Publications

Real-time modelling of the SARS-CoV-2 pandemic in England 2020–2023: a challenging data integration

Birrell PJ. et al, (2026), Journal of the Royal Statistical Society Series A: Statistics in Society, 189, 898 - 922

Transmission of rifampicin-resistant tuberculosis in Ho Chi Minh City, Viet Nam: a prospective genomic epidemiology study

Spies R. et al, (2026)

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing

Reding C. et al, (2026)

Advancing monitoring of antimicrobial resistance trajectories using flexible spatiotemporal modelling: a change-point analysis

Allel K. et al, (2026), Wellcome Open Research, 10, 326 - 326

Predicting pyrazinamide resistance in Mycobacterium tuberculosis using a graph convolutional network

Dissanayake D. et al, (2026), BMC Microbiology

Longitudinal Epidemiology and Variant Dynamics of SARS-CoV-2 in Coastal Kenya (2020–2025): Clinical Features and Wave Patterns

Lambisia AW. et al, (2026), Open Forum Infectious Diseases, 13

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Hunt M. et al, (2026), Nature Methods, 23, 653 - 662

The potential of a centrally implemented system for national surveillance of bloodstream infections in England, compared to current local surveillance, 2023–2024

Cregan J. et al, (2026), Journal of Hospital Infection, 169, 5 - 14

Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate

Nagy D. et al, (2026), Microbial Genomics, 12

Body Composition Changes in Children Living With HIV Initiated on Dolutegravir or Protease Inhibitors in the CHAPAS-4 Trial

Natukunda E. et al, (2026), Pediatric Infectious Disease Journal

Longitudinal changes in bone mineral density among children living with HIV over 96 weeks following switch to second-line antiretroviral therapy in Uganda

Natukunda E. et al, (2026), PLOS Global Public Health, 6, e0005979 - e0005979

Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens: diagnostic accuracy study

Sanderson ND. et al, (2026)

Evaluation of an Oxford Nanopore sequencing workflow for mycobacteria from primary MGIT culture

Baker CS. et al, (2026)

Pharmacokinetics and safety of fosfomycin and flomoxef administered as part of neonatal sepsis treatment (NeoSep1 Part 1)

Bekker A. et al, (2026), Antimicrobial Agents and Chemotherapy, 70

Defining recurrent urinary tract infection and reinfection risk: electronic health record study

Vazquez-Montes MDLA. et al, (2026), BJGP Open, BJGPO.2025.0239 - BJGPO.2025.0239

Short-Lived Success: Carbapenem-Resistant Enterobacterales Recolonization in Sinks Following Repeated Peroxide-Peracetic Acid-Based Foam Disinfection

Kotay S. et al, (2026)

ALARUM: Active One Health surveillance in LMICs to monitor and predict Antimicrobial Resistance Using Metagenomics – a cross-sectional study protocol

van der Sande MAB. et al, (2026), BMJ Open, 16, e107465 - e107465

A benchmark of expert-level academic questions to assess AI capabilities

Phan L. et al, (2026), Nature, 649, 1139 - 1146

Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance

Kotay SM. et al, (2026), npj Antimicrobials and Resistance, 4

The cumulative incidence and infection hospitalization risk of SARS-CoV-2 by variant: a longitudinal study in England

Gaughan C. et al, (2026), American Journal of Epidemiology, 195, 188 - 197

Individual and spatial heterogeneity of praziquantel efficacy against Schistosoma mansoni within the context of repeated mass drug administration

Iacovidou MA. et al, (2026)

Sotrovimab versus usual care in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Abani O. et al, (2026), The Lancet Infectious Diseases, 26, 34 - 45

Malaria vaccine protection against intradermal or venous parasites: a randomized phase 2b human challenge trial

Kapulu MC. et al, (2026), Nature Medicine, 32, 178 - 185

How ready are we to use artificial intelligence in our fight against antimicrobial resistance? An ESGAID and EAAS perspective.

Giacobbe DR. et al, (2026), Expert review of anti-infective therapy, 24, 39 - 61

Low-dose yellow fever vaccination in infants: a randomised, double-blind, non-inferiority trial.

Kimathi D. et al, (2026), Lancet (London, England), 407, 497 - 504

Treatment of enteric fever (typhoid and paratyphoid fever) with cephalosporins: a Cochrane review

Kuehn R. et al, (2026), EMERGENCIAS, 38, 66 - 68

External validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score and the added impact of acute clinical response: a prospective cohort study

Cross ELA. et al, (2025), BMC Infectious Diseases, 25

Epidemiological, microbiological, and genomic risk factors for healthcare-associated Carbapenemase producing Enterobacterales (CPE) outbreaks: A systematic review

Nagy D. et al, (2025)

The spatiotemporal distribution of substandard and falsified antimalarial medicines in Africa, 1996-2019

Adipo LB. et al, (2025)

It never rains but pours: disseminated nocardiosis in a renal transplant patient from Nigeria – a case report

Whitehead T. et al, (2025), BMC Infectious Diseases, 26

Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663 Mycobacterium tuberculosis samples

Westhead J. et al, (2025), Microbial Genomics, 11

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

Peto L. et al, (2025), eLife, 13

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

Peto L. et al, (2025)

Benchmarking transformer-based models for medical record de-identification in a single center multi-specialty evaluation

Kuo R. et al, (2025), iScience, 28, 113732 - 113732

Evaluating 12 automated, whole-genome sequencing analysis pipelines for Mycobacterium tuberculosis complex: a comparative study

Spies R. et al, (2025), The Lancet Microbe, 6, 101210 - 101210

2025 ICM: Use of Newer Antibiotics and Fluoroquinolone-Resistance

Sadek FZ. et al, (2025), The Journal of Arthroplasty, 41, S196 - S205

Enhancement of midwives' and child healthcare nurses' attitudes towards the WHO's recommendations following breastfeeding training: A quasi-experimental study.

Blixt I. et al, (2025), Sexual & reproductive healthcare : official journal of the Swedish Association of Midwives, 46

Estimating the association of antimicrobial resistance genes with minimum inhibitory concentration in Escherichia coli: an observational study

Lipworth S. et al, (2025), The Lancet Microbe, 6, 101183 - 101183

HCV response-guided therapy: is shorter always better? – Authors' reply

Cooke GS. et al, (2025), The Lancet, 406, 2540 - 2540

Rapid, accurate, and reproducible de novo prediction of resistance to antituberculars

Zhang X. et al, (2025), mSphere, 10

Predicting pyrazinamide resistance in Mycobacterium tuberculosis using a graph convolutional network

Dissanayake D. et al, (2025)

Case ascertainment of a potential centrally-implemented, automated system for national surveillance of healthcare-associated infections, England, 2016 to 2023

Cregan J. et al, (2025), Eurosurveillance, 30

Letter: Generative AI Dual-Use Risks in Infectious Diseases: An Overlooked Challenge for Global Health

Rizzo A. et al, (2025), NEJM AI, 2

Optimisation of whole cell human depletion provides increased sensitivity and microbial genome coverage from respiratory metagenomic assays

Doyle RM. et al, (2025)

Implementing rapid pan-microbial metagenomics in paediatric intensive care

Hammond R. et al, (2025)

Rapidly and reproducibly building a comprehensive catalogue of resistance-associated variants for M. tuberculosis

Adlard D. et al, (2025)

An electronic health record-wide association study to identify populations at increased risk of E. coli bacteraemia

Pritchard E. et al, (2025), Journal of Infection, 91, 106612 - 106612

Plasmid dynamics driving carbapenemase gene dissemination in healthcare environments: a nationwide analysis of closed Enterobacterales genomes.

Koh V. et al, (2025), Nature communications, 16

Escherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase

Matlock W. et al, (2025), Nature Communications, 16

Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue

Street TL. et al, (2025), Microbial Genomics, 11

A collaborative large language model for drug analysis

Zhou H. et al, (2025), Nature Biomedical Engineering

Cardiac output measurement in Malawian children ages 2 months–12 years hospitalised with severe anaemia (COM-TRACT)

Chintolo E. et al, (2025), International Health

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

Nagy D. et al, (2025)

Induction of an early IFN-γ cellular response and high plasma levels of SDF-1α are inversely associated with COVID-19 severity and residence in rural areas in Kenyan patients

Wanjiku P. et al, (2025), PLOS One, 20, e0316967 - e0316967

Subpopulations in clinical samples of M. tuberculosis can give rise to rifampicin resistance and shed light on how resistance is acquired

Brunner VM. and Fowler PW., (2025), JAC-Antimicrobial Resistance, 7

Laboratory evaluation of 185 commercial assays for detecting SARS-CoV-2: the UK response for mass testing

Bown A. et al, (2025), eClinicalMedicine, 87, 103416 - 103416

SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study

Ghafari M. et al, (2025), The Lancet Microbe, 6, 101154 - 101154

Evaluation of SARS-CoV-2 lateral flow device sensitivity: a comparison of systematic laboratory assessments with manufacturer-reported sensitivity

Kulasegaran-Shylini R. et al, (2025), eClinicalMedicine, 87, 103454 - 103454

To heal or harm: A systematic review of the role of fluoroquinolones in periprosthetic joint infections

Tevell S. et al, (2025), CMI Communications, 2, 105103 - 105103

Conference report: The second Bacterial Genome Sequencing Pan-European Network conference

Wei KC. et al, (2025), Microbes and Infection, 27, 105557 - 105557

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