Matthew Colpus

This study validates an optimized Oxford Nanopore sequencing workflow for mycobacteria from primary MGIT cultures, showing high concordance with Illumina for species identification and SNP detection.

This study compares long-read and short-read sequencing for tuberculosis drug resistance and outbreak analysis, finding they are comparable with minimal differences in key clinical outputs.

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 evaluates the performance of the gnomonicus tool for predicting antibiotic resistance in Mycobacterium tuberculosis using a diverse testset of 2,663 samples and compares it to TB-Profiler.

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.

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

This paper evaluates the accuracy of bacterial genome reconstruction using Oxford Nanopore R10.4.1 long-read-only sequencing and finds it produces accurate assemblies at 40x depth, competitive with hybrid Illumina-Nanopore assemblies.