HPRU Papers

PAPERS PUBLISHED IN 2024

• Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification. Pouwels KB, Eyre DW, House T, Aspey B, Matthews PC, Stoesser N, et al.

https://www.nature.com/articles/s41467-024-49201-4 

• Towards quantifying plasmid similarity. Matlock W, Shaw LP, Sheppard SK, and Feil E.

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001290 

• Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin. Farrar A, Feehily C, Turner P, Zagajewski A, Chatzimichail S,Crook D, et al.

https://www.nature.com/articles/s41598-024-69341-3#citeas

• Associations between BMI and hospital resource use in patients hospitalised for COVID-19 in England: a community-based cohort study. Altunkaya J, Piernas C, Pouwels KB, Jebb SA, Clarke P, Astbury NM, et al.

https://www.thelancet.com/journals/landia/article/PIIS2213-8587(24)00129-3/fulltext 

• Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile. Dingle KE, Freeman J, Didelot X, Quan TP, Eyre DW, Swann J, et al. 

https://journals.asm.org/doi/10.1128/mbio.00243-23

• High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent. Chau KK, Goodall T, Bowes M, Easterbrook K, Brett H, Hughes J, et al. 

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000983

• Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey. Lythgoe KA, Golubchik T, Hall M, House T, Cahuantzi R, MacIntyre-Cockett G, et al. 

https://royalsocietypublishing.org/doi/10.1098/rspb.2023.1284

• Prevalence of persistent SARS-CoV-2 in a large community surveillance study. Ghafari M, Hall M, Golubchik T, Ayoubkhani D, House T, MacIntyre-Cockett G, et al. 

https://www.nature.com/articles/s41586-024-07029-4

• Employment outcomes of people with Long Covid symptoms: community-based cohort study. Ayoubkhani D, Zaccardi F, Pouwels KB, Walker AS, Houston D, Alwan NA, et al. 

https://academic.oup.com/eurpub/advance-article/doi/10.1093/eurpub/ckae034/7616634

• Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli. Davies TJ, Swann J, Sheppard AE, Davies TJ, Swann J, Sheppard AE, et al. 

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001151#header

• Development and validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score. Cross ELA, Quan TP, Hayward GN, Walker AS, Llewelyn MJ. 

https://www.journalofinfection.com/article/S0163-4453(23)00593-5/fulltext

• Epidemiology and microbiology of recurrent UTI in women in Oxfordshire, UK. Vazquez-Montes MDL, Fanshawe TR, Stoesser N, Walker AS, Butler C, Hayward G. 

https://academic.oup.com/jacamr/article/6/1/dlad156/7514314

• Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population. Wei J, Stoesser N, Matthews PC, Khera T, Gethings O, Diamond I, et al. 

https://www.nature.com/articles/s41467-024-44973-1

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

https://www.nature.com/articles/s41467-023-44325-5

• The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies. Lipworth S, Matlock W, Shaw L, Vihta K, Rodger G, Chau K, et al.

https://www.nature.com/articles/s41467-024-45761-7

• SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort. Dietz E, Pritchard E, Pouwels K, Ehsaan M, Blake J, Gaughan C, et al.

https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-024-03351-w

• Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches. Carter JJ, Walker TM, A Sarah Walker, Whitfield MG, Morlock GP, Lynch CI, et al. 

https://academic.oup.com/jacamr/article/6/2/dlae037/7630603

• No evidence of difference in mortality with amoxicillin versus co-amoxiclav for hospital treatment of community-acquired pneumonia. Wei J, Uppal A, Nganjimi C, Warr H, Ibrahim Y, Gu Q, et al.

https://www.journalofinfection.com/article/S0163-4453(24)00095-1/fulltext

• Distinct patterns of vital sign and inflammatory marker responses in adults with suspected bloodstream infection. Gu Q, Wei J, Yoon CH, Yan K, Jones N, Brent A, et al.

https://www.journalofinfection.com/article/S0163-4453(24)00090-2/fulltext

• Impact of interventions to reduce nosocomial transmission of SARS-CoV-2 in English NHS Trusts: a computational modelling study. Evans S, Stimson J, Pople D, White PJ, Mark HW, Robotham J. 

https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-024-09330-z

• Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23. Cane J, Sanderson N, Barnett S, Vaughan A, Pott M, Kapel N, et al.

https://www.journalofinfection.com/article/S0163-4453(24)00098-7/fulltext

• Costs-effectiveness and cost components of pharmaceutical and non-pharmaceutical interventions affecting antibiotic resistance outcomes in hospital patients: a systematic literature review. Allel K, Hernández-Leal MJ, Naylor NR, Undurraga EA, Abou Jaoude GJ, Bhandari P, et al.

https://gh.bmj.com/content/9/2/e013205.info

• Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches. Carter JJ, Walker TM, A Sarah Walker, Whitfield MG, Morlock GP, Lynch CI, et al.

https://academic.oup.com/jacamr/article/6/2/dlae037/7630603

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

https://www.nature.com/articles/s41467-023-44325-5

• Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis. Brunner, VM, Fowler, PW. 

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001187

PAPERS PUBLISHED IN 2023

• Deep reinforcement learning for multi-class imbalanced training: applications in healthcare. Yang J, El-Bouri R, O’Donoghue O, Lachapelle AS, Soltan AAS, Eyre DW, et al. 

https://link.springer.com/article/10.1007/s10994-023-06481-z

• Algorithmic fairness and bias mitigation for clinical machine learning with deep reinforcement learning. Yang, J., Soltan, A.A.S., Eyre, D.W., Clifton D.

https://www.nature.com/articles/s42256-023-00697-3 

• Interpretable machine learning-based decision support for prediction of antibiotic resistance for complicated urinary tract infections. Yang, J., Eyre, D.W., Lu, L., Clifton D.

https://www.nature.com/articles/s44259-023-00015-2  

• Health record hiccups—5,526 real-world time series with change points labelled by crowdsourced visual inspection. Quan TP, Lacey B, Peto TEA, Walker AS.

https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad060/7232826

• Effect of second booster vaccinations and prior infection against SARS-CoV-2 in the UK SIREN healthcare worker cohort. Kirwan PD, Hall VJ, Foulkes S, Otter AD, Munro K, Sparkes D, et al. 

https://www.thelancet.com/journals/lanepe/article/PIIS2666-7762(23)00228-4/fulltext

• Stakeholders’ views and experiences on implementing new diagnostics in primary care to support management of community-acquired acute respiratory tract infections: a qualitative study. Hoste ME, Colman E, Wanat M, Hayward G, Tissier JL, Postma M, et al.

https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2023.1216940/full

• Effectiveness of BNT162b2 mRNA vaccine third doses and previous infection in protecting against SARS-CoV-2 infections during the Delta and Omicron variant waves; the UK SIREN cohort study September 2021 to February 2022. Hall VJ, Ferdinando Insalata, Foulkes S, Kirwan P, Sparkes D, Atti A, et al. 

https://www.journalofinfection.com/article/S0163-4453(23)00553-4/fulltext

• Performance of antigen lateral flow devices in the UK during the alpha, delta, and omicron waves of the SARS-CoV-2 pandemic: a diagnostic and observational study. Eyre DW, Futschik M, Tunkel S, Wei J, Cole-Hamilton J, Saquib R, et al.

https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00129-9/fulltext

• The burden and dynamics of hospital-acquired SARS-CoV-2 in England. Cooper BS, Evans S, Jafari Y, Pham TM, Mo Y, Lim C, et al.

https://www.nature.com/articles/s41586-023-06634-z

• Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance inMycobacterium tuberculosis. JAC-antimicrobial resistance. Brankin AE, Fowler PW.

https://academic.oup.com/jacamr/article/5/2/dlad039/7103433

• Impact of the COVID-19 pandemic on antimicrobial stewardship support for general practices in England: a qualitative interview study. Campbell A, Borek AJ, McLeod M, Tonkin-Crine S, Pouwels KB, Roope LS, et al.

https://bjgpopen.org/content/7/3/BJGPO.2022.0193

• Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance in  Brankin AE, Fowler PW.
  

https://academic.oup.com/jacamr/article/5/2/dlad039/7103433

• The quality of vital signs measurements and value preferences in electronic medical records varies by hospital, specialty, and patient demographics. Jackson N, Woods J, Watkinson P, Brent A, Peto TEA, Walker AS, et al

 https://www.nature.com/articles/s41598-023-30691-z

• Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK. Wei J, Matthews PC, Stoesser N, Newton JN, Diamond I, Studley R, et al. 

https://www.nature.com/articles/s41467-023-38275-1

• Molnupiravir plus usual care versus usual care alone as early treatment for adults with COVID-19 at increased risk of adverse outcomes (PANORAMIC): an open-label, platform-adaptive randomised controlled trial. Butler CC, Hobbs FDR, Gbinigie OA, Rahman NM, Hayward G, Richards DB, et al.

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)02597-1/fulltext

• Performance of antigen lateral flow devices in the UK during the alpha, delta, and omicron waves of the SARS-CoV-2 pandemic: a diagnostic and observational study. Eyre DW, Futschik M, Tunkel S, Wei J, Cole-Hamilton J, Saquib R, et al.

https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00129-9/fulltext

• Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction. Sanderson ND, Kapel N, Rodger G, Webster H, Lipworth S, Street TL, et al.

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000910

• A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone. Smith RP, May HE, AbuOun M, Stubberfield E, Gilson D, Chau KK, et al.

https://www.frontiersin.org/articles/10.3389/fmicb.2023.1070340/full

• Implementing antibiotic stewardship in high-prescribing English general practices: a mixed-methods study. Br J Gen Pract. Tonkin-Crine S, McLeod M, Borek AJ, Campbell A, Anyanwu P, Costelloe C, et al.

https://bjgp.org/content/73/728/e164

• Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing. Yokoyama M, Peto L, Budgell EP, Jones N, Sheridan E, Liu J, et al.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0282584

• Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis. Orlek A, Anjum MG, Mather A, Stoesser N, Walker AS. 

 https://www.nature.com/articles/s41598-023-29530-y 

• The burden and dynamics of hospital-acquired SARS-CoV-2 in England. Cooper BS, Evans S, Jafari Y, Pham TM, Mo Y, Lim C, et al.

https://www.nature.com/articles/s41586-023-06634-z

• Evaluating the impact of testing strategies for the detection of nosocomial COVID-19 in English hospitals through data-driven modeling. Evans S, Stimson J, Pople D, Wilcox MH, Hope R, Robotham JV.

https://www.frontiersin.org/articles/10.3389/fmed.2023.1166074/full

• Stakeholders’ views and experiences on implementing new diagnostics in primary care to support management of community-acquired acute respiratory tract infections: a qualitative study. Hoste ME, Colman E, Wanat M, Hayward G, Tissier JL, Postma M, et al.

https://www.frontiersin.org/articles/10.3389/fpubh.2023.1216940/full

• In Impact of the COVID-19 pandemic on antimicrobial stewardship support for general practices in England: a qualitative interview study. Campbell A, Borek AJ, McLeod M, Tonkin-Crine S, Pouwels KB, Roope LS, et al.

https://bjgpopen.org/content/7/3/BJGPO.2022.0193

• Re-examining advice to complete antibiotic courses: a qualitative study with clinicians and patients. Borek AJ, Edwards G, Santillo M, Wanat M, Glogowska M, Butler CC, et al..

https://bjgpopen.org/content/7/2/BJGPO.2022.0170?utm_source=TrendMD&utm_medium=cpc&utm_campaign=BJGP_Open_TrendMD_0 

• Cycle threshold values as indication of increasing SARS-CoV-2 new variants, England, 2020–2022. Harrison RE, Hamada A, Haswell N, Groves A, Vihta K, Cella K, et al.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521603/

• COVID-19 vaccination, risk-compensatory behaviours, and contacts in the UK. Buckell J, Jones J, Matthews PC, Sir Ian Diamond, Rourke E, Studley R, et al.

https://www.nature.com/articles/s41598-023-34244-2

• Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK. Wei J, Matthews PC, Stoesser N, Newton JN, Diamond I, Studley R, et al. 

https://www.nature.com/articles/s41467-023-38275-1

• Health record hiccups-5,526 real-world time series with change points labelled by crowdsourced visual inspection. Quan TP, Lacey B, Peto TEA, Walker AS.

https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad060/7232826

• Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance in M. tuberculosis. Brankin AE, Fowler PW

https://academic.oup.com/jacamr/article/5/2/dlad039/7103433

• Hostile: accurate decontamination of microbial host sequences. Constantinides B, Hunt M, Crook D.

https://academic.oup.com/bioinformatics/article/39/12/btad728/7457481

• Effectiveness of BNT162b2 mRNA vaccine third doses and previous infection in protecting against SARS-CoV-2 infections during the Delta and Omicron variant waves; the UK SIREN cohort study September 2021 to February 2022. Hall VJ, Insalata F, Foulkes S, et al.

https://pubmed.ncbi.nlm.nih.gov/37926119/

• Demonstrating the learning and impact of embedding participant involvement in a pandemic research study: the experience of the SARS-CoV-2 immunity & reinfection evaluation (SIREN) study UK, 2020–2023. Howells, A., Aquino, E.N., Bose, D. et al.

https://researchinvolvement.biomedcentral.com/articles/10.1186/s40900-023-00506-6

• Antibody correlates of protection against Delta infection after vaccination: A nested case-control within the UK-based Siren Study. Atti, A., Insalata, F., Carr, E. J., et al.

https://linkinghub.elsevier.com/retrieve/pii/S0163445323003808

• A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing. G Rodger, K Chau, P Aranega-Bou, et al.

https://www.journalofhospitalinfection.com/article/S0195-6701(23)00410-3/fulltext

• Model-based evaluation of admission screening strategies for the detection and control of carbapenemase-producing Enterobacterales in the English hospital setting. Pople D, Kypraios T, Donker T, et al.

https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-023-03007-1

PAPERS PUBLISHED IN 2022

• Mixed-methods evaluation of a behavioural intervention package to identify and amend incorrect penicillin allergy records in UK general practice. Wanat M, Santillo M, Galal U, Davoudianfar M, Bongard E, Savic S, et al.

e057471.full.pdf (bmj.com)

• Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria. Lipworth S, Vihta K, Davies T, et al. 

https://www.nature.com/articles/s43856-022-00161-0

• Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399. Ledda A, Cummins M, Shaw LP, et al. 

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000675

• Risk of Long COVID in People Infected With Severe Acute Respiratory Syndrome Coronavirus 2 After 2 Doses of a Coronavirus Disease 2019 Vaccine: Community-Based, Matched Cohort Study. Ayoubkhani D, Bosworth M L, King S, et al.

https://academic.oup.com/ofid/article/9/9/ofac464/6696170

• Trajectory of long covid symptoms after covid-19 vaccination: community based cohort study. Ayoubkhani D, Bermingham C, Pouwels K B, et al.

https://www.bmj.com/content/377/bmj-2021-069676

• Conducting rapid qualitative interview research during the COVID-19 pandemic – Reflections on methodological choices. Wanat M, Borek A J, Pilbeam C, et al.

https://www.frontiersin.org/articles/10.3389/fsoc.2022.953872/full

• How can behavioural science contribute to qualitative research on antimicrobial stewardship in primary care? Borek A J, Santillo M, Butler C C, et al.

https://academic.oup.com/jacamr/article/4/1/dlac007/6523943

• Predicting antibiotic resistance in complex protein targets using alchemical free energy methods. Brankin A, Fowler P W.

https://onlinelibrary.wiley.com/doi/10.1002/jcc.26979

• Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms. The CRyPTIC Consortium.

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001755

• Systematic review of wastewater surveillance of antimicrobial resistance in human populations. Chau K K, Barker L, Budgell E P, et al.

https://www.sciencedirect.com/science/article/pii/S0160412022000976?via%3Dihub

• The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance. Duggett N, AbuOun M, Randall L, et al.

https://www.nature.com/articles/s41598-020-76877-7

• Assessment[MW1]  of an institutional guideline for vancomycin dosing and identification of predictive factors associated with dose and drug trough levels. Gu Q, Jones N, Drennan P, et al.

https://www.journalofinfection.com/article/S0163-4453(22)00403-0/fulltext

• Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants. Eyre D W, Taylor D, Purver M, et al.

https://www.nejm.org/doi/full/10.1056/nejmoa2116597

• Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis. The CRyPTIC Consortium.

https://erj.ersjournals.com/content/60/4/2200239

• Enhancing opportunistic recruitment and retention in primary care trials: lessons learned from a qualitative study embedded in the Cranberry for Urinary Tract Infection (CUTI) feasibility trial. Gbinigie O A, Boylan A, Butler C C, et al.

https://bmcprimcare.biomedcentral.com/articles/10.1186/s12875-022-01796-7

• Non-antibiotic treatment of acute urinary tract infection in primary care: a qualitative study. Gbinigie O A, Tonkin-Crine S, Butler C C, et al.

https://bjgp.org/content/72/717/e252

• Inferring risks of coronavirus transmission from community household data. House T, Riley H, Pellis L, et al.

https://journals.sagepub.com/doi/full/10.1177/09622802211055853

• ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads. Hunt M, Swann J, Constantinides B, et al.

https://academic.oup.com/bioinformatics/article/38/12/3291/6585329

• The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020. Knight G M, Mui Pham T, Stimson J, et al.

https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-022-07490-4

• An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status. Lumley S F, Rodger G, Constantinides, et al.

https://academic.oup.com/cid/article/74/7/1208/6314286

• K-mer based prediction of Clostridioides difficile relatedness and ribotypes. Moore M P, Wilcox M H, Walker A S, et al.

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000804

• Quantifying the primary and secondary effects of antimicrobial resistance on surgery patients: Methods and data sources for empirical estimation in England. Naylor N R, Evans S, Pouwels K B, et al.

https://www.frontiersin.org/articles/10.3389/fpubh.2022.803943/full

• Methodological and Ethical Considerations when Conducting Qualitative Interview Research With Healthcare Professionals: Reflections and Recommendations as a Result of a Pandemic. Pilbeam C, Anthierens S, Vanderslott, et al.

https://journals.sagepub.com/doi/10.1177/16094069221077763

• Primary care preparedness for the SARS-CoV-2 pandemic: a survey of NHS GPs. Family Practice. Pilbeam C, Edwards G, Tonkin-Crine S, et al.

https://academic.oup.com/fampra/article/39/3/332/6454248

• Burden of SARS-CoV-2 infection in healthcare workers during second wave in England and impact of vaccines: prospective multicentre cohort study (SIREN) and mathematical model. Pople D, Monk E J M, Evans S, et al.

https://www.bmj.com/content/378/bmj-2022-070379

• Estimation of the impact of hospital-onset SARS-CoV-2 infections on length of stay in English hospitals using causal inference. Stimson J, Pouwels K B, Hope R, et al.

https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-022-07870-w

• daiquiri: Data Quality Reporting for Temporal Datasets. Quan T P

https://joss.theoj.org/papers/10.21105/joss.05034

• Health worker experiences of implementing TB infection prevention and control: A qualitative evidence synthesis to inform implementation recommendations. Van der Westhuizen H, Dorward J, Roberts N, et al.

https://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0000292

• The experience of European hospital-based health care workers on following infection prevention and control procedures and their wellbeing during the first wave of the COVID-19 pandemic. Van Hout D, Hutchinson P, Wanat M, et al.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245182

• Symptoms and SARS-CoV-2 positivity in the general population in the UK. Vihta K, Pouwels K B, Peto T E A, et all.

https://academic.oup.com/cid/article/75/1/e329/6423489

• Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections. Vihta K, Gordon N C, Stoesser N, et al.

https://www.nature.com/articles/s41598-021-02755-5

• Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom. Vihta K, Pouwels K B, Peto T E A, et al.

https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciac613/6653436

• Symptoms and SARS-CoV-2 positivity in the general population in the UK. Vihta K, Pouwels K B, Peto T E A, et al.

https://academic.oup.com/cid/article/75/1/e329/6423489

• Patients’ and clinicians’ perspectives on the primary care consultations for acute respiratory infections during the first wave of the COVID-19 pandemic: an eight-country qualitative study in Europe. Wanat M, Hoste M, Gobat N, et al.

https://bjgpopen.org/content/6/2/BJGPO.2021.0172

• The value, challenges and practical considerations of conducting qualitative research on antimicrobial stewardship in primary care. Wanat M, Santillo M, Borek A J, et al.

https://academic.oup.com/jacamr/article/4/2/dlac026/6551005

• Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines. Wei J, Pouwels K B, Stoesser N, et al.

https://www.nature.com/articles/s41591-022-01721-6

• SARS-CoV-2 antibody trajectories after a single COVID-19 vaccination with and without prior infection. Wei J, Matthews P C, Stoesser N, et al.

https://www.nature.com/articles/s41467-022-31495-x

• Eliciting risk preferences that predict risky health behaviour: A comparison of two approaches. Yang M, Roope L S J, Buchanan J, et al.

https://onlinelibrary.wiley.com/doi/10.1002/hec.4486

• Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records. Yoon C, Bartlett s, Stoesser N, et al.

https://academic.oup.com/jac/article/77/9/2536/6611841

PAPERS PUBLISHED IN 2021

• Management of penicillin allergy in primary care: a qualitative study with patients and primary care physicians. Wanat M, Anthierens S, Butler C, et al. 

https://bmcprimcare.biomedcentral.com/articles/10.1186/s12875-021-01465-1

• A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Abuoun M, Jones H, Stubberfield E et al.

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000630

• Prospective trial of different antimicrobial treatment durations for presumptive canine  urinary tract infections. Allerton F, Pouwels K B, Bazelle J, et al.

https://bmcvetres.biomedcentral.com/articles/10.1186/s12917-021-02974-y

• Surveillance of Antibacterial Usage during the COVID-19 Pandemic in England, 2020. Andrews A, Budd E L, Hendrick A, et al.

https://www.mdpi.com/2079-6382/10/7/841

• Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK. Auguet O, Niehus R, Gweon H, et al.

https://www.sciencedirect.com/science/article/pii/S2589537021001905?via%3Dihub

• Development of an intervention to support the implementation of evidence-based strategies for optimising antibiotic prescribing in general practice. Borek A J, Campbell A, Dent E, et al.

https://implementationsciencecomms.biomedcentral.com/articles/10.1186/s43058-021-00209-7

• Implementing interventions to reduce antibiotic use: a qualitative study in high-prescribing practices. Borek A J, Campbell A, Dent E, et al.

https://bmcprimcare.biomedcentral.com/articles/10.1186/s12875-021-01371-6

• Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: A qualitative interview study with general practitioners in England. Borek A J, Maitland K, MeLeod M, et al.

https://www.mdpi.com/2079-6382/10/12/1531

• Preferences for Medical Consultations from Online Providers: Evidence from a Discrete Choice Experiment in the United Kingdom. Buchanan J, Roope L S J, Morrell L, et al.

https://link.springer.com/article/10.1007/s40258-021-00642-8

• Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission. Eyre D W, Laager M, Walker A S, et al.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008417

• Quantitative SARS-CoV-2 anti-spike responses to Pfizer–BioNTech and Oxford–AstraZeneca vaccines by previous infection status. Eyre D W, Lumley S F, Wei J. et al.

https://www.sciencedirect.com/science/article/pii/S1198743X21002895?via%3Dihub

• Feasibility and Acceptability of Community Coronavirus Disease 2019 Testing Strategies (FACTS) in a University Setting. Hirst J, Logan M, Fanshawe T R, et al.

https://academic.oup.com/ofid/article/8/12/ofab495/6380918

• Utility of Whole Genome Sequencing in Assessing and Enhancing Partner Notification of Neisseria gonorrhoeae Infection. Kong L Y, Wilson J D, Moura I B, et al.

https://journals.lww.com/stdjournal/Fulltext/2021/10000/Utility_of_Whole_Genome_Sequencing_in_Assessing.11.aspx

• Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity by Viral Load, S Gene Variants and Demographic Factors, and the Utility of Lateral Flow Devices to Prevent Transmission. Lee L Y W, Rozmanowski S, Pang M, et al.

https://academic.oup.com/cid/article/74/3/407/6273394

• Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections. Lipworth S, Vihta K, Chau K K, et al.

https://academic.oup.com/cid/article/74/3/407/6273394

• Epidemiology of Mycobacterium abscessus in England: an observational study. Lipworth S, Hough N, Weston N, et al.

https://www.sciencedirect.com/science/article/pii/S2666524721001282?via%3Dihub

• Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection. Lipworth S, Peto T EA, Crook D W, et al.

https://www.sciencedirect.com/science/article/pii/S2666524721001518?via%3Dihub

• Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Lipworth S, Vihta K, Barker L, et al.

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00947-2

• The Duration, Dynamics, and Determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Responses in Individual Healthcare Workers. Lumley S F, Wei J, O’Donnell D, et al.

https://academic.oup.com/cid/article/73/3/e699/6064824

• Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers. Lumley S F, O’Donnell D, Stoesser N E, et al.

https://www.nejm.org/doi/10.1056/NEJMoa2034545

• Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals. Lumley S F, Constantinides B, Sanderson N, et al.

https://www.sciencedirect.com/science/article/pii/S0163445321003777?via%3Dihub

• Changes in paediatric respiratory infections at a UK teaching hospital 2016–2021; impact of the SARS-CoV-2 pandemic. Lumley S F, Richens N, Lees E, et al.

https://www.sciencedirect.com/science/article/pii/S0163445321005405?via%3Dihub

• Perspectives on COVID-19 testing policies and practices: a qualitative study with scientific advisors and NHS health care workers in England. Martindale A, Pilbeam C, Mableson H, et al.

https://bmcpublichealth.biomedcentral.com/articles/10.1186/s12889-021-11285-8

• Genomic network analysis of environmental and livestock F-type 1 plasmid populations. Matlock W, Chau K K, AbuOun M, et al.

https://www.nature.com/articles/s41396-021-00926-w

• Flanker: a tool for comparative genomics of gene flanking regions. Matlock W, Lipworth S, Constantinides B, et al.

https://www.nature.com/articles/s41396-021-00926-w

• Public preferences for delayed or immediate antibiotic prescriptions in UK primary care: a choice experiment. Morrell L, Buchanan J, Roope L S J, et al.

https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1003737

• Sociodemographic inequality in COVID-19 vaccination coverage among elderly adults in England: a national linked data study. Nafilyan V, Dolby T, Razieh C, et al.

https://bmjopen.bmj.com/content/11/7/e053402

• Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework. Nicholson G, Lehmann B, Padellini T, et al.

https://www.nature.com/articles/s41564-021-01029-0

• Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing. Peto L, Rodger G, Carter D P, et al.

https://journals.asm.org/doi/10.1128/JCM.03271-20

• COVID-19: Rapid antigen detection for SARS-CoV-2 by lateral flow assay: A national systematic evaluation of sensitivity and specificity for mass-testing. Peto T.

https://www.sciencedirect.com/science/article/pii/S2589537021002042?via%3Dihub

• Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK. Pouwels K B, Pritchard E, Matthews P C, et al.

https://www.nature.com/articles/s41591-021-01548-7

• Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance. Pritchard E, Jones J, Vihta K, et al.

https://www.sciencedirect.com/science/article/pii/S2666776221002684?via%3Dihub

• Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom. Pritchard E, Matthews P C, Stoesser N, et al.

https://www.nature.com/articles/s41591-021-01410-w

• Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. Shaw L P, Chau K K, Kavanagh J, et al.

https://www.science.org/doi/10.1126/sciadv.abe3868

• Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time. Walker A S, Pritchard E, House T, et al.

https://elifesciences.org/articles/64683

• Tracking the Emergence of SARS-CoV-2 Alpha Variant in the United Kingdom. Walker A S, Vihta K, Gethings O, et al.

https://www.nejm.org/doi/full/10.1056/NEJMc2103227

• Supporting Primary Care Professionals to Stay in Work During the COVID-19 Pandemic: Views on Personal Risk and Access to Testing During the First Wave of Pandemic in Europe. Wanat M, Hoste M, Gobat N, et al.

https://www.frontiersin.org/articles/10.3389/fmed.2021.726319/full

• Perceptions on undertaking regular asymptomatic self-testing for COVID-19 using lateral flow tests: a qualitative study of university students and staff. Wanat M, Logan M, Hirst J A, et al.

https://bmjopen.bmj.com/content/11/9/e053850

• Anti-spike antibody response to natural SARS-CoV-2 infection in the general population. Wei J, Matthews P C, Stoesser N, et al.

https://www.nature.com/articles/s41467-021-26479-2

• Antibody responses to SARS-CoV-2 vaccines in 45,965 adults from the general population of the United Kingdom. Wei J, Stoesser N, Matthews P C, et al.

https://www.nature.com/articles/s41564-021-00947-3

• An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction. Yang Y, Walker T M, Kouchaki S, et al.

https://academic.oup.com/bib/article/22/6/bbab299/6355133

• Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study. Young B C, Wu C, Charlesworth J, et al.

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000700

 PAPERS PUBLISHED IN 2020 

• Social and contextual influences on antibiotic prescribing and antimicrobial stewardship: A qualitative study with clinical commissioning group and general practice professionals. Borek AJ, Anthierens S, Allison R, et al

https://www.mdpi.com/2079-6382/9/12/859

• Evaluation of methods for detecting human reads in microbial sequencing datasets. Bush S J, Connor T R, Peto T E A, et al

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000393

• Read trimming has minimal effect on bacterial SNP-calling accuracy. Bush S J

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000434

• Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Constantinides B, Chau K K, Quan T P et al

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000391

• Differential occupational risks to healthcare workers from SARS-CoV-2: A prospective observational study. Eyre D W, Lumley S F, O’Donnell D, et al

https://elifesciences.org/articles/60675

• Assessing a novel, lab-free, point-of-care test for SARS-CoV-2 (CovidNudge): a diagnostic accuracy study. Gibani M M, Toumazou C, Sohbati M et al

https://www.sciencedirect.com/science/article/pii/S266652472030121X?via%3Dihub

• Delayed antibiotic prescription by general practitioners in the UK: a stated-choice study. Morrell L, Buchanan J, Roope L S J, et al

https://www.mdpi.com/2079-6382/9/9/608

• Risk factors associated with carbapenemase-producing enterobacterales (CPE) positivity in the hospital wastewater environment. Park S C, Parikh H, Vegesana K, et al

https://journals.asm.org/doi/10.1128/AEM.01715-20

• Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison. The National SARS-CoV-2 Serology Assay evaluation Group.

https://www.sciencedirect.com/science/article/pii/S1473309920306344?via%3Dihub

• Awareness of appropriate antibiotic use in primary care for influenza-like illness: evidence of improvement from UK population-based surveys. Pouwels K B, Roope L S J, Buchanan J et al.

https://www.mdpi.com/2079-6382/9/10/690

• Community prevalence of SARS-CoV-2 in England from April to November, 2020: results from the ONS Coronavirus Infection Survey. Pouwels K B, House T, Pritchard E et al.

https://www.sciencedirect.com/science/article/pii/S2468266720302826?via%3Dihub

• Estimating the effect of healthcare-associated infections on excess length of hospital stay using inverse-probability weighted survival curves. Pouwels K B, Vansteelandt S, Batra R et al.

https://academic.oup.com/cid/article/71/9/e415/5734540

• Combining Charlson and Elixhauser scores with varying lookback predicated mortality better than using individual scores. Pritchard E, Fawcett N, Quan T P, et al

https://www.sciencedirect.com/science/article/abs/pii/S0895435620311069?via%3Dihub

• Reducing expectations for antibiotics in primary care: a randomised experiment to test the response to fear based messages about antimicrobial resistance. Roope L S J, Tonkin-Crine S, Herd N et al

https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-020-01553-6

• Optimizing COVID-19 surveillance in long-term care facilities: a modelling study. Smith D R M, Duval A, Pouwels K B, et al.

https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-020-01553-6

• Optimising Interventions for Catheter-Associated Urinary Tract Infections (CAUTI) in Primary, Secondary and Care Home Settings. Wanat M, Borek A J, Atkins L et al.

https://www.mdpi.com/2079-6382/9/7/419