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Infection Biology

Characterising pathogen interactions with the host at an atomic, molecular, and tissue level to tackle infection and antimicrobial resistance

Promoter evolution and infection links

Streptococcus pneumoniae and Escherichia coli are two of the most clinically relevant bacterial pathogens, responsible for a wide range of infectious diseases and increasingly associated with antimicrobial resistance. Understanding the molecular mechanisms that drive their adaptation and virulence is therefore a public health priority. A key but underexplored such mechanism is promoter sequence variation, which allows bacteria to modulate gene expression and infection outcomes in a more plastic, low-cost, and less disruptive way than mutations affecting coding sequences. Yet intraspecific promoter diversity has never been characterised at the scale of an entire species. This project aims to fill that gap by developing a methodology to systematically extract and analyse promoter variation across the full publicly available genomic breadth of both pathogens. I will leverage large curated datasets (the AllTheBacteria and Global Pneumococcal Sequencing projects), using hundreds of thousands of high-quality assemblies from them. I will identify promoter variants in core genes, correlate them with strain lineages, and assess their association with resistance and invasiveness. This project is a natural foundation for a broader research programme at the intersection of regulatory genomics, antimicrobial resistance, and bacterial ecology.

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