Bacterial sepsis: Assessing novel molecular methods for rapid diagnosis, improved patient outcomes and reduced antimicrobial resistance

Project Summary

Sepsis is common in acute hospitals and is a medical emergency. It is a ‘life-threatening organ dysfunction caused by a detrimental host response to infection’, which may be triggered by a range of pathogens. Early diagnosis of the causative agents is critical for targeted treatment – including good antimicrobial stewardship – and patient prognosis. Standard diagnosis currently relies on 48-hour bacterial culture and susceptibility testing, resulting in prolonged use of broad-spectrum antibiotics. This project will assess the utility of a cutting-edge clinical metagenomics approach for detecting and characterising the bacterial causes of sepsis with the aim of informing timely targeted treatment.

Through this project the student will gain valuable skills in molecular biology (including MinION sequencing), microbiology and bioinformatics, working at the forefront of rapidly expanding and broadly applicable methodologies. This would put the student in a competitive position to continue in academic research, or to work within government or industry settings.

Project Team and where the student will be based

The student will be supervised by Dr Taya Forde (molecular epidemiologist) from the Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM) and Dr Paul Everest (microbiologist) from the School of Veterinary Medicine, with additional support from Dr Kirstyn Brunker (expertise in MinION sequencing) and Dr Katarina Oravcova (expertise in antimicrobial resistance) from IBAHCM. They will be based at the OHRBID lab (One Health Research into Bacterial Infectious Diseases), a newly refurbished laboratory space with strong capacity for molecular and microbiology research. The rapidly growing research team at OHRBID provides a vibrant and collaborative learning environment. As part of IBAHCM (Athena Swan Silver), the student will join a highly multidisciplinary group, offering regular seminars, shared interest groups, and a multitude of social events.


  • Academic qualifications - A Masters degree in a relevant field (e.g. molecular biology, microbiology, bioinformatics, infectious diseases, medical or veterinary science, or relevant field in life sciences).
  • Experience - Some laboratory experience in microbiological techniques or basic molecular biology would be useful.
  • Skills/Attributes - Basic skills in microbiology (bacterial culture) and molecular biology (e.g. DNA extraction, PCR), and/or basic familiarity working with sequence data and/or with bioinformatics software would be assets. The candidate should be willing to learn new skills (including computational). Independence (ability to take initiative) and a demonstrated ability to contribute and work as part of a team.


Enquiries about this project should be directed to Dr Taya