Leveraging sequencing technologies to advance identification of bacterial pathogens

Institute of Systems, Molecular and Integrative Biology
University of Liverpool

Dr Yu Wan
Prof N Williams
Prof Steve Paterson

Applications accepted all year round
Self-Funded PhD Students Only

About the Project

This four-year PhD project aims to advance sequencing-based bioinformatics methods for identification and characterisation of bacterial pathogens in diverse clinical and surveillance samples. Methodological and knowledge breakthroughs from this study will improve the diagnosis, monitoring, prevention, and control of bacterial infectious diseases, addressing the pressing threat of antimicrobial resistance.

Identification of bacterial pathogens is essential for diagnosis, outbreak investigation, infection prevention and control, and surveillance. High-throughput sequencing has become a powerful tool in bacterial genomics, facilitating high-resolution tracking of pathogen transmission and patterns of antimicrobial resistance (AMR). While short-read sequencing (such as Illumina sequencing) has been widely used in diagnostic laboratories, since the last decade long-read sequencing technologies (such as PacBio’s Single Molecule Real-time Sequencing and Oxford Nanopore Technologies’s nanopore sequencing) have revolutionised bacterial genomics by improving genome assembly, variant detection, and reconstruction of complex genomic features. Integrating both short-read and long-read sequencing approaches can improve the accuracy of pathogen identification, enabling high-resolution characterisation of pathogens. This four-year PhD project focuses on advancing bioinformatics methods for identification and characterisation of bacterial pathogens in high-throughput sequencing data.

Aims

1. Develop bioinformatics methods for pathogen identification and characterisation.
2. Advance understandings of pathogen and AMR dissemination.

Project structure

• Year 1: Conduct a pilot study to generate sequencing data from available isolates and explore current methods for understanding the spread of bacterial pathogens and AMR.
• Years 2 and 3: Develop bioinformatics methods and experimental protocols to improve pathogen identification and characterisation.
• Years 3 and 4: Apply the new methods to investigate the epidemiology of pathogens and AMR.
• Year 4: Write-up.

Training

Mandatory training

• Graduate School First Year Skills Workshop
• Graduate School Career Skills Workshop
• Departmentally provided subject specific skills training
• Poster presentation on an annual University Postgraduate Poster Day

Scientific skills

• Experiments for microbiology and DNA sequencing
• Advanced bioinformatics and programming
• Collation and sharing of sequence data
• Statistics and infectious disease epidemiology

Transferable skills

• Communications
• Critical thinking
• Multidisciplinary collaboration within a diverse research environment
• Time management

Career development

Please email the following information to supervisor Dr Yu Wan (yu.wan@liverpool.ac.uk), with a citation of this project’s title and reference number:

• Cover letter, enclosing a motivation statement, research interests, expertise, relevant experience, probable start date, a study plan, and contact details of two referees
• Curriculum vitae
• University transcripts relevant to this PhD project
• A list of your accessible publications (preferably, peer-reviewed first/last-author journal articles, and we accept other types of publications, such as blogs, forum posts, software documentation, etc) or a 1000-word sample of scientific writing

Candidates should register and apply through the University of Liverpool Application Portal. You’ll receive an email acknowledgment once you have submitted your application. We will be in touch by email with further details about what happens next. This application may close once a suitable candidate is found

Funding Notes

The Hill Abram Prize Endowment provides the successful candidate with a waiver of tuition fees, charged at the UK and Republic of Ireland student rate, for up to four years if the project begins before 31 July 2026.

References

1. E. Jauneikaite, K. S. Baker, J. G. Nunn, et al., Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities. The Lancet Microbe (2023). https://doi.org/10.1016/S2666-5247(23)00282-3.
2. R. R. Wick, L. M. Judd, K. E. Holt, Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. PLOS Computational Biology 19, e1010905 (2023). https://doi.org/10.1371/journal.pcbi.1010905.
3. D. M. Aanensen, C. C. Carlos, P. Donado-Godoy, et al., Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae. Clinical Infectious Diseases 73, S255–S257 (2021). https://doi.org/10.1093/cid/ciab795.