David W. Eyre

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.

This paper develops an automated method to build a comprehensive catalogue of resistance-associated variants for M. tuberculosis, achieving comparable performance to existing catalogues without expert rules.

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.

This study uses genomic data to trace the introduction and transmission of Candida auris in the UK between 2014 and 2019, identifying at least three introductions and multiple transmission events.

The paper evaluates metagenomic, 16S rRNA gene, and ultra-plexed PCR-based sequencing methods for taxonomic and AMR gene profiling in polymicrobial samples, finding that AmpliSeq and shotgun metagenomics perform best for resistome profiling.

This paper uses MinHash to rapidly approximate genomic distances and predict ribotypes in Clostridioides difficile genomes, reducing computational demands for transmission analysis.

The paper compares core genome MLST (cgMLST) with CE-PCR ribotyping and SNP analysis for C. difficile typing, finding cgMLST offers better discrimination but may require adjusted thresholds for outbreak detection.

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

This study identifies COPB2 haploinsufficiency as a cause of a coatopathy with osteoporosis and developmental delay, showing disrupted collagen trafficking and potential treatment with ascorbic acid.

This study evaluates SNP calling pipelines' performance on bacterial data, finding that reference genome selection strongly impacts accuracy, with Snippy performing consistently well across diverse genomes.