Publications

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), Microbial genomics, 9

Evaluation of sequence hybridization for respiratory viruses using the Twist Bioscience Respiratory Virus Research panel and the OneCodex Respiratory Virus sequence analysis workflow.

Kapel N. et al, (2023), Microbial genomics, 9

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

Chau KK. et al, (2023), Microbial genomics, 9

Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile

Dingle KE. et al, (2023), mBio

Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK.

Matlock W. et al, (2023), eLife, 12

Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis.

Hall MB. et al, (2023), The Lancet. Microbe, 4, e84 - e92

A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone.

Smith RP. et al, (2023), Front Microbiol, 14

Virus Detection and Identification in Minutes Using Single-Particle Imaging and Deep Learning.

Shiaelis N. et al, (2022), ACS nano

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

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

Yoon CH. et al, (2022), Journal of Antimicrobial Chemotherapy, 77, 2536 - 2545

High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region.

Dreyer V. et al, (2022), Genome medicine, 14

Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom

Vihta1 KD. et al, (2022), Clinical Infectious Diseases

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

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

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

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

Sanderson N. et al, (2022)

The bacteriology of pleural infection (TORPIDS): an exploratory metagenomics analysis through next generation sequencing.

Kanellakis NI. et al, (2022), The Lancet. Microbe, 3, e294 - e302

Mycobacterium Tuberculosis Transmission in Birmingham, UK, 2009-19: A Prospective Observational Study

Walker TM. et al, (2021)

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

Wei J. et al, (2021)

Symptoms and SARS-CoV-2 positivity in the general population in the UK

Vihta K-D. et al, (2021)

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Liu C. et al, (2021), Cell, 184, 4220 - 4236.e13

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

Fowler PW. et al, (2021)

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

Wei J. et al, (2021)

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

Eyre DW. et al, (2021)

Amplification-Free Detection of Viruses in Minutes using Single-Particle Imaging and Machine Learning

Shiaelis N. et al, (2021), Biophysical Journal, 120, 195a - 195a

Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison

Ainsworth M. et al, (2020), The Lancet Infectious Diseases, 20, 1390 - 1400

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

Stoesser N. et al, (2019)

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

Bush SJ. et al, (2019)

Prediction of Pyrazinamide Resistance in <i>Mycobacterium Tuberculosis</i> Using Structure-Based Machine Learning Approaches

Carter JJ. et al, (2019)

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

Peto L. et al, (2019)

Prediction of pyrazinamide resistance inMycobacterium tuberculosisusing structure-based machine learning approaches

Carter JJ. et al, (2019)

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Publications