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Author: Derrick W Crook

  • ORCiD: http://orcid.org/0000-0002-0590-2850
  • Most recently observed institution: Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK

Rankings

  • All-time downloads: 289,947 (rank: 248 )
  • Categories:
    • bioinformatics: 14,708 (rank: 572 (tie) )
    • epidemiology: 34,272 (rank: 714 )
    • genomics: 5,730 (rank: 4,890 (tie) )
    • infectious diseases: 174,923 (rank: 206 )
    • microbiology: 48,338 (rank: 375 )

Downloads per author, site-wide

Preprints

Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays

infectious diseases more details view paper
  • Downloaded 123,716 times
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    • Site-wide: 55
    • In infectious diseases: 21
  • Year to date:
    • Site-wide: 540
  • Since beginning of last month:
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Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

epidemiology more details view paper
  • Downloaded 35,029 times
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    • Site-wide: 287
    • In epidemiology: 62
  • Year to date:
    • Site-wide: 249
  • Since beginning of last month:
    • Site-wide: 2,638

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

microbiology more details view paper
  • Downloaded 27,009 times
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    • Site-wide: 390
    • In microbiology: 39
  • Year to date:
    • Site-wide: 2,245
  • Since beginning of last month:
    • Site-wide: 18,866

Virus detection and identification in minutes using single-particle imaging and deep learning

infectious diseases more details view paper
  • Downloaded 11,781 times
  • Download rankings, all-time:
    • Site-wide: 1,062
    • In infectious diseases: 340
  • Year to date:
    • Site-wide: 5,248
  • Since beginning of last month:
    • Site-wide: 19,846

Antibodies to SARS-CoV-2 are associated with protection against reinfection

infectious diseases more details view paper
  • Downloaded 11,542 times
  • Download rankings, all-time:
    • Site-wide: 1,087
    • In infectious diseases: 345
  • Year to date:
    • Site-wide: 10,424
  • Since beginning of last month:
    • Site-wide: 20,166

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

bioinformatics more details view paper
  • Downloaded 8,772 times
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    • Site-wide: 1,528
    • In bioinformatics: 75
  • Year to date:
    • Site-wide: 57,397
  • Since beginning of last month:
    • Site-wide: 76,882

Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

infectious diseases more details view paper
  • Downloaded 7,154 times
  • Download rankings, all-time:
    • Site-wide: 1,993
    • In infectious diseases: 554
  • Year to date:
    • Site-wide: 20,448
  • Since beginning of last month:
    • Site-wide: 28,190

Differential occupational risks to healthcare workers from SARS-CoV-2: A prospective observational study

infectious diseases more details view paper
  • Downloaded 4,869 times
  • Download rankings, all-time:
    • Site-wide: 3,362
    • In infectious diseases: 769
  • Year to date:
    • Site-wide: 60,759
  • Since beginning of last month:
    • Site-wide: 56,981

Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status

infectious diseases more details view paper
  • Downloaded 4,791 times
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    • Site-wide: 3,448
    • In infectious diseases: 937
  • Year to date:
    • Site-wide: 1,601
  • Since beginning of last month:
    • Site-wide: 2,154

Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing

infectious diseases more details view paper
  • Downloaded 4,586 times
  • Download rankings, all-time:
    • Site-wide: 3,659
    • In infectious diseases: 862
  • Year to date:
    • Site-wide: 1,879
  • Since beginning of last month:
    • Site-wide: 3,552

An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status

infectious diseases more details view paper
  • Downloaded 4,157 times
  • Download rankings, all-time:
    • Site-wide: 4,168
    • In infectious diseases: 920
  • Year to date:
    • Site-wide: 10,296
  • Since beginning of last month:
    • Site-wide: 6,715

Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.

genomics more details view paper
  • Downloaded 3,363 times
  • Download rankings, all-time:
    • Site-wide: 5,683
    • In genomics: 493
  • Year to date:
    • Site-wide: 144,459
  • Since beginning of last month:
    • Site-wide: 162,819

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches

microbiology more details view paper
  • Downloaded 3,115 times
  • Download rankings, all-time:
    • Site-wide: 6,374
    • In microbiology: 379
  • Year to date:
    • Site-wide: 61,574
  • Since beginning of last month:
    • Site-wide: 47,246

Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis

microbiology more details view paper
  • Downloaded 3,086 times
  • Download rankings, all-time:
    • Site-wide: 6,468
    • In microbiology: 422
  • Year to date:
    • Site-wide: 12,012
  • Since beginning of last month:
    • Site-wide: 21,697

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

bioinformatics more details view paper
  • Downloaded 2,440 times
  • Download rankings, all-time:
    • Site-wide: 9,077
    • In bioinformatics: 892
  • Year to date:
    • Site-wide: 65,419
  • Since beginning of last month:
    • Site-wide: 88,871

MinION Nanopore Sequencing of Multiple Displacement Amplified Mycobacteria DNA Direct from Sputum

microbiology more details view paper
  • Downloaded 2,172 times
  • Download rankings, all-time:
    • Site-wide: 10,805
    • In microbiology: 676
  • Year to date:
    • Site-wide: 15,600
  • Since beginning of last month:
    • Site-wide: 24,040

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

microbiology more details view paper
  • Downloaded 2,163 times
  • Download rankings, all-time:
    • Site-wide: 10,876
    • In microbiology: 580
  • Year to date:
    • Site-wide: 160,572
  • Since beginning of last month:
    • Site-wide: 105,620

SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 and correlates of protection in the UK general population

infectious diseases more details view paper
  • Downloaded 2,152 times
  • Download rankings, all-time:
    • Site-wide: 10,966
    • In infectious diseases: 1,768
  • Year to date:
    • Site-wide: 3,174
  • Since beginning of last month:
    • Site-wide: 33,069

Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance

infectious diseases more details view paper
  • Downloaded 1,575 times
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    • Site-wide: 17,595
    • In infectious diseases: 3,494
  • Year to date:
    • Site-wide: 1,128
  • Since beginning of last month:
    • Site-wide: 1,683

Stringent thresholds for SARS-CoV-2 IgG assays result in under-detection of cases reporting loss of taste/smell

infectious diseases more details view paper
  • Downloaded 1,508 times
  • Download rankings, all-time:
    • Site-wide: 18,786
    • In infectious diseases: 2,054
  • Year to date:
    • Site-wide: 131,119
  • Since beginning of last month:
    • Site-wide: 93,810

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

bioinformatics more details view paper
  • Downloaded 1,418 times
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    • Site-wide: 20,709
    • In bioinformatics: 2,205
  • Year to date:
    • Site-wide: 67,229
  • Since beginning of last month:
    • Site-wide: 52,146

Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

microbiology more details view paper
  • Downloaded 1,414 times
  • Download rankings, all-time:
    • Site-wide: 20,797
    • In microbiology: 1,093
  • Year to date:
    • Site-wide: 166,327
  • Since beginning of last month:
    • Site-wide: 153,683

Severe infections emerge from the microbiome by adaptive evolution

genomics more details view paper
  • Downloaded 1,385 times
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    • Site-wide: 21,464
    • In genomics: 1,762
  • Year to date:
    • Site-wide: 152,872
  • Since beginning of last month:
    • Site-wide: 187,203

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

microbiology more details view paper
  • Downloaded 1,363 times
  • Download rankings, all-time:
    • Site-wide: 22,012
    • In microbiology: 1,149
  • Year to date:
    • Site-wide: 180,140
  • Since beginning of last month:
    • Site-wide: 150,193

Validating a 14-drug microtitre plate containing bedaquiline and delamanid for large-scale research susceptibility testing of Mycobacterium tuberculosis

microbiology more details view paper
  • Downloaded 1,358 times
  • Download rankings, all-time:
    • Site-wide: 22,133
    • In microbiology: 1,224
  • Year to date:
    • Site-wide: 81,881
  • Since beginning of last month:
    • Site-wide: 67,083

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

genomics more details view paper
  • Downloaded 981 times
  • Download rankings, all-time:
    • Site-wide: 36,501
    • In genomics: None
  • Year to date:
    • Site-wide: 2,297
  • Since beginning of last month:
    • Site-wide: 2,526

Flanker: a tool for comparative genomics of gene flanking regions

bioinformatics more details view paper
  • Downloaded 974 times
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    • Site-wide: 36,942
    • In bioinformatics: 4,461
  • Year to date:
    • Site-wide: 27,682
  • Since beginning of last month:
    • Site-wide: 10,463

High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

microbiology more details view paper
  • Downloaded 893 times
  • Download rankings, all-time:
    • Site-wide: 42,121
    • In microbiology: 2,216
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    • Site-wide: 183,097
  • Since beginning of last month:
    • Site-wide: 180,197

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

bioinformatics more details view paper
  • Downloaded 876 times
  • Download rankings, all-time:
    • Site-wide: 43,307
    • In bioinformatics: 4,168
  • Year to date:
    • Site-wide: 125,440
  • Since beginning of last month:
    • Site-wide: 60,837

Time of day of vaccination affects SARS-CoV-2 antibody responses in an observational study of healthcare workers

infectious diseases more details view paper
  • Downloaded 668 times
  • Download rankings, all-time:
    • Site-wide: 64,161
    • In infectious diseases: 3,909
  • Year to date:
    • Site-wide: 80,095
  • Since beginning of last month:
    • Site-wide: 83,866

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

microbiology more details view paper
  • Downloaded 659 times
  • Download rankings, all-time:
    • Site-wide: 65,322
    • In microbiology: 3,646
  • Year to date:
    • Site-wide: 122,603
  • Since beginning of last month:
    • Site-wide: 136,187

Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation

infectious diseases more details view paper
  • Downloaded 644 times
  • Download rankings, all-time:
    • Site-wide: 67,472
    • In infectious diseases: None
  • Year to date:
    • Site-wide: 4,482
  • Since beginning of last month:
    • Site-wide: 18,425

BashTheBug: a crowd of volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates.

microbiology more details view paper
  • Downloaded 630 times
  • Download rankings, all-time:
    • Site-wide: 69,335
    • In microbiology: 4,542
  • Year to date:
    • Site-wide: 52,060
  • Since beginning of last month:
    • Site-wide: 97,142

Nested Russian Doll-like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC

microbiology more details view paper
  • Downloaded 597 times
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    • Site-wide: 74,360
    • In microbiology: 4,184
  • Year to date:
    • Site-wide: 172,500
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    • Site-wide: 179,791

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

genomics more details view paper
  • Downloaded 582 times
  • Download rankings, all-time:
    • Site-wide: 76,865
    • In genomics: 4,752
  • Year to date:
    • Site-wide: 157,874
  • Since beginning of last month:
    • Site-wide: 190,564

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

microbiology more details view paper
  • Downloaded 571 times
  • Download rankings, all-time:
    • Site-wide: 78,552
    • In microbiology: 4,565
  • Year to date:
    • Site-wide: 133,335
  • Since beginning of last month:
    • Site-wide: 159,517

DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform

microbiology more details view paper
  • Downloaded 564 times
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    • Site-wide: 79,901
    • In microbiology: 4,707
  • Year to date:
    • Site-wide: 142,768
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    • Site-wide: 95,481

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

microbiology more details view paper
  • Downloaded 548 times
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    • Site-wide: 82,696
    • In microbiology: 4,734
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    • Site-wide: 172,252
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Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

microbiology more details view paper
  • Downloaded 513 times
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    • Site-wide: 89,612
    • In microbiology: 5,454
  • Year to date:
    • Site-wide: 108,632
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    • Site-wide: 80,486

Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the hospital environment: a bacterial genome-wide association study

infectious diseases more details view paper
  • Downloaded 497 times
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    • Site-wide: 92,812
    • In infectious diseases: 4,830
  • Year to date:
    • Site-wide: 67,824
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    • Site-wide: 97,981

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

genomics more details view paper
  • Downloaded 494 times
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    • Site-wide: 93,287
    • In genomics: 5,544
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    • Site-wide: 115,923
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    • Site-wide: 70,124

Identifying mixed Mycobacterium tuberculosis infection and laboratory cross-contamination during Mycobacterial sequencing programs

microbiology more details view paper
  • Downloaded 483 times
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    • Site-wide: 95,758
    • In microbiology: 5,669
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    • Site-wide: 160,422
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    • Site-wide: 121,343

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

microbiology more details view paper
  • Downloaded 471 times
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    • Site-wide: 98,469
    • In microbiology: 6,098
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    • Site-wide: 133,171
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    • Site-wide: 35,328

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopaedic Device Infection

infectious diseases more details view paper
  • Downloaded 466 times
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    • Site-wide: 99,654
    • In infectious diseases: 5,318
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    • Site-wide: 38,915
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    • Site-wide: None

Molecular diagnosis of orthopaedic device infection direct from sonication fluid by metagenomic sequencing

microbiology more details view paper
  • Downloaded 449 times
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    • Site-wide: 103,606
    • In microbiology: 6,203
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    • Site-wide: 174,213
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    • Site-wide: 180,293

Hash-based core genome multi-locus sequencing typing for Clostridium difficile

microbiology more details view paper
  • Downloaded 426 times
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    • Site-wide: 108,982
    • In microbiology: 6,558
  • Year to date:
    • Site-wide: 179,038
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    • Site-wide: 182,090

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

microbiology more details view paper
  • Downloaded 421 times
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    • Site-wide: 110,304
    • In microbiology: 7,221
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    • Site-wide: 99,911
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    • Site-wide: 78,722

Genomic network analysis of an environmental and livestock IncF plasmid population

bioinformatics more details view paper
  • Downloaded 397 times
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    • Site-wide: 116,298
    • In bioinformatics: 9,018
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    • Site-wide: 146,050
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    • Site-wide: None

The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

microbiology more details view paper
  • Downloaded 379 times
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    • Site-wide: 121,014
    • In microbiology: 7,455
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    • Site-wide: 183,767
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    • Site-wide: 162,537

Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline

microbiology more details view paper
  • Downloaded 365 times
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    • Site-wide: 125,058
    • In microbiology: 7,689
  • Year to date:
    • Site-wide: 194,678
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    • Site-wide: 184,203

The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination

infectious diseases more details view paper
  • Downloaded 363 times
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    • Site-wide: 125,535
    • In infectious diseases: 5,926
  • Year to date:
    • Site-wide: 25,255
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    • Site-wide: 99,113

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

infectious diseases more details view paper
  • Downloaded 342 times
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    • Site-wide: 131,536
    • In infectious diseases: None
  • Year to date:
    • Site-wide: 12,556
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    • Site-wide: 25,785

Enterobacterales-associated plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches: a genomic surveillance study in Oxfordshire, UK

genomics more details view paper
  • Downloaded 336 times
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    • Site-wide: 133,250
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  • Year to date:
    • Site-wide: 12,932
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    • Site-wide: 19,362

When do big problems far away become smaller than the problems closer to home: Lessons for antimicrobial resistance from Father Ted

epidemiology more details view paper
  • Downloaded 315 times
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    • Site-wide: 139,412
    • In epidemiology: 5,420
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    • Site-wide: 172,906
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    • Site-wide: 101,547

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

bioinformatics more details view paper
  • Downloaded 313 times
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    • Site-wide: 140,018
    • In bioinformatics: 10,172
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    • Site-wide: 191,263
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    • Site-wide: 191,624

Selective culture enrichment and sequencing of faeces to enhance detection of antimicrobial resistance genes

microbiology more details view paper
  • Downloaded 300 times
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    • Site-wide: 143,853
    • In microbiology: 9,349
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    • Site-wide: 165,877
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Using hospital network-based surveillance for antimicrobial resistance as a more robust alternative to self-reporting

epidemiology more details view paper
  • Downloaded 287 times
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    • Site-wide: 147,563
    • In epidemiology: 5,628
  • Year to date:
    • Site-wide: 192,318
  • Since beginning of last month:
    • Site-wide: 160,431

Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records

infectious diseases more details view paper
  • Downloaded 246 times
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    • Site-wide: 159,303
    • In infectious diseases: 6,932
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    • Site-wide: 21,605
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    • Site-wide: 120,916

Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

infectious diseases more details view paper
  • Downloaded 234 times
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    • Site-wide: 162,814
    • In infectious diseases: 6,507
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    • Site-wide: 167,131
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    • Site-wide: 191,396

Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting

epidemiology more details view paper
  • Downloaded 218 times
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    • Site-wide: 166,960
    • In epidemiology: 6,785
  • Year to date:
    • Site-wide: 66,990
  • Since beginning of last month:
    • Site-wide: 115,785

Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic.

infectious diseases more details view paper
  • Downloaded 188 times
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    • Site-wide: 174,349
    • In infectious diseases: 6,954
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    • Site-wide: 94,933
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Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples

genomics more details view paper
  • Downloaded 157 times
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    • Site-wide: 180,934
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    • Site-wide: 40,885
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    • Site-wide: 28,521

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

genomics more details view paper
  • Downloaded 101 times
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    • Site-wide: 190,218
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  • Year to date:
    • Site-wide: 63,295
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    • Site-wide: 5,232

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

microbiology more details view paper
  • Downloaded 81 times
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    • Site-wide: 192,686
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    • Site-wide: 39,520

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