Sarah J Oakley

OxBreaker is a species-agnostic pipeline for analyzing bacterial and plasmid outbreaks using nanopore sequencing, offering high accuracy and accessibility for real-time genomic surveillance.

The paper shows that E. coli phylogeny influences blaTEM-1 expression and co-amoxiclav resistance through lineage-specific regulatory differences.

This paper compares direct cDNA and PCR-cDNA Nanopore sequencing of E. coli isolates, finding PCR-based amplification improves yield but introduces minor GC-content bias.

The paper investigates plasmid sharing among Enterobacterales in human infections, livestock, wastewater, and waterways in Oxfordshire, finding shared plasmid backbones and rapid accessory gene changes across niches.