News

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.

A substantial update to Clann, the maximum likelihood supertree inference tool. V5.1 introduces proper ML optimality criteria based on Steel & Rodrigo (2008), Robinson–Foulds distance scoring, ML topology tests (Kishino–Hasegawa and Shimodaira–Hasegawa), parallel heuristic search, source-tree weighting schemes, supertree landscape clustering analysis, and a modernised interactive CLI. The codebase has been fully refactored into modular components. The project has been revived after years of dormancy—legacy phylogenetics methods deserve a second life.

This paper addresses a fundamental challenge in multilocus phylogenetics — how to handle cases where different genes cover different subsets of taxa, leading to ineffective overlap. Published in Systematic Biology.

A genomic study of pathogenic Enterobacteriaceae isolated from leafy vegetables, examining antibiotic resistance profiles and the public health implications of resistance gene transfer through the food supply. Published in Environment International.

Lab member John-Paul Wilkins contributed to this study demonstrating that combining individual clinical and wastewater whole genome sequencing significantly improves SARS-CoV-2 surveillance. Published in Water Research.

A landmark large-scale study cataloguing previously unexplored microbial diversity across 2,500 food metagenomes and revealing links to the human gut microbiome. Published in Cell.

Chris Creevey co-authored this FAO report on the sustainable use and conservation of rumen microorganisms, highlighting the importance of microbial diversity for efficient and sustainable ruminant digestion. Published by the Food & Agriculture Organisation of the United Nations.

A collaborative study exploring the plant interactions and biogeochemical role of Acidobacteriota — one of the most widespread but poorly understood bacterial phyla in the soil microbiome. Published in Soil Biology and Biochemistry.

Lab members Lucy Dillon, Nick Dimonaco, and Chris Creevey show that accessory genes — those present in some but not all strains of a species — play a defining role in the routes bacteria take towards antibiotic resistance. Published in Life Science Alliance.