Dr Mathew Upton

Dr Mathew Upton

Associate Professor (Reader) in Medical Microbiology

School of Biomedical & Healthcare Sciences (Plymouth University Peninsula Schools of Medicine and Dentistry)


ORCID ID - orcid.org/0000-0003-4287-6396

May 2013 - Reader in Medical Microbiology, University of Plymouth

April 2014 - Co-founder and Director at Spectromics Ltd (http://www.spectromics.com/)

June 2011 - Senior Lecturer in Medical Microbiology, University of Manchester

June 2001 - Lecturer in Medical Microbiology, University of Manchester

Following BSc and PhD studies in Newcastle, I completed a number of postdoc projects in Aberdeen, Antarctica, Bristol, Liverpool and New Zealand, before taking up a lectureship in Manchester.


BSc (Hons) Microbiology, University of Newcastle

PhD Microbial Ecology, University of Newcastle

Professional membership

Society for General Microbiology

Society for Applied MicrobiologyAmerican Society for Microbiology

European Society for Clinical Microbiology

Roles on external bodies

Editor, Journal of Medical Microbiology
Editor, Journal of Applied Microbiology
Editor, Letters in Applied Microbiology
Panel member and author, HigherEducation Academy National Subject Profile in Microbiology (2008)

Teaching interests

Areas of teaching interest relate to medical microbiology, bacterial genomics and antibiotic resistance.

Research interests

Understanding the inner workings of bacterial pathogens

The vast majority of bacteria that live in and on our bodies contribute significantly to our health and well-being. However, sometimes we succumb to bacterial infections and, increasingly, these are becoming harder to treat due to antibiotic resistance. My group focuses on investigation of E. coli strains that cause urinary tract infections, a very common infection that is often mild, but can lead to severe debilitation, or death. The introduction of next generation DNA sequencing technologies has revolutionized the way we examine the mechanisms that pathogenic bacteria use to cause disease or evade the action of antibiotics. By studying their genomes, we aim to understand these bacteria and will be able to develop specific molecular assays for rapid detection and for outbreak investigation.

The above work is carried out in collaboration with colleagues at University of Queesnland, Brisbane (Drs Scott Beatson and Makrina Totsika and Prof Mark Schembri) and University of Liverpool (Prof Craig Winstanley).

Plugging the gaps in the antibiotic discovery pipeline

The WHO have declared that antibiotic resistance is one of the major threats to human health. Very recently, the Chief Medical Officer raised this issue nationally and the topic was even highlighted at the G8 summit in June 2013. However, there is still a real need to discover novel antibiotics. Infections caused by drug resistant pathogens are a significant cause of morbidity and  mortality and pan-resistant organisms are becoming less rare. My group runs a programme of natural product screening for discovery of bacteriocins, antimicrobial peptides produced by bacteria. The programme is supported by use of next generation sequencing methods to determine bacterial genome sequences and generate metagenomic datasets that can be interrogated with various software tools for identification of putative bacteriocins.

Lead compounds are being developed towards clinical use with commercially focused funding from BBSRC and other sources.


Scopus author ID - 35593933700

ResearchGate profile - Mathew_Upton

Research degrees awarded to supervised students

I have supervised 16 PhD students and over 70 MSc research projects. These projects have all been in the field of medical microbiology and have involved collaborators at UK universities, Public Health England (formerly HPA) and NHS Trusts.

Grants & contracts

Recent funding

Innovate UK/BBSRC Efficient production of first in class antimicrobial therapeutics from an integrated synthetic biology approach. Industrial Biocatalyst award with Ingenza Ltd, Edinburgh - May 2015-APril 2017 (Lead Academic, awarded £217,000)

Public Health England. PhD Studentship Co-infection during influenza. October 2014 - September 2017 (Co-I; £90,000)

Healthcare Infection Society. MRSA genome sequence analysis. March 2014 (PI; £9,900)

Plymouth Hospitals NHS Trust Charitable Funds. Investigation of water-borne pathogens in Critical Care Areas using genomic approaches. May 2013 (Co-I; £11,850) 

BBSRC, Follow on Fund. Development of epidermicin for nasaldecolonisationof MRSA carriage. March 2012 (PI; £132,000)

UMIP, University of Manchester. Development of methods for rapid detection of UTI. August 2012 (Co-PI; £102,000)

UMIP, University of Manchester. Recombinant expression of antimicrobial peptides. July 2011 (PI; £23,000)

Department of Health, UK National Innovation Centre and UMIP,University of Manchester, Development of point of care diagnostics forurinary tract infection. July 2011 (Co-PI; £54,000)

Department of Health, UK National Innovation Centre and UMIP,University of Manchester, Development of an in-situ indicator of cathetercolonisation. July 2011 (Co-PI; £80,000)

Welcome Trust, Understanding UPEC biology. March 2011 (CoI with C Winstanley, Liverpool;£113,500)

BBSRC, Regulatory and market consultancy for a novel antibiotic.September 2010 (PI; £15,500)

UMIP, University of Manchester. Antimicrobial peptides activeagainst staphylococci. December 2008 (PI; £75,000)

Key publications are highlighted

Handley KM, Upton M, Beatson SA, Héry M & Lloyd JR 2013 'Genome Sequence of Hydrothermal Arsenic-Respiring Bacterium Marinobacter santoriniensis NKSG1T' Genome Announc 1, (3) Author Site , DOI
AlRabiah H, Correa E, Upton M & Goodacre R 2013 'High-throughput phenotyping of uropathogenic E. coli isolates with Fourier transform infrared spectroscopy' Analyst 138, (5) 1363-1369 Author Site , DOI
Govindji N, Wills P, Upton M, Tirelli N, Yeates S & Webb M 2013 'The antibiofilm effects of Byotrol™ G32' J Appl Microbiol 114, (5) 1285-1293 Author Site , DOI
Upton M, Cotter P & Tagg J 2012 'Antimicrobial peptides as therapeutic agents' Int J Microbiol 2012, Author Site , DOI
Floyd RV, Upton M, Hultgren SJ, Wray S, Burdyga TV & Winstanley C 2012 'Escherichia coli-mediated impairment of ureteric contractility is uropathogenic E. coli specific' J Infect Dis 206, (10) 1589-1596 Author Site , DOI
Gibreel TM, Dodgson AR, Cheesbrough J, Bolton FJ, Fox AJ & Upton M 2012 'High metabolic potential may contribute to the success of ST131 uropathogenic Escherichia coli' J Clin Microbiol 50, (10) 3202-3207 Author Site , DOI
Sandiford S & Upton M 2012 'Identification, characterization, and recombinant expression of epidermicin NI01, a novel unmodified bacteriocin produced by Staphylococcus epidermidis that displays potent activity against Staphylococci' Antimicrob Agents Chemother 56, (3) 1539-1547 Author Site , DOI
Gibreel TM, Dodgson AR, Cheesbrough J, Fox AJ, Bolton FJ & Upton M 2012 'Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from Northwest England' J Antimicrob Chemother 67, (2) 346-356 Author Site , DOI
Al-Mahrous MM & Upton M 2011 'Discovery and development of lantibiotics; antimicrobial agents that have significant potential for medical application' Expert Opin Drug Discov 6, (2) 155-170 Author Site , DOI
Al-Hamad A, Burnie J & Upton M 2011 'Enhancement of antibiotic susceptibility of Stenotrophomonas maltophilia using a polyclonal antibody developed against an ABC multidrug efflux pump' Can J Microbiol 57, (10) 820-828 Author Site , DOI
Al-Mahrous MM, Jack RW, Sandiford SK, Tagg JR, Beatson SA & Upton M 2011 'Identification of a haemolysin-like peptide with antibacterial activity using the draft genome sequence of Staphylococcus epidermidis strain A487' FEMS Immunol Med Microbiol 62, (3) 273-282 Author Site , DOI
Totsika M, Beatson SA, Sarkar S, Phan M-D, Petty NK, Bachmann N, Szubert M, Sidjabat HE, Paterson DL & Upton M 2011 'Insights into a Multidrug Resistant Escherichia coli Pathogen of the Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms' PLOS ONE 6, (10) Author Site , DOI
Wescombe PA, Upton M, Renault P, Wirawan RE, Power D, Burton JP, Chilcott CN & Tagg JR 2011 'Salivaricin 9, a new lantibiotic produced by Streptococcus salivarius' Microbiology 157, (Pt 5) 1290-1299 Author Site , DOI
Ben-Darif E, De Pinna E, Threlfall EJ, Bolton FJ, Upton M & Fox AJ 2010 'Comparison of a semi-automated rep-PCR system and multilocus sequence typing for differentiation of Salmonella enterica isolates' J Microbiol Methods 81, (1) 11-16 Author Site , DOI
Ben-Darif E, Jury F, De Pinna E, Threlfall EJ, Bolton FJ, Fox AJ & Upton M 2010 'Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes' J Clin Microbiol 48, (4) 1055-1060 Author Site , DOI
Daly KM, Upton M, Sandiford SK, Draper LA, Wescombe PA, Jack RW, O'Connor PM, Rossney A, Goetz F & Hill C 2010 'Production of the Bsa Lantibiotic by Community-Acquired Staphylococcus aureus Strains' JOURNAL OF BACTERIOLOGY 192, (4) 1131-1142 Author Site , DOI
Al-Mahrous M, Sandiford SK, Tagg JR & Upton M 2010 'Purification and characterization of a novel delta-lysin variant that inhibits Staphylococcus aureus and has limited hemolytic activity' Peptides 31, (9) 1661-1668 Author Site , DOI
Lau SH, Cheesborough J, Kaufmann ME, Woodford N, Dodgson AR, Dodgson KJ, Bolton EJ, Fox AJ & Upton M 2010 'Rapid identification of uropathogenic Escherichia coli of the O25:H4-ST131 clonal lineage using the DiversiLab repetitive sequence-based PCR system' Clin Microbiol Infect 16, (3) 232-237 Author Site , DOI
Moat J, Cargill J, Shone J & Upton M 2009 'Application of a novel decontamination process using gaseous ozone' Can J Microbiol 55, (8) 928-933 Author Site , DOI
Cargill JS & Upton M 2009 'Low concentrations of vancomycin stimulate biofilm formation in some clinical isolates of Staphylococcus epidermidis' J Clin Pathol 62, (12) 1112-1116 Author Site , DOI
Al-Hamad A, Upton M & Burnie J 2009 'Molecular cloning and characterization of SmrA, a novel ABC multidrug efflux pump from Stenotrophomonas maltophilia' J Antimicrob Chemother 64, (4) 731-734 Author Site , DOI
Clermont O, Dhanji H, Upton M, Gibreel T, Fox A, Boyd D, Mulvey MR, Nordmann P, Ruppe E & Sarthou JL 2009 'Rapid detection of the O25b-ST131 clone of Escherichia coli encompassing the CTX-M-15-producing strains' JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY 64, (2) 274-277 Author Site , DOI
Macintosh RL, Brittan JL, Bhattacharya R, Jenkinson HF, Derrick J, Upton M & Handley PS 2009 'The terminal A domain of the fibrillar accumulation-associated protein (Aap) of Staphylococcus epidermidis mediates adhesion to human corneocytes' J Bacteriol 191, (22) 7007-7016 Author Site , DOI
Kwan PSL, Birtles A, Bolton FJ, French NP, Robinson SE, Newbold LS, Upton M & Fox AJ 2008 'Longitudinal study of the molecular epidemiology of Campylobacter jejuni in cattle on dairy farms' Appl Environ Microbiol 74, (12) 3626-3633 Author Site , DOI
Lau SH, Reddy S, Cheesbrough J, Bolton FJ, Willshaw G, Cheasty T, Fox AJ & Upton M 2008 'Major uropathogenic Escherichia coli strain isolated in the northwest of England identified by multilocus sequence typing' J Clin Microbiol 46, (3) 1076-1080 Author Site , DOI
Kwan PSL, Barrigas M, Bolton FJ, French NP, Gowland P, Kemp R, Leatherbarrow H, Upton M & Fox AJ 2008 'Molecular epidemiology of Campylobacter jejuni populations in dairy cattle, wildlife, and the environment in a farmland area' Appl Environ Microbiol 74, (16) 5130-5138 Author Site , DOI
Jones GL, Warren RE, Skidmore SJ, Davies VA, Gibreel T & Upton M 2008 'Prevalence and distribution of plasmid-mediated quinolone resistance genes in clinical isolates of Escherichia coli lacking extended-spectrum beta-lactamases' JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY 62, (6) 1245-1251 Author Site , DOI
Lau SH, Kaufmann ME, Livermore DM, Woodford N, Willshaw GA, Cheasty T, Stamper K, Reddy S, Cheesbrough J & Bolton FJ 2008 'UK epidemic Escherichia coli strains A-E, with CTX-M-15 beta-lactamase, all belong to the international O25:H4-ST131 clone' J Antimicrob Chemother 62, (6) 1241-1244 Author Site , DOI
Kwan PSL, Bolton FJ, Upton M & Fox AJ 2007 'A lack of polymorphic tandem repeats in Campylobacter jejuni genome limits the development of multiple-locus variable number of tandem repeat analysis typing schemes' ZOONOSES AND PUBLIC HEALTH 54, 40-40 Author Site
Banner MA, Cunniffe JG, Macintosh RL, Foster TJ, Rohde H, Mack D, Hoyes E, Derrick J, Upton M & Handley PS 2007 'Localized tufts of fibrils on Staphylococcus epidermidis NCTC 11047 are comprised of the accumulation-associated protein' J Bacteriol 189, (7) 2793-2804 Author Site , DOI
Hyink O, Wescombe PA, Upton M, Ragland N, Burton JP & Tagg JR 2007 'Salivaricin A2 and the novel lantibiotic salivaricin B are encoded at adjacent loci on a 190-kilobase transmissible megaplasmid in the oral probiotic strain Streptococcus salivarius K12' Appl Environ Microbiol 73, (4) 1107-1113 Author Site , DOI
Kwan PSL, Barrigas M, Bolton FJ, Gowland P, Kemp R, Leatherbarrow H, French NP, Upton M & Fox AJ 2007 'The molecular epidemiology of Campylobacter jejuni populations in a farmland environment' ZOONOSES AND PUBLIC HEALTH 54, 137-138 Author Site
Wescombe PA, Upton M, Dierksen KP, Ragland NL, Sivabalan S, Wirawan RE, Inglis MA, Moore CJ, Walker GV & Chilcott CN 2006 'Production of the lantibiotic salivaricin A and its variants by oral streptococci and use of a specific induction assay to detect their presence in human saliva' Appl Environ Microbiol 72, (2) 1459-1466 Author Site , DOI
Jury F, Al-Mahrous M, Apostolou M, Sandiford S, Fox A, Ollier W & Upton M 2006 'Rapid cost-effective subtyping of meticillin-resistant Staphylococcus aureus by denaturing HPLC' J Med Microbiol 55, (Pt 8) 1053-1060 Author Site , DOI
Upton M, Tagg JR, Wescombe P & Jenkinson HF 2001 'Intra- and interspecies signaling between Streptococcus salivarius and Streptococcus pyogenes mediated by SalA and SalA1 lantibiotic peptides' JOURNAL OF BACTERIOLOGY 183, (13) 3931-3938 Author Site , DOI
Upton M, Hill B, Edwards C, Saunders JR, Ritchie DA & Lloyd D 2000 'Combined molecular ecological and confocal laser scanning microscopic analysis of peat bog methanogen populations' FEMS Microbiol Lett 193, (2) 275-281 Author Site
McDonald IR, Upton M, Hall G, Pickup RW, Edwards C, Saunders JR, Ritchie DA & Murrell JC 1999 'Molecular ecological analysis of methanogens and methanotrophs in blanket bog peat' MICROBIAL ECOLOGY 38, (3) 225-233 Author Site , DOI
Upton M & Upton C 1999 'Novel nitrated derivatives of 5,8-diazabenzo[c] phenanthrene and 9,14-diazadibenz[a,e] acephenanthrylene: new classes of potent mutagenic compounds' MUTAGENESIS 14, (6) 587-593 Author Site , DOI
Nercessian D, Upton M, Lloyd D & Edwards C 1999 'Phylogenetic analysis of peat bog methanogen populations' FEMS MICROBIOLOGY LETTERS 173, (2) 425-429 Author Site , DOI
Edwards C, Hales BA, Hall GH, McDonald IR, Murrell JC, Pickup R, Ritchie DA, Saunders JR, Simon BM & Upton M 1998 'Microbiological processes in the terrestrial carbon cycle: Methane cycling in peat' ATMOSPHERIC ENVIRONMENT 32, (19) 3247-3255 Author Site , DOI
Lloyd D, Thomas KL, Hayes A, Hill B, Hales BA, Edwards C, Saunders JR, Ritchie DA & Upton M 1998 'Micro-ecology of peat: minimally invasive analysis using confocal laser scanning microscopy, membrane inlet mass spectrometry and PCR amplification of methanogen-specific gene sequences' FEMS MICROBIOLOGY ECOLOGY 25, (2) 179-188 Author Site , DOI
Upton M, Jaeda MI & Upton C 1998 'Novel 5,8-diazabenzo[c]phenanthrenes: Synthesis and mutagenicity' JOURNAL OF PHARMACY AND PHARMACOLOGY 50, (5) 475-482 Author Site
Upton M, Pennington TH, Haston W & Forbes KJ 1997 'Detection of human commensals in the area around an Antarctic research station' ANTARCTIC SCIENCE 9, (2) 156-161 Author Site
Upton M, Carter PE, Orange G & Pennington TH 1996 'Genetic heterogeneity of M type 3 group A streptococci causing severe infections in Tayside, Scotland' J Clin Microbiol 34, (1) 196-198 Author Site
Upton M, Carter PE, Morgan M, Edwards GF & Pennington TH 1995 'Clonal structure of invasive Streptococcus pyogenes in Northern Scotland' Epidemiol Infect 115, (2) 231-241 Author Site
Conference Papers
Abdellatif E, Upton M & Freemont AJ 2012 'Synovial Fluid (SF) Antibacterial Effect and the Possibility of Using this Feature as a Diagnostic Test for Septic Arthritis (SA)' //0 //0 S32-S32

Other academic activities

Patents granted or filed

  1. Tagg, JR., K. Dierksen & M. Upton. Salivaricin B, a novelstreptococcal lantibiotic with therapeutic potential. 500261 (NZ, October2000); 09/913,763(USA August 2004).
  2. Upton, M., & SK. Sandiford. Novel peptide antibiotic. PCT/GB2010/052106. Filed December 2010.
  3. Two additional patents filed in 2014, both now progressed to PCT

I have acted as a consultant for the following external organisations:

Omnia-Chem - 2012

SGS International - 2010

Footprint International Ltd - 2010

TrueReflections – 2009