D. W. Crook

This paper predicts pyrazinamide resistance in Mycobacterium tuberculosis using machine learning models trained on pncA mutations and structural features, achieving 80.2% sensitivity and 76.9% specificity.

This study evaluates direct-from-sputum whole-genome sequencing for tuberculosis diagnosis, lineage determination, and drug susceptibility prediction using different sequencing technologies.

This study identifies microvariation in M. tuberculosis strains using sequencing data from England, finding that mixed infections are associated with increased tuberculosis transmission.

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.

BashTheBug uses crowdsourced volunteers to accurately measure MICs of 13 antitubercular drugs from microdilution plates, showing median/mode of classifications is sufficient.

The paper analyzes the pangenome dynamics of Enterobacteriaceae from environmental sources, finding that plasmids carry more AMR genes and are influenced by niche and geography rather than phylogeny.

This study shows that replacing contaminated sink drains with new plumbing increases antimicrobial resistance genes and Enterobacterales abundance due to disrupted biofilms.

The paper shows hospital sink drains are colonized by diverse E. coli and Klebsiella strains, including resistant ones, and may contribute to patient infections.

This paper develops a thermo-protection buffer to enable direct whole genome sequencing of Mycobacteria from clinical samples using Nanopore technology, achieving high coverage at low bacterial concentrations.

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 shows that amoxicillin-clavulanate resistance in E. coli is quantitative, not binary, and that WGS-based predictions outperform traditional phenotyping methods.

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

This study uses metagenomic Nanopore sequencing to detect influenza virus in clinical respiratory samples, achieving high sensitivity and complete genome sequencing.

This study evaluates fosfomycin susceptibility testing in KPC-producing Klebsiella pneumoniae isolates and finds that fosA gene presence affects test accuracy, with sodium phosphonoformate improving results.

This study evaluates how sequencing depth affects taxonomic composition and AMR gene detection in metagenomic samples, finding that higher depth is needed for AMR gene richness.

This study develops a hybrid protocol combining culture enrichment and plasmid extraction to improve detection of antimicrobial resistance genes in faecal samples.

The paper validates a 14-drug microtitre plate for measuring MICs of anti-TB compounds in M. tuberculosis isolates, finding optimal reading with the Vizion system after 14 days incubation.

This paper introduces AMyGDA, a software tool for automated detection of M. tuberculosis growth on 96-well plates to determine drug susceptibility.

The paper develops metrics to detect mixed Mycobacterium tuberculosis infections and cross-contamination in sequencing data from tuberculosis diagnostic labs.

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 study evaluates MIRU-VNTR typing against whole-genome sequencing to identify Mycobacterium tuberculosis transmission, finding low predictive value of MIRU-VNTR and lineage-specific performance.

The paper identifies genomic regions in Mycobacterium tuberculosis that contribute to artefactual variation in bacterial similarity searches and proposes a method to reduce such variation.

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

This paper develops a low-cost WGS method for TB diagnosis and surveillance using direct respiratory samples, achieving rapid results with high concordance with reference labs.