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Publications

Utilising large and diverse bacterial genome datasets to improve the detection and identification of Streptococcus pneumoniae via PCR-based diagnostics

Ahlers FM. et al, (2025), Microbial Genomics

Benchmarking transformer-based models for medical record deidentification: A single centre, multi-specialty evaluation

Kuo R. et al, (2025)

Molecular clock complexities of Clostridioides difficile.

Vernon JJ. et al, (2025), Anaerobe, 93

Identification of undetected SARS-CoV-2 infections by clustering of Nucleocapsid antibody trajectories

Zwerwer LR. et al, (2025), Nature Communications

The impact of antimicrobial stewardship ward rounds on antimicrobial use and predictors of advice, uptake, and outcomes

EYRE D. et al, (2025), Journal of Infection

Rapid clinical diagnosis and treatment of common, undetected, and uncultivable bloodstream infections using metagenomic sequencing from routine blood cultures with Oxford Nanopore

Govender KN. and Eyre DW., (2025)

Machine learning and clinician predictions of antibiotic resistance in Enterobacterales bloodstream infections.

Yuan K. et al, (2024), J Infect

Addition of macrolide antibiotics for hospital treatment of community-acquired pneumonia

Wei J. et al, (2024), Journal of Infectious Diseases

Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey

Lees E. et al, (2024), Microbial Genomics

Developing a Framework for Tracking Antimicrobial Resistance Gene Movement in a Persistent Environmental Reservoir

Mathers A. et al, (2024), npj Antimicrobials and Resistance

Corrigendum to "No evidence of difference in mortality with amoxicillin versus co-amoxiclav for hospital treatment of community-acquired pneumonia" [J Infect 88 (2024) 106161].

Wei J. et al, (2024), J Infect, 89

Predicting individual patient and hospital-level discharge using machine learning

Wei J. et al, (2024), Communications Medicine

Comparative evaluation of large-language models and purpose-built software for medical record de-identification

Kuo R. et al, (2024)

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from Escherichia coli isolates.

Rodger G. et al, (2024), Microb Genom, 10

Global burden of bacterial antimicrobial resistance 1990-2021: a systematic analysis with forecasts to 2050.

GBD 2021 Antimicrobial Resistance Collaborators None., (2024), Lancet, 404, 1199 - 1226

Predicting future hospital antimicrobial resistance prevalence using machine learning

VIHTA K-D. et al, (2024), Communications Medicine

Developing a novel approach to complex evolution of antimicrobial resistance via mobile genetic elements from a persistent environmental biofilm

Mathers A. et al, (2024)

Expanding the use of mathematical modeling in healthcare epidemiology and infection prevention and control.

Grant R. et al, (2024), Infect Control Hosp Epidemiol, 1 - 6

Global, regional, and national incidence and mortality burden of non-COVID-19 lower respiratory infections and aetiologies, 1990-2021: a systematic analysis from the Global Burden of Disease Study 2021.

GBD 2021 Lower Respiratory Infections and Antimicrobial Resistance Collaborators None., (2024), Lancet Infect Dis, 24, 974 - 1002

Epidemiology and excess mortality of antimicrobial resistance in bacteraemias among cancer patients: a cohort study using routinely collected health data from regional hospital trusts in Oxford and Oslo, 2008-2018

Danielsen AS. et al, (2024)

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