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List of works by Derrick W Crook

'Caveat emptor': the cautionary tale of endocarditis and the potential pitfalls of clinical coding data-an electronic health records study

scientific article published on 04 September 2019

'Feral' and 'wild'-type methicillin-resistant Staphylococcus aureus in the United Kingdom

scientific article published on 14 December 2009

505. Making of a “Super-Duper Bug”: Plasmid-Mediated Resistance Accumulation in a Carbapenemase-Producing Klebsiella quasipneumoniae from Patients and the Environment

A Candida auris Outbreak and Its Control in an Intensive Care Setting

article

A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control

scientific article published on 26 November 2018

A Mal functional variant is associated with protection against invasive pneumococcal disease, bacteremia, malaria and tuberculosis

scientific journal article

A Quantitative Evaluation of MIRU-VNTR Typing Against Whole-Genome Sequencing for Identifying Mycobacterium tuberculosis Transmission: A Prospective Observational Cohort Study

article

A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated PCR Ribotype 078

scientific article published on 12 March 2019

A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database.

scientific article

A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples

scientific article

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

scholarly article published 5 November 2017

A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance

scientific article (publication date: 2012)

A role for tetracycline selection in the evolution ofClostridium difficilePCR-ribotype 078

A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis

scientific article published on 28 December 2017

Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences

scientific article published on 27 August 2018

Acquisition of Streptococcus pneumoniae and Nonspecific Morbidity in Infants and Their Families

scientific article published on 01 February 2005

Aiming for zero tuberculosis transmission in low-burden countries

scientific article published on 12 October 2017

Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism

scientific article published on 14 October 2020

An improved antiserum agar method for detecting carriage of Haemophilus influenzae type b

scientific article published on 01 March 1993

Antibiotic Review Kit for Hospitals (ARK-Hospital): study protocol for a stepped-wedge cluster-randomised controlled trial

scientific article published on 11 July 2019

Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe

scientific article published on 02 December 2019

Antibiotic use and clinical outcomes in the acute setting under management by an infectious diseases acute physician versus other clinical teams: a cohort study

scientific article published on 23 August 2016

Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers

scientific article published on 23 December 2020

Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel

scientific article published on 20 April 2020

Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel

Application of machine learning techniques to tuberculosis drug resistance analysis

scholarly article by Samaneh Kouchaki et al published 21 November 2018 in Bioinformatics

Are there better methods of monitoring MRSA control than bacteraemia surveillance? An observational database study ⬇️

scientific article

Assessing a novel, lab-free, point-of-care test for SARS-CoV-2 (CovidNudge): a diagnostic accuracy study

scientific article published on 17 September 2020

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study

scientific article

Asymptomatic Clostridium difficile colonisation and onward transmission

scientific article (publication date: 2013)

Author Correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

scientific article published on 21 February 2020

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

scientific article published on 23 October 2018

Awareness of Appropriate Antibiotic Use in Primary Care for Influenza-Like Illness: Evidence of Improvement from UK Population-Based Surveys

scientific article published on 13 October 2020

BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness

scientific article

Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study

scientific article

Capsular Typing Method for Streptococcus agalactiae Using Whole-Genome Sequence Data

scientific article

Capsular serotype-specific attack rates and duration of carriage of Streptococcus pneumoniae in a population of children

scientific article

Capsular type and the pneumococcal human host-parasite relationship

scientific article published on 17 January 2006

Cardiac transplantation and immunisation against Haemophilus influenzae

scientific article published on 01 November 1993

Changes in serogroup and genotype prevalence among carried meningococci in the United Kingdom during vaccine implementation

scientific article

Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing ⬇️

scientific article

Characteristics of CTX-M ESBL-producing Escherichia coli isolates from the Lao People's Democratic Republic, 2004-09 ⬇️

scientific article published on October 10, 2011

Characterization of capsular genes in Haemophilus influenzae isolates from H. influenzae type b vaccine recipients

scientific article published on 01 April 1995

Characterization of genetic and phenotypic diversity of invasive nontypeable Haemophilus influenzae

scientific article

Characterization of plasmids

scientific article

Chloramphenicol treatment for acute infective conjunctivitis in children in primary care: a randomised double-blind placebo-controlled trial

scientific article published in July 2005

Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, blaKPC, in Klebsiella Species Is Elusive but Not Rare

scientific article

Clinical Clostridium difficile: clonality and pathogenicity locus diversity

scientific article

Clonal Relationships between Invasive and Carriage Streptococcus pneumoniae and Serotype‐ and Clone‐Specific Differences in Invasive Disease Potential

scientific article published on 04 April 2003

Clostridium difficile in England: can we stop washing our hands? - Authors' reply ⬇️

scientific article published in May 2017

Clostridium difficile mixed infection and reinfection

scientific article published on 9 November 2011

Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage

scientific article

Clostridium difficile: Investigating Transmission Patterns Between Infected and Colonized Patients Using Whole Genome Sequencing ⬇️

article

Colistin resistance gene mcr-1 and pHNSHP45 plasmid in human isolates of Escherichia coli and Klebsiella pneumoniae

scientific article

Colonization with Enterobacteriaceae producing ESBLs in children attending pre-school childcare facilities in the Lao People's Democratic Republic

scientific article published on 12 February 2015

Combining Charlson and Elixhauser scores with varying lookback predicated mortality better than using individual scores

scientific article published on 28 September 2020

Common NFKBIL2 polymorphisms and susceptibility to pneumococcal disease: a genetic association study

scientific article

Comparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution

scientific article published on 08 October 2020

Comparison of Control of Clostridium difficile Infection in Six English Hospitals Using Whole-Genome Sequencing ⬇️

scientific article published on 29 May 2017

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

scientific article published on 30 August 2019

Comparison of multilocus variable-number tandem-repeat analysis and whole-genome sequencing for investigation of Clostridium difficile transmission ⬇️

scientific article published on 09 October 2013

Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.

scientific article

Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.

scientific article published on 06 September 2016

Construction of a novel shuttle vector for use in Haemophilus influenzae and H. parainfluenzae ⬇️

scientific article published on September 16, 2010

Contribution to Clostridium Difficile Transmission of Symptomatic Patients With Toxigenic Strains Who Are Fecal Toxin Negative ⬇️

scientific article

Control of Artifactual Variation in Reported Intersample Relatedness during Clinical Use of a Mycobacterium tuberculosis Sequencing Pipeline.

scientific article published on 26 July 2018

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

scientific article published on 01 May 2019

Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.

scientific article published on 20 April 2016

Corrigendum: Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.

scientific article published on 29 March 2018

Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission. ⬇️

scientific article published on 7 August 2017

DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples

scientific article published on 22 July 2020

DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing.

scientific article published on 10 January 2018

Decline of meticillin-resistant Staphylococcus aureus in Oxfordshire hospitals is strain-specific and preceded infection-control intensification

scientific article

DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis

scholarly article by Yang Yang et al published 28 January 2019 in Computer applications in the biosciences : CABIOS

DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis

scholarly article by Timothy M Walker et al published 28 January 2019 in Bioinformatics

Detection of Viral Pathogens With Multiplex Nanopore MinION Sequencing: Be Careful With Cross-Talk

scientific article published in 2018

Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission

scientific article (publication date: 2013)

Determinants of acquisition and carriage of Staphylococcus aureus in infancy

scientific article

Differences in outcome according to Clostridium difficile testing method: a prospective multicentre diagnostic validation study of C difficile infection

scientific article published on 03 September 2013

Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study

scientific article published on 21 August 2020

Direct detection of the multidrug resistance genome of Haemophilus influenzae in cerebrospinal fluid of children: implications for treatment of meningitis

scientific article published in January 2008

Dissemination of multiple carbapenem resistance genes in an in vitro gut model simulating the human colon

scientific article published on 01 July 2019

Diverse sources of C. difficile infection identified on whole-genome sequencing

scientific article published on September 2013

Diversity of antibiotic resistance integrative and conjugative elements among haemophili

scientific article published in June 2007

Don't overlook the little guy: An evaluation of the frequency of small plasmids co-conjugating with larger carbapenemase gene containing plasmids

scientific article published on 27 March 2019

Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Rosenbach 1884

scientific article published on 25 April 2019

Dynamic linkage of COVID-19 test results between Public Health England's Second Generation Surveillance System and UK Biobank

scientific article published on 18 June 2020

Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing

scientific article published on 3 January 2015

Dynamics of acquisition and loss of carriage of Staphylococcus aureus strains in the community: the effect of clonal complex

scientific article published on 04 January 2014

Effect of age on treatment outcomes in Clostridium difficile infection

scientific article published on 4 February 2013

Effect of antibiotic prescribing on antibiotic resistance in individual children in primary care: prospective cohort study

scientific article

Effects of control interventions on Clostridium difficile infection in England: an observational study ⬇️

scientific article published on 24 January 2017

Effects of proton pump inhibitors and histamine-2 receptor antagonists on response to fidaxomicin or vancomycin in patients with Clostridium difficile-associated diarrhoea

scientific article

Emergence and spread of predominantly community-onset Clostridium difficile PCR ribotype 244 infection in Australia, 2010 to 2012.

scientific article published on 12 March 2015

Enhanced Klebsiella pneumoniae Carbapenemase Expression from a Novel Tn4401 Deletion

scientific article

Enhanced determination of Streptococcus pneumoniae serotypes associated with invasive disease in Laos by using a real-time polymerase chain reaction serotyping assay with cerebrospinal fluid

scientific article

Enhanced invasiveness of bovine-derived neonatal sequence type 17 group B streptococcus is independent of capsular serotype

scientific article published on 22 February 2006

Epidemiological studies of large resistance plasmids in Haemophilus

scientific article published on 01 May 2000

Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: Risk factors for colonization and carriage, and genetic overlap with regional C. difficile infection strains ⬇️

scientific article published on 16 August 2017

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

scientific article published on 16 August 2017

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

scientific article published on 12 March 2019

Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping

scientific article

Evaluation of a cluster-randomized controlled trial of a package of community-based maternal and newborn interventions in Mirzapur, Bangladesh

scientific article

Evaluation of methods for detecting human reads in microbial sequencing datasets

scientific article published on 19 June 2020

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera

scientific article published in February 2021

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

scientific article published on 22 March 2016

Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus

scientific article published on 2 September 2015

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

scientific article published on 5 March 2012

Evolutionary history of the Clostridium difficile pathogenicity locus ⬇️

scientific article

Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

scholarly article published 6 November 2015

Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses

scientific article published on 22 April 2015

Fairness of financial penalties to improve control of Clostridium difficile

scientific article published on 20 November 2008

Fidaxomicin attains high fecal concentrations with minimal plasma concentrations following oral administration in patients with Clostridium difficile infection

scientific article

Fidaxomicin versus vancomycin for Clostridium difficile infection: meta-analysis of pivotal randomized controlled trials.

scientific article

Fidaxomicin versus vancomycin for infection with Clostridium difficile in Europe, Canada, and the USA: a double-blind, non-inferiority, randomised controlled trial

article

First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131.

scientific article published on 31 May 2016

Functional polymorphisms in the FCN2 gene are not associated with invasive pneumococcal disease

scientific article

Genetic diversity and carriage dynamics of Neisseria lactamica in infants

scientific article

Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting

scientific article published on 29 September 2014

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines

scientific article published on 01 February 2020

Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital

scientific article published on 01 April 2020

Genomic epidemiology of complex, multi-species, plasmid-borne bla KPC carbapenemase in Enterobacterales in the UK, 2009-2014

scientific article published on 24 February 2020

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli.

scientific article

Genomic islands: tools of bacterial horizontal gene transfer and evolution

scientific article published on 29 October 2008

Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

scientific article published on 18 June 2020

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

scientific article

Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study

scientific article published on 12 July 2017

Gonorrhoea treatment failure caused by a strain with combined ceftriaxone and high-level azithromycin resistance, England, February 2018

article

Haemophilus influenzae type b carriage and immunity four years after receiving the Haemophilus influenzae oligosaccharide-CRM197 (HbOC) conjugate vaccine

scientific article published on 01 June 1993

Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile

scientific article published on 23 December 2019

Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone

scientific article published on 21 December 2013

High confidence prediction of essential genes in Burkholderia cenocepacia ⬇️

scientific article

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

scientific article published on 01 September 2020

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

scientific article published on 10 October 2017

Hospital exposure in a UK population, and its association with bacteraemia

scientific article published on 19 November 2007

Hybrid Vibrio vulnificus.

scientific article published on January 2005

Hyperinvasive neonatal group B streptococcus has arisen from a bovine ancestor

scientific article

Identification of another module involved in the horizontal transfer of the Haemophilus genomic island ICEHin1056 ⬇️

scientific article published on June 10, 2013

Identification of serotype in culture negative pneumococcal meningitis using sequential multiplex PCR: implication for surveillance and vaccine design

scientific article

Identifying Mixed Mycobacterium tuberculosis Infection and Laboratory Cross-Contamination during Mycobacterial Sequencing Programs

scientific article published on 25 October 2018

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

scientific article published on 04 April 2016

IkappaB genetic polymorphisms and invasive pneumococcal disease

scientific article

Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania

scientific article published on 8 December 2017

Impact of Meningococcal Serogroup C Conjugate Vaccines on Carriage and Herd Immunity

scientific article published on 01 March 2008

Impact of waterborne outbreak of cryptosporidiosis on AIDS and renal transplant patients

scientific article published on 01 June 1990

Improved Performance Predicting Clarithromycin Resistance in Mycobacterium abscessus on an Independent Data Set

scientific article published on 25 July 2019

Improved workflows for high throughput library preparation using the transposome-based Nextera system

scientific article

Increasing burden of community-acquired pneumonia leading to hospitalisation, 1998-2014

scientific article

Increasing incidence of Escherichia coli bacteraemia is driven by an increase in antibiotic-resistant isolates: electronic database study in Oxfordshire 1999-2011.

scientific article published on 21 March 2012

Infectious disease training: challenges and opportunities

scientific article published on 01 January 2002

Insidious Risk of Severe Mycobacterium chimaera Infection in Cardiac Surgery Patients.

scientific article published on 7 December 2016

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

scientific article published in Scientific Reports

Intensive Care Unit Wastewater Interventions to Prevent Transmission of Multi-species Klebsiella pneumoniae Carbapenemase (KPC) Producing Organisms

scientific article published on 2 February 2018

Invasive pneumococcal disease in England and Wales: vaccination implications

scientific article published on 21 December 2000

Invasive pneumococcal disease in Oxford, 1985-2001: a retrospective case series

scientific article

Invasive pneumococcal disease: epidemiology in children and adults prior to implementation of the conjugate vaccine in the Oxfordshire region, England

scientific article published in April 2008

Investigation of the impact of the NICE guidelines regarding antibiotic prophylaxis during invasive dental procedures on the incidence of infective endocarditis in England: an electronic health records study

scientific article published on 02 April 2020

Is MRSA admission bacteraemia community-acquired? A case control study

scientific article

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing

scientific article

Klebsiella quasipneumoniae Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment.

scientific article published on 24 May 2019

MBL genotype and risk of invasive pneumococcal disease: a case-control study

scientific article published on 01 May 2002

MRSA bacteraemia in patients on arrival in hospital: a cohort study in Oxfordshire 1997-2003.

scientific article

Machine Learning for Classifying Tuberculosis Drug-Resistance from DNA Sequencing Data.

scientific article published on 12 December 2017

Management of patients with suspected infectious diarrhoea in hospitals in England ⬇️

scientific article

Mannose-binding lectin genotypes: lack of association with susceptibility to thoracic empyema

scientific article

Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya

scientific article published on 23 May 2016

Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples

scientific article published on 23 December 2019

Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

scientific article published on 19 June 2019

Microbiological lung surveillance in mechanically ventilated patients, using non-directed bronchial lavage and quantitative culture

article

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

scientific article

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.

scientific article

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing

scientific article published on 10 May 2017

Molecular Typing of Bacteria Directly from Cerebrospinal Fluid

scientific article published on 01 August 2000

Molecular basis of resistance displayed by highly ciprofloxacin-resistant Salmonella enterica serovar Typhi in Bangladesh

scientific article

Molecular epidemiology of Clostridium difficile strains in children compared with that of strains circulating in adults with Clostridium difficile-associated infection

scientific article published on 21 September 2011

Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing.

scientific article published on 30 April 2015

Mortality after Staphylococcus aureus bacteraemia in two hospitals in Oxfordshire, 1997-2003: cohort study

scientific article

Mortality risks associated with emergency admissions during weekends and public holidays: an analysis of electronic health records

scientific article

Multi-Label Random Forest Model for Tuberculosis Drug Resistance Classification and Mutation Ranking

scientific article published on 22 April 2020

Multi-site and nasal swabbing for carriage of Staphylococcus aureus: what does a single nose swab predict?

scientific article published on 30 January 2017

Multidrug-resistant Escherichia coli soft tissue infection investigated with bacterial whole genome sequencing

scientific article published on 19 October 2014

Multilocus sequence typing of Clostridium difficile

scientific article

Multiple-strain colonization in nasal carriers of Staphylococcus aureus

scientific article published on 05 February 2014

Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures

scientific article published on 28 January 2015

Mycobacterium chimaera Isolates from Heater-Cooler Units, United Kingdom

scientific article published on July 2017

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

scientific article published on 23 April 2020

Nanopore metagenomic sequencing to investigate nosocomial transmission of human metapneumovirus from a unique genetic group among haematology patients in the United Kingdom

scientific article published on 22 February 2020

Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation

scientific article (publication date: 16 May 2016)

Near patient testing for influenza in children in primary care: comparison with laboratory test

scientific article

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

scientific article published on 11 April 2016

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

article

Novel type IV secretion system involved in propagation of genomic islands

scientific article published on 22 November 2006

Occurrence and characterization of Escherichia coli ST410 co-harbouring blaNDM-5, blaCMY-42 and blaTEM-190 in a dog from the UK

scientific article published on 01 May 2019

Occurrence and characterization of mcr-1-harbouring Escherichia coli isolated from pigs in Great Britain from 2013 to 2015.

scientific article

Optimized use of Oxford Nanopore flowcells for hybrid assemblies

scientific article published on 11 November 2020

Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples

scientific article published on 24 February 2020

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids

scientific article published on 9 March 2017

Outcome following staphylococcal peritonitis.

scientific article published in March 2000

Outcome of invasive pneumococcal disease: a UK based study. Oxford Pneumococcal Surveillance Group

scientific article

PTPN22 and invasive bacterial disease

article

Panton-Valentine leucocidin is the key determinant of pyomyositis in a bacterial GWAS

scientific article published on 22 February 2019

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

Patient and strain characteristics associated with Clostridium difficile transmission and adverse outcomes ⬇️

scientific article published on 12 April 2018

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

scientific article published on 09 February 2017

Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event

scientific article published on 29 January 2012

Population structure of group B streptococcus from a low-incidence region for invasive neonatal disease

scientific article published on 01 June 2005

Population-based Incidence and Etiology of Community-acquired Neonatal Viral Infections in Bangladesh: A Community-based and Hospital-based Surveillance Study

scientific article

Population-based incidence and etiology of community-acquired neonatal bacteremia in Mirzapur, Bangladesh: an observational study

scientific article

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data.

scientific article

Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing.

scientific article published on 05 February 2014

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

scientific article published on 26 September 2018

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches.: Supplemental Tables

scholarly article published 11 January 2019

Predictors of first recurrence of Clostridium difficile infection: implications for initial management ⬇️

scientific article

Prevalence of Staphylococcus aureus protein A (spa) mutants in the community and hospitals in Oxfordshire

scientific article

Prospective evaluation of criteria for microbiological diagnosis of prosthetic-joint infection at revision arthroplasty. The OSIRIS Collaborative Study Group

scientific article

Prosthetic joint infection due to Candida parapsilosis in the UK: case report and literature review

scientific article published on September 1, 1992

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

scientific article

Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study ⬇️

scientific article

Rare variants in MYD88, IRAK4 and IKBKG and susceptibility to invasive pneumococcal disease: a population-based case-control study

scientific article

Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus

scientific article published on 20 January 2017

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

scientific article published on 27 September 2018

Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing

scientific article published on 29 November 2012

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

scientific article published on 23 March 2020

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

scholarly article published 7 January 2019

Reducing demand for antibiotic prescriptions: evidence from an online survey of the general public on the interaction between preferences, beliefs and information, United Kingdom, 2015

scientific article published on 01 June 2018

Reducing expectations for antibiotics in primary care: a randomised experiment to test the response to fear-based messages about antimicrobial resistance

scientific article published on 23 April 2020

Reduction in invasive pneumococcal disease following implementation of the conjugate vaccine in the Oxfordshire region, England

scientific article published on 23 September 2010

Reduction of invasive pneumococcal disease 3 years after the introduction of the 13-valent conjugate vaccine in the Oxfordshire region of England

scientific article published on 9 April 2014

Regarding "Clostridium difficile ribotype does not predict severe infection".

scientific article published on 18 February 2013

Relationship between bacterial strain type, host biomarkers, and mortality in Clostridium difficile infection ⬇️

scientific article published on 5 March 2013

Relationship between microbiology of throat swab and clinical course among primary care patients with acute cough: a prospective cohort study

scientific article published on 17 December 2019

Renal impairment and clinical outcomes of Clostridium difficile infection in two randomized trials.

scientific article published on 20 June 2013

Reply to Mills and Linkin

scientific article published on 20 May 2014

Reply to Walk et al.

scientific article published on 8 May 2013

Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches

scientific article published on 9 June 2017

Respiratory infections for which general practitioners consider prescribing an antibiotic: a prospective study.

scientific article published on 16 March 2007

Risk Factors for Clostridium difficile Acquisition in Infants: Importance of Study Design

scientific article published on 26 February 2013

Risk factors associated with carbapenemase-producing Enterobacterales (CPE) positivity in the hospital wastewater environment

scientific article published on 11 September 2020

Risk factors for Klebsiella pneumoniae carbapenemase (KPC) gene acquisition and clinical outcomes across multiple bacterial species

scientific article published on 10 January 2020

Robust Prediction of Resistance to Trimethoprim in Staphylococcus aureus.

scientific article published on 4 January 2018

SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus

scientific article published in 2020

SARS-CoV-2 antibody prevalence, titres and neutralising activity in an antenatal cohort, United Kingdom, 14 April to 15 June 2020

scientific article published on 01 October 2020

SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex

scholarly article by Samuel Lipworth et al published March 2019 in Emerging Infectious Diseases

Safe intravenous antibiotic therapy at home: experience of a UK based programme

scientific article published on May 1996

Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples

scientific article

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

scholarly article published 19 December 2016

School‐Aged Children: A Reservoir for Continued Circulation ofHaemophilus influenzaeType b in the United Kingdom

scientific article published on 01 May 2008

Secular trends in nosocomial bloodstream infections: antibiotic-resistant bacteria increase the total burden of infection.

scientific article published on 7 December 2012

Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae

scientific article published on 08 November 2019

Sequence and functional analyses of Haemophilus spp. genomic islands

scientific article

Severe infections emerge from commensal bacteria by adaptive evolution

scientific article published on 19 December 2017

Severe infections emerge from the microbiome by adaptive evolution

Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease ⬇️

scientific article (publication date: 2013)

Site-specific recombination with the chromosomal tRNA(Leu) gene by the large conjugative Haemophilus resistance plasmid

scientific article published on May 2002

Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays

scientific article published on 30 January 2017

Stability of serotypes during nasopharyngeal carriage of Streptococcus pneumoniae

scientific article

Stable and noncompetitive RNA internal control for routine clinical diagnostic reverse transcription-PCR

scientific article published on March 2004

Staphylococcus aureus in critical care - Authors' reply.

scientific article

Streptococcus pneumoniae serotype-2 childhood meningitis in Bangladesh: a newly recognized pneumococcal infection threat

scientific article (publication date: 2012)

Surveillance of infection severity: a registry study of laboratory diagnosed Clostridium difficile

scientific article (publication date: 2012)

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

scientific article published on 23 March 2018

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

article

Temporal and Geographic Stability of the Serogroup‐Specific Invasive Disease Potential of Streptococcus pneumoniae in Children

scientific article published on 25 August 2004

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

scientific article published on 07 January 2021

Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK

scientific article published on 03 September 2021

The Hospital Water Environment as a Reservoir for Carbapenem-Resistant Organisms Causing Hospital-Acquired Infections-A Systematic Review of the Literature

scientific article

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

scientific article published on 24 September 2019

The Stealthy Superbug: the Role of Asymptomatic Enteric Carriage in Maintaining a Long-Term Hospital Outbreak of ST228 Methicillin-Resistant Staphylococcus aureus

scientific article published on 19 January 2016

The complexity and diversity of the Pathogenicity Locus in Clostridium difficile clade 5

scientific article

The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers

scientific article published on 06 January 2021

The evolution of genetic structure in the marine pathogen, Vibrio vulnificus.

scientific article published on 20 July 2007

The hospital microbiome project: meeting report for the UK science and innovation network UK-USA workshop ‘beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance’, October 14th 2013

article

The impact of conjugate vaccine on carriage of Haemophilus influenzae type b

scientific article published on 01 January 1995

The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance

scientific article published on 16 November 2020

The relative importance of large problems far away versus small problems closer to home: insights into limiting the spread of antimicrobial resistance in England

scientific article published on 27 April 2017

The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak

scientific article published on 21 June 2018

The usefulness of whole genome sequencing in the management of Staphylococcus aureus infections.

scientific article published on 18 January 2013

Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands

scientific article published on December 2004

Transforming clinical microbiology with bacterial genome sequencing.

scientific article

Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing

scientific article

Treatment of first recurrence of Clostridium difficile infection: fidaxomicin versus vancomycin

scientific article

Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998-2016: a study of electronic health records

scientific article published on 17 August 2018

Tuberculosis is changing.

scientific article published on 10 March 2017

Two Distinct Patterns of Clostridium Difficile Diversity Across Europe Indicates Contrasting Routes of Spread ⬇️

scientific article published on 6 April 2018

Two cases of Clostridium difficile infection in unrelated oncology patients attributable to a single clone of C. difficile PCR ribotype 126

scientific article published in 2015

Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence

scientific article published on 10 June 2008

Using hospital network-based surveillance for antimicrobial resistance as a more robust alternative to self-reporting

scientific article published on 25 July 2019

Using linked electronic health records to report healthcare-associated infections

scientific article published in PLoS ONE

Vaccine escape recombinants emerge after pneumococcal vaccination in the United States

scientific article

Validating a 14-Drug Microtiter Plate Containing Bedaquiline and Delamanid for Large-Scale Research Susceptibility Testing of Mycobacterium tuberculosis

scientific article published on 27 August 2018

WGS to determine the extent of Clostridioides difficile transmission in a high incidence setting in North Wales in 2015

article

WGS to predict antibiotic MICs for Neisseria gonorrhoeae

scientific article published on 10 March 2017

Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England ⬇️

scientific article

Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing.

scientific article

Whole genome sequencing for predicting clarithromycin resistance in

scientific article published on 21 December 2018

Whole genome sequencing for predicting clarithromycin resistance in Mycobacterium abscessus

article

Whole genome sequencing in the prevention and control of Staphylococcus aureus infection.

scientific article

Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation.

scientific article

Whole-genome sequencing demonstrates that fidaxomicin is superior to vancomycin for preventing reinfection and relapse of infection with Clostridium difficile

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Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

scientific article published on 23 June 2015

Whole-genome sequencing identifies nosocomial transmission of extra-pulmonary M. tuberculosis

scientific article published on 22 December 2016

Whole-genome sequencing identifies nosocomial transmission of extra-pulmonary M. tuberculosis-response

scientific article published on September 2017

Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit

scientific article published on 12 December 2013

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

scientific article

Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study

scientific article published on 11 July 2016

Within-host evolution of Staphylococcus aureus during asymptomatic carriage.

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Within-host evolution of bacterial pathogens

scientific article

mcr-1 and mcr-2 (mcr-6.1) variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015.

scientific article published in October 2018

mcr-1 and mcr-2 variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015.

scientific article published in October 2017

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