Derrick W. Crook

Validation of an optimised Oxford Nanopore sequencing workflow versus Illumina for mycobacteria from primary MGIT culture

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.

Long-read sequencing of Mycobacterial tuberculosis is comparable to short-read sequencing for antimicrobial resistance prediction and epidemiological studies.

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.

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

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

Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 Mycobacterium tuberculosis samples

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.

Rapidly and reproducibly building a comprehensive catalogueof resistance-associated variants for M. tuberculosis

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.

An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in M. tuberculosis using a reproduciblealgorithmic approach.

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: fast sequence filtering and contaminant depletion

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.

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of Escherichia coli isolates

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.

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

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: accurate host decontamination of microbial sequences

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

Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK

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.

Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

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.

High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent

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: a tool for comparative genomics of gene flanking regions

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

Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission

Transmission of pre-XDR and XDR-TB in the Mumbai Metropolitan Region, India

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.

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

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

Genomic network analysis of an environmental and livestock IncF plasmid population

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: within-species genome-wide dN/dS estimation from over 10,000 genomes

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

Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

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

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

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.

Phenotypically distinct human sequence is widespread in publicly archived microbial reads: an evaluation of methods for its detection

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.

Genomic epidemiology of a complex, multi-species plasmid-borne blaKPC carbapenemase outbreak in Enterobacterales in the UK, 2009-2014

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.

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

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.

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

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

Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study

Detection of viral pathogens with multiplex Nanopore MinION sequencing: be careful with cross-talk

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

Severe infections emerge from the microbiome by adaptive evolution

Severe S. aureus infections arise from the nasal microbiome through adaptive evolution, with specific mutations enriched in infecting bacteria compared to colonizing ones.