Dr Mathew Upton

Research interests

Discovery and development of first in class antibiotics

The WHO have declared that antibiotic resistance is one of the major threats to human health. England's Chief Medical Officer has often 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. The UK Government commissioned O'Neill review suggests that drug resistant infections will kill 10 million people a year by 2050 if we are not able to slow the development and spread of these infections.

I run 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. Candidate antimicrobials are screened against clinically relevant pathogens, examined for toxicity and efficacy in vivo (including the Galleria mellonella insect assay). Working with industrial biotechnology leaders, Ingenza, we are developing systems for commercially viable production of bacteriocins, some that will be produced using cognitive computing design approaches, in collaboration with the National Physical Laboratory. Most recently, I have begun to explore the biodiversity and bioactivity of marine sponges in collaboration with members of the University of Plymouth Marine Institute.

Lead compounds are being developed towards clinical use with commercially focused funding from BBSRC, Innovate UK, Society for Applied Microbiology and other sources.

Collaborators in this work are located in Plymouth (Dr Howell, University of Plymouth Marine Institute), Scotland (Dr Ian Fotheringham, Ingenza Ltd), London (Dr Max Ryadnov, National Physical Laboratory) and Denmark (Prof Jenssen, Roskilde University)

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 in Plymouth (Dr Peter Jenks, Derriford Hospital) and at University of Queesnland, Brisbane (Drs Scott Beatson and Makrina Totsika and Prof Mark Schembri) and King Abdullah Medical Research Centre, Riyadh, Saudi Arabia (Dr Algohribi).

Scopus author ID - 35593933700

ResearchGate profile - Mathew_Upton

Research degrees awarded to supervised students

I have supervised 17 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

Societyfor Applied Microbiology. Mining deep-sea sponges for novel antimicrobial biologics. Oct 2017-Sept 2020. (PI awarded £65k)

InnovateUK. Biomedical Catalyst. Developing a pipeline of bacteriocin-based antibiotics. Aug 2017-July 2020. (Lead Academic awarded £299k with Ingenza and National Physical Laboratory; total award £933k)

InnovateUK. Industrial Strategy Challenge Fund. Economic Biosecurity Surveillance Service. Sept 2017-April 2018. (Lead Academic awarded £33k, with Applied Genomics Ltd; Total award £150k)

InnovateUK. Capital Equipment for AMR research. Jan-March 2017.(Lead Academic awarded £85k, with Ingenza Ltd; total award £143k)

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. May2013 (Co-I; £11,850) 

BBSRC, Follow on Fund. Development of epidermicin for nasal decolonisation of 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 ofantimicrobial peptides. July 2011 (PI; £23,000)

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

Department of Health, UK National Innovation Centre and UMIP, Universityof Manchester, Development of an in-situ indicator of catheter colonisation. July2011 (Co-PI; £80,000)

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

BBSRC, Regulatory and market consultancy for a novel antibiotic. September2010 (PI; £15,500)

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