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Publications

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

Stoesser N. et al, (2024), JAC Antimicrob Resist, 6

Double testing with lateral flow antigen test devices for COVID-19: does a second test in quick succession add value?

Futschik ME. et al, (2024), Journal of Virological Methods, 329

Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin.

Farrar A. et al, (2024), Sci Rep, 14

Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum.

Read DS. et al, (2024), Water Res, 264

Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning.

CRyPTIC consortium None., (2024), PLoS Comput Biol, 20

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Peto L. et al, (2024)

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Peto L. et al, (2024)

Improving the representativeness of UK's national COVID-19 Infection Survey through spatio-temporal regression and post-stratification.

Pouwels KB. et al, (2024), Nat Commun, 15

Rifampicin resistant Mycobacterium tuberculosis in Vietnam, 2020-2022.

Van Nguyen H. et al, (2024), J Clin Tuberc Other Mycobact Dis, 35

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

Sanderson N. et al, (2024), Microbial Genomics

Author Correction: The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies.

Lipworth S. et al, (2024), Nat Commun, 15

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

Carter JJ. et al, (2024), JAC Antimicrob Resist, 6

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Peto L. et al, (2024)

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population.

Wei J. et al, (2024), Nat Commun, 15

The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies

Lipworth S. et al, (2024), Nature Communications

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

CRyPTIC Consortium None., (2024), Nat Commun, 15

MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis

Roberts LW. et al, (2024), The Lancet Microbe

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

Davies TJ. et al, (2023), Microb Genom, 9

Hostile: accurate decontamination of microbial host sequences.

Constantinides B. et al, (2023), Bioinformatics, 39

Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli.

Zagajewski A. et al, (2023), Commun Biol, 6

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