Professor Mathew Upton

August 2018 – Professor of Medical Microbiology, University of PlymouthJune 2018 – Founder and Chief Scientific Officer at Amprologix Ltd (@amprologix)
April 2014 – July 2022 Co-founder and Director at Spectromics Ltd (http://www.spectromics.com/)
May 2013 – Reader in Medical Microbiology, University of Plymouth
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.
Lead for Antibiotic Resistant Pathogens Research Group
Current lab members:

BSc (Hons) Microbiology, University of NewcastlePhD Microbial Ecology, University of Newcastle

Fellow of the Royal Society of BiologyMember of the Microbiology Society
Member of the American Society for Microbiology
Member of the European Society for Clinical Microbiology
Member of the British Society for Antimicrobial Chemotherapy

WHO Technical Advisory Group on Vaccines for AMR - Observer, 2022-2023
Guest Associate Editor
Frontiers in Microbiology, 2022 – Bacteriocins and other Ribosomally Synthesised and Post-translationally modified Peptides (RiPPs) as modulators of the microbiome

Areas of teaching interest relate to medical microbiology, bacterial genomics and antibiotic resistance.
MSc Biomedical Sciences
Contributing to modules BIOM5003 (Contemporary Aspects of Infection and Immunity), BIOM5005 (Project Design and Development), BIOM5006 (Research Project), BIOM5008 (Clinical Microbiology), BIOM5010 (Personalised Medicine).
BSc Biomedical Sciences.
Contributing to Modules BIOM3001, BIOM3003, BIOM3015, BIOM3016.

Research overview
I am a microbiologist with over 20 years of research experience in topics related to human infections. My expertise also includes commercialisation of my research findings, most recently through the formation of Amprologix in 2018, a University of Plymouth spin-out company. My main focus is on working to address the global health threat of antimicrobial resistance (AMR). The WHO have declared that AMR is one of the major threats to human health. The topic has gained national and international attention at the highest levels, with sessions at the 2021 G7 meetings and discussions at the World Economic Forum in addition to AMR being included in the UN's high level discussion in 2016 (with a repeat planned in 2024). 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.
It is clear that AMR is a highly complex issue that will only be addressed by taking a 'One Health' approach - this means we need to work in human, animal and environmental systems collectively to solve the threat effectively. My research is conducted in all three settings.
Lead for Antibiotic Resistant Pathogens Research Group
Major current projects in antibiotic discovery and vaccine development are listed here
Discovery and development of first in class antibiotics - responding to AMR, the 'silent pandemic'
There is a real need for novel antibiotics; in 2021 the WHO looked at all antibiotics in development and concluded that there are not enough to meet current or future clinical needs. Infections caused by drug resistant pathogens are a significant cause of morbidity and mortality and pan-resistant organisms are becoming less rare. In 2022, it was reported that AMR infections killed 1.27 million people globally in 2019.
I run a programme of natural product screening for discovery of antibiotics and 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. I gave a TedX talk on this topic in 2018.
Lead compounds are being developed towards clinical use with commercially focused funding from BBSRC, MRC, Department of Health and Social Care, 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)
The Antibiotic Discovery Accelerator (ABX) Network - https://www.antibioticdiscovery.com/
We have established the ABX Network to improve antibiotic discovery in the UK. The aims are to - 

Funding for the ABX Network has come from the University of Plymouth & the Hospital Saturday Fund

 
Vaccination can be a highly effective way to address AMR by reducing infections in humans, but also in animals. Although significant progress has been made in recent years, we still need to reduce the amount of antimicrobials used in farming and agriculture as these are major drivers of increasing AMR. One approach is to vaccinate animals so that they do not develop infections that require use of antibiotics. In much of this work, I collaborate with experts at The Vaccine Group, a recent University of Plymouth spin-out company. We are developing vaccines for use in pigs and cattle to address some of the biggest causes of infection and antibiotic use in animals. This includes a major programme with collaborators in China, where a new commercial vaccine candidate is now being trialled. In line with the 'One Health' approach mentioned above, we are now developing vaccines for use in humans; clearly this will also reduce infections and the need for antibiotics.
We are using cutting edge bioinformatic tools to identify novel vaccine antigens in bacterial genomes and cloning the genes encoding the antigens into novel vectors. The approaches are more effective than many previous methods for identifying vaccine antigens and the vectors bring additional benefits, like opportunities for single dose activity and the ability to vaccinate with antigens for more than one target pathogen at the same time. This is an exciting and growing area of research with excellent future opportunities; we're probably now much more aware how important vaccines are for preventing infections.
 

I have supervised nearly 30 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, UKHSA (formerly Public Health England & HPA) and NHS Trusts.
Current PhD students (Director of studies)
Neil Powell (2020-2024) - Penicillin allergy patient classification
Jack Kay (2020-2023) - Discovery and design of of novel antimicrobial peptides
Sean Kelly (2021-2025) - Emerging human respiratory pathogens
Current PhD students (Co-supervisor)
Jazmin Conway (2021-2024) - Marine biodiscovery for AMR
Kudzai Hwengwere (2021-2025) - Antarctic marine microbial ecology and natural product discovery
Braith Grey (2021-2024) - Toward a low-cost, rapid point-of-care biosensor for detection of Antibiotic Resistant Urinary Tract Infections
Matthew McKracken (2022-2025) - Biocide resistance in human pathogens
Darshana Srivastava (2023-2027) - Novel antimicrobials from flowering plants


Current ReM students (co-supervisor)
Alistair White (2022-2024) - Novel molecular diagnostics for AMR
Recent PhD Graduates (Director of studies)
Matthew Koch (2017-2021) - SfAM PhD Studentship Discovery of novel antimicrobials from deep sea sponges
Abdu Aldarhami (2015-2019) - Novel antimicrobials for therapy of Gram positive infections
Nizar Saeedi (2014-2018) - Pathogenenesis of ST127 uropathogenic E coli
Rob O'Hara (2015-2018) - Epidemiology of ST127 uropathogenic E coli
Recent PhD Graduates (co-supervisor)
James Butler (2018-2022) - Novel antimicrobial surfaces to reduce healthcare associated infections
Poppy Best (2017-2021) - Bioactivity and ecology of bacteria from deep sea sponges
Sam Gould (2015-2018) - 3D models to study oral infections
Connor Wood (2015-2018) - Superinfection of influenza virus
Barbara Durante (2015-2018) - Immunological effects of antimicrobial peptides

Recent funding
Enterprise solutions, University of Plymouth; R&D solutions fund. Studies in oral microbiology with Modus Labs Ltd, Plymouth Science Park June 2022 (PI awarded £18k, with Dr Tina Joshi)
British Antarctic Survey. Metagenomic sequencing for biodiscovery in Antarctic marine samples, July 2021 (Co-I with Prof Melody Clarke, BAS, awarded £62k)
Wolfson Foundation. University of Plymouth Proteomics Core Facility equipment grant July 2021 (Co-I award of £350k matched by £400k from University of Plymouth and small donations of £50k, total award £800k)
NERC/ARIES DTP. University of Plymouth PhD Studentship as part of ARIES DTP with British Antarctic Survey, March 2021. Co-I with Prof Mel Clarke (PI), Prof Lloyd Peck - BAS; and Prof Kerry Howell - UoP. Award value £75k
Newton Fund/MRC/South African MRC. Harnessing the chemical diversity of natural products to develop new antimicrobial drugs for combating bacterial pathogens - the South Africa UK Antibiotic Accelerator. July 2020-June 2023. (UK PI with Prof Rosie Dorrington as South African PI. International consortium awarded £1.9m) - https://www.plymouth.ac.uk/news/uk-nil-south-africa-research-team-to-establish-hub-for-discovery-of-new-antibiotics
SBRI/InnovateUK/Department of Health and Social Care. AMR in Humans call. Feb 2019-Jan 2021. (PI on behalf of Amprologix Ltd, awarded contract of £1.18m) - https://www.plymouth.ac.uk/news/university-spinout-receives-_12million-to-tackle-antimicrobial-resistance
UKRI GCRF One Ocean Hub. April 2019 - March 2024. (Co-I awarded £100k as part of University of Plymouth work package. Lead organisation, University of Strathclyde. International consortium awarded £19m).
InnovateUK/Department of Health and Social Care. UK-China AMR call. Development of attenuated bovine herpesvirus-4 as a safe,inexpensive, single dose vaccine to control Streptococcus suis infection indomestic pigs. April 2019-March 2022. (Lead academic awarded £294k, with The Vaccine Group; total project award £700k) - https://www.plymouth.ac.uk/news/university-researchers-to-tackle-drug-resistant-disease-that-jumps-from-pigs-to-humans
BactiVac Network/MRC. Development of novel vaccines for prevention of mastitis in cattle. Sept 2018 - Aug 2019 (Co-I. Total project awarded £50k)
 Society for 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 StudentshipCo-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)

Patents granted or filed
 
 
 

 

 

 

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


Omnia-Chem - 2012
SGS International - 2010
Footprint International Ltd - 2010
TrueReflections – 2009