Overview
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.
About this opportunity
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
- Develop bioinformatics methods for pathogen identification and characterisation.
- 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