the transmission of S. aureus in dairy cows by a former PhD student in the group, Laura Garcia Alvarez. The original isolate was whole genome sequenced and analysed in collaboration with the Wellcome Trust Sanger Institute by Matt Holden (now at St Andrews) and Julian Parkhill. We subsequently obtained funding from Defra and the MRC to investigate the discovery further.  

Milk sampling during our MRSA studiesIn collaboration with Prof Alexander Tomasz’s lab at Rockefeller University we have  published the results of a study into the function of the PBP2a produced by the mecC gene showing that it was differentially resistant to cephalosporins. We continue to work on the biology, evolution and epidemiology of mecC MRSA.
We have developed a Hi-C metagenomics wet-lab and bioinformatics pipeline able to examine antimicrobial resistance (AMR) genes within individual species within microbiomes of interest. We have completed studies comparing high antibiotic use farms with low antibiotic use farms, groups of pigs over the course of antibiotic treatment, experimental infections of chickens with and without antibiotic treatment, and other studies looking at the dynamics of AMR genes in complex microbiomes.
We are members of the DETECTIVE consortium looking at AMR in Chinese hospitals with Prof Alan McNally and colleagues at the University of Birmingham. We lead the NEOSTAR project, a cross-disciplinary social science/microbiology project looking at links between agricultural and human antibiotic resistance in North East India.

Mark 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

Key Publications

Google Scholar - list of all publications

Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid. Ba X, Harrison EM, Lovering AL, Gleadall N, Zadoks R, Parkhill J, Peacock SJ, Holden MT, Paterson GK, Holmes MA. Antimicrob Agents Chemother. 2015 Dec;59(12):7396-404. Epub 2015 Sep 21.

Detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015. Hadjirin NF, Lay EM, Paterson GK, Harrison EM, Peacock SJ, Parkhill J, Zadoks RN, Holmes MA. Euro Surveill. 2015 Jun 18;20(24). pii: 21156.

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Paterson GK, Harrison EM, Murray GG, Welch JJ, Warland JH, Holden MT, Morgan FJ, Ba X, Koop G, Harris SR, Maskell DJ, Peacock SJ, Herrtage ME, Parkhill J, Holmes MA. Nat Commun. 2015 Mar 27;6:6560. doi: 10.1038/ncomms7560.

A shared population of epidemic methicillin-resistant Staphylococcus aureus 15 circulates in humans and companion animals. 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.
MBio. 2014 May 13;5(3):e00985-13. doi: 

Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. García-Álvarez L, Holden MT, Lindsay H, Webb CR, Brown DF, Curran MD, Walpole E, Brooks K, Pickard DJ, Teale C, Parkhill J, Bentley SD, Edwards GF, Girvan EK, Kearns AM, Pichon B, Hill RL, Larsen AR, Skov RL, Peacock SJ, Maskell DJ, Holmes MA. Lancet Infect Dis. 2011 Aug;11(8):595-603.

 Mark Holmes

Profesor Mark Holmes

Professor of Microbial Genomics and Veterinary Science

Associate Dean for Research

Group members: Dr Xiaoliang (Ibrahim) Ba, Dr Stefan De Vries,  Dr Srishti Gupta, Dr Michael Bateman, Ms Nazreen Hadjarin, Ms Claire Raisen

    Plain English

    The main theme of my current research is in looking at how resistance to antibiotics develops and is maintained in the bacteria that live in human and animal hosts.

    mecC MRSA isolates
    Location of original human and bovine mecC MRSA isolates