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Publications

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HPRU PUBLICATIONS

2026

  • Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance. Kotay SM, Parikh HI, Hyun SG, Barry K, Stoesser N, Walker AS, et al. 

https://www.nature.com/articles/s44259-025-00176-2  

  • Defining recurrent urinary tract infection and reinfection risk: electronic health record study. Vazquez-Montes MDLA, Fansshawe TR, Smith MC, Ahmed H, Stoesser N, Walker AS, et al. 

https://bjgpopen.org/content/early/2025/12/24/BJGPO.2025.0239

  • Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate. Nagy D, Pennetta V, Rodger G, Hopkins K, Jones CR, The NEKSUS Consortium et al. 

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001631?emailalert=true#html_fulltext

  • Antibiotic prescribing and use in United Kingdom general practices in socio-economically deprived areas: a critical interpretive synthesis.  Bell A, Ford T, Roberts N, Blane D, Tonkin-Crine S, Borek AJ.

https://www.tandfonline.com/doi/full/10.1080/29944694.2025.2606722#abstract

  • Widening access to penicillin allergy assessment in the United Kingdom—a proposed implementation plan for the National Health Service (NHS). Porter CE, Roleston C, Bethune C, Jenny B, Brown CS, Clarke I, et al. 

https://academic.oup.com/jacamr/article/8/1/dlaf240/8416145#550580291

  • Acceptability of self-sampling and self-testing for infections: a rapid systematic review on public users’ views. Borek AJ, Roleston C, Lazzarino R, Cooray M, Hayward G, Roberts N et al. 

https://link.springer.com/article/10.1186/s12889-025-21773-w#Ack1

2025

  • Assessing a penicillin allergy de-labelling implementation intervention in a UK hospital: a process evaluation reporting healthcare workers’ experiences. Powell N, Upton M, Kent B, Sandoe JAT, Tonkin-Crine S. 

https://academic.oup.com/jacamr/article/7/5/dlaf174/8279672#535440084 

  • The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study. Peto L, Fawcett N, Kamfose MM, Scarborough C, Peniket A, Danby R, et al. 

https://elifesciences.org/articles/97751#abstract

  • Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663 Mycobacterium tuberculosis samples. Westhead J, Baker CS, Brouard M, Colpus M, Constantinides B, Hall A et al.

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001592#header

  • The potential of a centrally implemented system for national surveillance of bloodstream infections in England, compared to current local surveillance, 2023–2024. Cregan J, Nsonwu O, Chudasama D, Hopkins S, Muller-Pebody B, Hope R et al.

https://www.journalofhospitalinfection.com/article/S0195-6701(25)00417-7/fulltext#sec-7

  • Combining demographic shifts with age-based resistance prevalence to estimate future antimicrobial resistance burden in Europe and implications for targets: A modelling study. Waterlow NR, Chandler CIR, Cooper BS, Moore CE, Robotham JV, Sartorious B et al.

https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1004579#ack

  • Assessing a penicillin allergy de-labelling implementation intervention in a UK hospital: a process evaluation reporting healthcare workers’ experiences. Powell N, Upton M, Kent B, Sandow JAT, Tonkin-Crine S.

 https://academic.oup.com/jacamr/article/7/5/dlaf174/8279672?login=false#535440084

  • Interplay between C-reactive protein responses and antibiotic prescribing in people with suspected infection. GuQ, Yuan K, Wei J, Yoon CH, Danielsen AS, Luk A, et al. 

https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-025-11381-9

  • Case ascertainment of a potential centrally-implemented, automated system for national surveillance of healthcare-associated infections, England, 2016 to 2023.  Cregan J, Nsonwu O. Chudasama D, Hopkins S, Muller-Pebody B, Hope R, et al. 

https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2025.30.42.2500066

  • Escherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase. Matlock W, Rodger G, Pritchard E, Colpus M, Kapel N, Barrett L, et al. 

https://www.nature.com/articles/s41467-025-63714-6

  • The impact of inter-infection time on antimicrobial resistance profiles in women with multiple urinary tract infections over time. Honda T, Vazquez-Montes MDLA, Fanshawe TR, Stoesser N, Butler CC, Walker AS, et al. 

https://pubmed.ncbi.nlm.nih.gov/40581812/

  • Estimating the effect of antimicrobial resistance genes on minimum inhibitory concentration in Escherichia coli. Lipworth S, Chau K, Oakley S, Barrett Lucinda, Crrok Derrick, Peto T, et al. 

https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(25)00111-9/fulltext

  • Evaluating 12 automated, whole-genome sequencing analysis pipelines for Mycobacterium tuberculosis complex: a comparative study. Spies R, Crook DW, Peto TEA, Fowler PW, Turner R, Thai H, et al. 

         https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(25)00138-7/fulltext

  • Rapid, accurate, and reproducible de novo prediction of resistance to antituberculars. Zhang X, Wan S, Bhati AP, Fowler PW, Coveney PV. 

        https://journals.asm.org/doi/10.1128/msphere.00571-25

  • An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in M. tuberculosis using a reproducible algorithmic approach. Adhlard D, Joseph L, Webster H, O'Reilly A, Knaggs J, Peto TEA, et al. 

         https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001429

  • An electronic health record-wide association study to identify populations at increased risk of E. coli bacteraemia. Pritchard E, Vihta K, Lipworth S, Pouwels KB, Stoesser N, Hope R, et al. 

        https://www.sciencedirect.com/science/article/pii/S0163445325002129

  • Subpopulations in clinical samples of M. tuberculosis can give rise to rifampicin resistance and shed light on how resistance is acquired. Brunner V, Fowler P. 

         https://academic.oup.com/jacamr/article/7/5/dlaf175/8279675?login=false

  • Dissemination of OXA-23 carbapenemase in Proteus mirabilis and Escherichia coli driven by transposon-carrying lineages. Zamudio R, Osman K, Pike R, Chaudhry A, Meunier D, Stoesser N, et al. 

         https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001502

  • Stop antibiotics when you feel better? Opportunities, challenges and research directions. Borek AJ, Ledda A, Pouwels KB, Butler CC, Hayward G, Walker AS et al. 

         https://academic.oup.com/jacamr/article/6/5/dlae147/7753463

  • Timeliness of a potential automated system for national surveillance of healthcare-associated infections in England. Quan TP, Eyre D, Shadwell S, West D, Hopkins S, Chudasama D, et al. 
    https://pubmed.ncbi.nlm.nih.gov/40288583/
  • General practice antibiotic prescriptions attributable to respiratory syncytial virus by age and antibiotic class: an ecological analysis of the English population. Miller L, Beaney T, Hope R, Cunningham M, Robotham J, Powels K, et al. 
    https://academic.oup.com/jac/article/80/4/1116/8023879
  • Rapid antibiotic susceptibility testing for urinary tract infections in secondary care in England: a cost-effectiveness analysis. Booton RD, Agnew E, Pople D, Evans S, Bock LJ, Sutton MJ, et al. 
    https://bmjopen.bmj.com/content/14/11/e081865