Publications

Antibiotic review kit for hospitals (ARK-Hospital): a stepped-wedge cluster-randomised controlled trial

Llewelyn MJ. et al, (2023), The Lancet Infectious Diseases, 23, 207 - 221

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

Sanderson ND. et al, (2023), Microbial Genomics, 9

Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing ofM. tuberculosis

(2022), European Respiratory Journal, 60, 2200239 - 2200239

Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity in the General Population in the United Kingdom

Vihta KD. et al, (2022), Clinical Infectious Diseases, 75, e329 - e337

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

(2022), PLOS Biology, 20, e3001721 - e3001721

Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms

(2022), PLOS Biology, 20, e3001755 - e3001755

Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum.

Tuekprakhon A. et al, (2022), Cell, 185, 2422 - 2433.e13

M. tuberculosis microvariation is common and is associated with transmission: Analysis of three years prospective universal sequencing in England

Wyllie D. et al, (2022), Journal of Infection, 85, 31 - 39

SARS-CoV-2 antibody trajectories after a single COVID-19 vaccination with and without prior infection.

Wei J. et al, (2022), Nat Commun, 13

Catwalk: identifying closely related sequences in large microbial sequence databases.

Volk D. et al, (2022), Microbial genomics, 8

Mycobacterium tuberculosis transmission in Birmingham, UK, 2009–19: An observational study

Walker TM. et al, (2022), The Lancet Regional Health - Europe, 17, 100361 - 100361

Mycobacterium tuberculosis transmission in Birmingham, UK, 2009–19: An observational study

Walker TM. et al, (2022), The Lancet Regional Health - Europe, 17, 100361 - 100361

Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.

Nutalai R. et al, (2022), Cell, 185, 2116 - 2131.e18

Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales.

Marimuthu K. et al, (2022), Nature communications, 13

Realising the Potential of Genomics for M. tuberculosis: A Silver Lining to the Pandemic?

Walker TM. and Crook DW., (2022), China CDC Weekly, 4, 437 - 439

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

Fowler PW. et al, (2022), eLife, 11

Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines

Wei J. et al, (2022), Nature Medicine, 28, 1072 - 1082

An Observational Cohort Study on the Incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and B.1.1.7 Variant Infection in Healthcare Workers by Antibody and Vaccination Status

Lumley SF. et al, (2022), Clinical Infectious Diseases, 74, 1208 - 1219

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

Street TL. et al, (2022), Journal of clinical microbiology, 60

Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies.

Jabeen MF. et al, (2022), Microbiology spectrum

Systematic review of wastewater surveillance of antimicrobial resistance in human populations.

Chau KK. et al, (2022), Environ Int, 162

Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines

Wei J. et al, (2022), Nature Medicine

Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance

Pritchard E. et al, (2022), The Lancet Regional Health - Europe, 13, 100282 - 100282

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Dejnirattisai W. et al, (2022), Cell, 185, 467 - 484.e15

Reduced neutralisation of SARS-CoV-2 omicron B.1.1.529 variant by post-immunisation serum.

Dejnirattisai W. et al, (2021), Lancet (London, England)

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.

Elliott P. et al, (2021), Science (New York, N.Y.), 374

Ten Years of Population-Level Genomic Escherichia coli and Klebsiella pneumoniae Serotype Surveillance Informs Vaccine Development for Invasive Infections

Lipworth S. et al, (2021), Clinical Infectious Diseases, 73, 2276 - 2282

Tracking the Emergence of SARS-CoV-2 Alpha Variant in the United Kingdom

Walker AS. et al, (2021), New England Journal of Medicine

Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Dejnirattisai W. et al, (2021)

Time of Day of Vaccination Affects SARS-CoV-2 Antibody Responses in an Observational Study of Health Care Workers

Wang W. et al, (2021), Journal of Biological Rhythms, 074873042110593 - 074873042110593

A haemagglutination test for rapid detection of antibodies to SARS-CoV-2

Townsend A. et al, (2021), Nature Communications, 12

Anti-spike antibody response to natural SARS-CoV-2 infection in the general population

Wei J. et al, (2021), Nature Communications, 12

Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections

Vihta K-D. et al, (2021), Scientific Reports, 11

Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

Pouwels KB. et al, (2021), Nature Medicine, 27, 2127 - 2135

Stringent thresholds in SARS-CoV-2 IgG assays lead to under-detection of mild infections

Eyre DW. et al, (2021), BMC Infectious Diseases, 21

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

Lipworth S. et al, (2021), Genome Medicine, 13

Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridization of viral RNA

Hepp C. et al, (2021), Scientific Reports, 11

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

Young BC. et al, (2021), Microbial Genomics, 7

Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity in the General Population in the United Kingdom

Vihta K-D. et al, (2021), Clinical Infectious Diseases

An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction

Yang Y. et al, (2021), Briefings in Bioinformatics, 22

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

Davies TJ. et al, (2021)

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

Wang W. et al, (2021)

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

Lumley SF. et al, (2021)

A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage

AbuOun M. et al, (2021), Microbial Genomics, 7

Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection

Lipworth S. et al, (2021), LANCET MICROBE, 2, E492 - E492

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

Lumley SF. et al, (2021), Journal of Infection

Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals

Lumley SF. et al, (2021), Journal of Infection, 83, 473 - 482

Epidemiology of Mycobacterium abscessus in England: an observational study

Lipworth S. et al, (2021), The Lancet Microbe, 2, e498 - e507

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

Eyre DW. et al, (2021), Clinical Microbiology and Infection, 27, 1516.e7 - 1516.e14

Flanker: a tool for comparative genomics of gene flanking regions

Matlock W. et al, (2021), Microbial Genomics, 7

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Publications