Welcome to the CreeveyLab

PhD student Emmet Campbell, with Timofey Skvortsov and Chris Creevey, developed Ptolemaea, a pipeline that reconciles bacterial antiviral (phage) defence-system annotations from PADLOC, DefenseFinder and a bidirectional BLAST search into a single consensus call per gene. Run across 700 genomes spanning E. coli and the ESKAPE pathogens, Ptolemaea recovered over 32,000 defence-system annotations, roughly twice as many as either existing tool alone, while making disagreements between tools explicit and resolvable. Preprint available on bioRxiv; the pipeline is freely available on GitHub.

Postdoc Lucy Dillon, with James McInerney and Chris Creevey, combined pangenomic and machine-learning analyses of over 16,000 E. coli and Pseudomonas aeruginosa genomes to test whether antimicrobial resistance simply accumulates gene by gene. Instead, they found sets of resistance genes that are mutually exclusive within a species, evidence of fitness trade-offs that constrain which combinations of resistance mechanisms can coexist, and gene pairings that cooperate in E. coli but actively work against each other in P. aeruginosa. The findings reframe multidrug resistance evolution as following genomically constrained pathways rather than open-ended accumulation, highlighting new targets for follow-up work on resistance-associated fitness costs. Preprint available on bioRxiv.

Chris organised and hosted the inaugural Biological Diversity Research Showcase as Theme Lead for the Sustaining Ecosystems and Biodiversity Theme at the QUB School of Biological Sciences, timed to coincide with the UN International Day for Biological Diversity. The event brought together researchers from across the school to exchange ideas and celebrate the breadth of biodiversity research at Queen’s. Keynote speaker Dr. Cathy Maguire headlined a packed programme of talks and discussions. Hopefully the first of many annual events.