I am delighted to be stepping into the role of co-director of the AMR Centre this month. My own research focus is genomic epidemiology of AMR pathogens, and so you may notice a genomics flavor to this week’s newsletter!

Microbial genomics is now an essential part of modern public health microbiology, as the COVID-19 pandemic has highlighted (see Genome Medicine special collection on The impact of genomics on precision public health).

Pathogen sequencing is particularly helpful in shedding light on the mechanisms, emergence and spread of AMR, but leads to many practical challenges both in the lab and in terms of data analytics.

This is why I spend much of my research time developing bioinformatics approaches for both raw sequence analysis (e.g. assembling bacterial genomes from rapid nanopore sequencing data) and genomic surveillance tools for specific AMR pathogens like Klebsiella pneumoniae (hospital acquired infections and neonatal sepsis), Shigella sonnei (dysentery) and Salmonella Typhi (typhoid fever).

Genomics also has a huge role to play in the development, targeting and assessment of vaccines against AMR pathogens, and this is a common theme in two new projects I am starting at the School.

The first is working with colleagues to establish the Global Typhoid Genomics Consortium, which aims to aggregate genomic data to monitor the emergence and spread of drug resistance and inform targeted public health action including potential roll-out of the new conjugate vaccine.

The second is partnering with Pathogenwatch and Institut Pasteur to improve our tools for genomic surveillance of Klebsiella, including developing genome-based antigen prediction to support sero-epidemiology for neonatal sepsis and inform choice of target antigens and strains for vaccine development.