Derrick W. Crook

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.

This study evaluates Nanopore long-read only genome assembly for clinical Enterobacterales isolates, finding Autocycler with Medaka polishing achieves accuracy comparable to hybrid assemblies.

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 develops an automated method to predict bedaquiline resistance in M. tuberculosis using a reproducible algorithmic approach, achieving high sensitivity and specificity in variant classification.

Deacon efficiently filters and depletes contaminant sequences from large genomic datasets using a human pangenome index, achieving high accuracy and speed with minimal computational resources.

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.

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 quantifies antibiotic resistance in tuberculosis using genomic data and MIC measurements to identify genetic determinants of resistance and hypersensitivity across multiple drugs.

Hostile is a tool for removing human host sequences from microbial sequencing data, achieving high accuracy in read removal while preserving target microbial sequences.

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.

This paper evaluates the performance of new Oxford Nanopore flowcells and chemistries for bacterial genome reconstruction, finding that while R10.4/Kit12 with 'super accuracy' basecalling shows promise, hybrid assembly remains more robust and cost-effective.

This study compares taxonomic and resistome variability between single-timepoint grab and 24H-composite wastewater samples, finding that composites better capture AMR genes and reduce temporal variability.

Flanker clusters gene flanking sequences to identify mobile genetic element patterns associated with antimicrobial resistance genes.

The paper analyzes whole genome sequencing data from tuberculosis strains in Mumbai to identify factors driving the pre-XDR and XDR-TB epidemic, finding lineage 2 strains are strongly associated with these resistant forms.

This study optimizes Oxford Nanopore Flowcell usage for hybrid assemblies by reducing sequencing time and cost through washing steps, enabling more isolates per flowcell.

The paper analyzes IncF plasmid diversity across environmental and livestock settings using network community analysis, revealing niche-driven partitioning and core gene-defined communities.

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

The paper develops a metagenomic metric to predict antibiotic resistance in Enterobacterales infections using pooled human faecal samples from LMICs and high-income settings.

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.

The paper evaluates methods for detecting human contamination in microbial sequencing data and finds that classification-based methods are most effective, though combining methods improves accuracy for short reads.

This study analyzes the genomic epidemiology of a blaKPC carbapenemase outbreak in Enterobacterales in the UK, revealing genetic plasticity and plasmid dynamics across multiple species and lineages.

This study compares hybrid assemblies of bacterial genomes using Illumina and long-read sequencing technologies, finding that combining ONT and Illumina reads provides high-quality, low-cost genome reconstruction.

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

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.

TETyper classifies transposable element variation and genetic contexts from whole-genome sequencing data, revealing high transposition diversity in KPC-associated Tn4401.

The paper assesses cross-talk in multiplex Nanopore MinION sequencing and finds 0.056% of reads are misassigned due to chimeric reads.