Author

D. Crook

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 10

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Organism:human· 5 Approach:statistical model· 5 Research Focus:variant calling· 5 Assay:whole-genome sequencing· 5 Approach:experimental assay· 4 Organism:bacteria (other)· 2 Research Focus:cell type annotation· 2 Approach:deep learning· 2

Frequent Co-Authors

J. Swann· 3 shared N. D. Sanderson· 3 shared N. Stoesser· 3 shared T. Peto· 3 shared A. J. Mentzer· 2 shared A. J. Pollard· 2 shared A. Tuekprakhon· 2 shared D. Skelly· 2 shared

Activity by Year

2017-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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3 shared papersMicrobiology

J. Swann

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10 papers

Recent·Most cited

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing

N. D. Sanderson, K. Hopkins, M. Colpus, M. Parker, S. Lipworth, D. Crook, N. Stoesser

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.

Microbial Genomics · May 7, 2024Peer-reviewedMicrobiology

Repeated evolution of bedaquiline resistance in Mycobacterium tuberculosis is driven by truncation of mmpR5

L. W. Roberts, K. M. Malone, M. Hunt, L. Joseph, P. Wintringer, J. Knaggs, D. Crook, M. R. Farhat, Z. Iqbal, S. V. Omar

The paper identifies truncation of mmpR5 as a driver of bedaquiline resistance in Mycobacterium tuberculosis through analysis of clinical isolates and MIC measurements.

bioRxiv · Dec 8, 2022 · PreprintMicrobiology

Further antibody escape by Omicron BA.4 and BA.5 from vaccine and BA.1 serum

A. Tuekprakhon, J. Huo, R. Nutalai, A. Dijokaite-Guraliuc, D. Zhou, H. M. Ginn, M. Sekvaraj, C. Liu, A. J. Mentzer, P. Supasa, H. M. E. Duyvesteyn, R. Das, D. Skelly, T. G. Ritter, A. Amini, , G. R. Screaton

This study shows that BA.4 and BA.5 variants are more resistant to neutralization by vaccine and BA.1 immune sera compared to BA.1 and BA.2.

bioRxiv · May 21, 2022 · PreprintMicrobiology

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

T. J. Davies, J. Swann, A. E. Sheppard, H. Pickford, S. Lipworth, M. AbuOun, M. Ellington, P. W. Fowler, S. Hopkins, K. Hopkins, D. Crook, T. E. Peto, M. F. Anjum, A. S. Walker, N. Stoesser

This study evaluates four AMR gene typing methods using simulated and real E. coli data, revealing significant discrepancies and highlighting issues with current bioinformatic approaches.

bioRxiv · Nov 3, 2021 · PreprintMicrobiology

Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2

W. - Dejnirattisai, D. - Zhou, P. - Supasa, C. - Liu, A. J. Mentzer, H. M. Ginn, Y. - Zhao, H. M. E. Duyvesteyn, A. Tuekprakhon, R. Nutalai, B. - Wang, G. C. Paesen, C. - Lopez-Camacho, J. - Slon-Campos, T. Walter, , Barne

This study compares antibody resistance of SARS-CoV-2 variants P.1, B.1.351, and B.1.1.7, finding P.1 is less resistant to antibodies despite similar ACE2 binding mutations.

bioRxiv · Mar 12, 2021Microbiology

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

N. D. Sanderson, J. Swann, L. Barker, J. Kavanagh, S. Hoosdally, D. Crook, the GonFast Investigators Group, T. L. Street, D. W. Eyre

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

bioRxiv · Feb 7, 2020Microbiology

Whole genome sequencing for predicting clarithromycin resistance in Mycobacterium abscessus

S. I. W. Lipworth, N. Hough, L. Leach, M. Morgan, K. Jeffrey, M. Andersson, E. Robinson, G. Smith, D. Crook, T. Peto, T. Walker

This study uses whole genome sequencing to predict clarithromycin resistance in Mycobacterium abscessus by identifying known and novel resistance-determining mutations.

bioRxiv · Sep 28, 2018Microbiology

A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing

S. I. W. Lipworth, R. Jajou, H. de Neeling, P. Bradley, W. van der Hoek, G. Maphalala, M. Bonnet, E. Sanchez-Padilla, R. Diel, S. Niemann, Z. Iqbal, G. Smith, T. Peto, D. Crook, T. M. Walker, D. van Soolingen

This paper introduces SNP-IT, a method using whole genome sequencing to identify subspecies and lineages of Mycobacterium tuberculosis complex, revealing high prevalence of M. orygis in UK clinical isolates.

bioRxiv · Jan 5, 2018Microbiology

Real-time analysis of nanopore-based metagenomic sequencing from orthopaedic device infection

N. D. Sanderson, T. L. Street, D. Foster, J. Swann, B. L. Atkins, A. J. Brent, M. A. McNally, S. Oakley, A. Taylor, T. E. A. Peto, D. Crook, D. W. Eyre

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.

bioRxiv · Nov 17, 2017Microbiology

Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

J. van Aartsen, C. Moore, C. Parry, P. Turner, N. Phot, S. Mao, K. Suy, T. Davies, A. Giess, A. Sheppard, T. Peto, N. Day, D. Crook, A. Walker, N. Stoesser

The paper investigates ESC-R-EC and ESC-R-KP colonization in Cambodian children, identifies risk factors, and characterizes resistance gene diversity and genetic contexts.

bioRxiv · Aug 16, 2017Microbiology