Project Reference: TRG27-GEN-KB1

Project title: Tracking antimicrobial resistance across borders through pathogen genomics

Project outline

The rapid expansion of pathogen genome sequencing has transformed our understanding of bacterial evolution, yet most genomic data are generated in high-income countries. An overlooked feature of these surveillance systems is that many bacterial isolates originate from international travellers returning from regions with high infectious disease burden. These genomes provide geographically structured snapshots of bacterial populations from around the world, creating an unprecedented opportunity to study bacterial evolution, antimicrobial resistance (AMR), and global pathogen movement.

This project will investigate how traveller-derived genomic datasets can be used to understand bacterial population structure and the evolution and dissemination of AMR across international borders. Working in collaboration with the UK Health Security Agency (UKHSA) and international partners, the student will analyse large-scale whole genome sequencing datasets from multiple bacterial pathogens to determine how global travel shapes bacterial diversity and the movement of clinically important lineages and resistance genes.

The project will address three key questions: (i) how accurately do traveller-derived genomes represent bacterial populations circulating in different geographical regions; (ii) how do bacterial lineages and AMR determinants spread through global human mobility; and (iii) how can large-scale genomic and epidemiological datasets be integrated to improve our understanding of bacterial population biology?

The student will receive interdisciplinary training in bacterial genomics, comparative genomics, phylogenetics, antimicrobial resistance prediction, large-scale bioinformatics, statistical analysis and reproducible computational biology. The project combines cutting-edge genomic technologies with internationally unique surveillance datasets and collaboration with UKHSA, providing an outstanding opportunity to develop skills in computational bioscience.

Principal Supervisor

Professor Kate Baker

Email address: kb827@cam.ac.uk

Department / Partner Institute: Genetics

Website: https://www.pdu.gen.cam.ac.uk/kate-s-baker 

BBSRC strategic theme

Bioscience for an integrated understanding of health