D. W. Eyre

The paper identifies amino acid substitutions in penicillin binding proteins (PBPs) PBP1 and PBP3 as a mechanism of cephalosporin resistance in C. difficile, which co-occurs with fluoroquinolone resistance in epidemic lineages.

This paper benchmarks taxonomic classifiers for metagenomic sequencing data, finding that Bracken with a standard database achieves the highest species-level classification accuracy across Illumina and Nanopore platforms.

This study identifies three ancient, toxigenic genomospecies within C. difficile using global phylogenomic analysis, reshaping its taxonomy and understanding of toxin gene evolution.

This study optimizes DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae directly from urine samples to enable culture-free whole-genome reconstruction.

This study develops a workflow for high-precision variant and antimicrobial resistance calling from metagenomic Nanopore sequencing of Neisseria gonorrhoeae.

The paper identifies RNA polymerase mutations in Neisseria gonorrhoeae that confer ceftriaxone resistance independently of penA mutations.

This paper introduces hash-cgMLST, a method for rapid genome comparison in Clostridium difficile, showing it matches standard cgMLST performance but with faster processing.

The paper investigates the evolutionary history of Clostridium difficile RT078, finding that tetracycline resistance genes, particularly tetM, were acquired independently in multiple clonal expansions, contributing to its increased prevalence.

This paper compares metagenomic sequencing using Illumina MiSeq and Oxford Nanopore MinION platforms for diagnosing prosthetic joint infections, demonstrating a real-time analysis pipeline for rapid bacterial detection.

This study shows metagenomic sequencing of sonication fluid can accurately diagnose prosthetic joint infections with high sensitivity and specificity.