Imperial College London

ProfessorAlisonHolmes

Faculty of MedicineDepartment of Infectious Disease

Professor of Infectious Diseases
 
 
 
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Contact

 

+44 (0)20 3313 1283alison.holmes

 
 
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Location

 

8N16Hammersmith HospitalHammersmith Campus

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Summary

 

Publications

Publication Type
Year
to

440 results found

Courtenay M, Castro-Sanchez E, Gallagher R, Gould D, Hawker Cet al., 2022, Delivery of antimicrobial stewardship competencies in UK pre-registration nurse education programmes: a national cross-sectional survey, JOURNAL OF HOSPITAL INFECTION, Vol: 121, Pages: 39-48, ISSN: 0195-6701

Journal article

Jadeja N, Zhu NJ, Lebcir RM, Sassi F, Holmes A, Ahmad Ret al., 2022, Using system dynamics modelling to assess the economic efficiency of innovations in the public sector - a systematic review, PLoS One, Vol: 17, Pages: 1-20, ISSN: 1932-6203

BackgroundDecision-makers for public policy are increasingly utilising systems approaches such as system dynamics (SD) modelling, which test alternative interventions or policies for their potential impact while accounting for complexity. These approaches, however, have not consistently included an economic efficiency analysis dimension. This systematic review aims to examine how, and in what ways, system dynamics modelling approaches incorporate economic efficiency analyses to inform decision-making on innovations (improvements in products, services, or processes) in the public sector, with a particular interest in health.Methods and findingsRelevant studies (n = 29) were identified through a systematic search and screening of four electronic databases and backward citation search, and analysed for key characteristics and themes related to the analytical methods applied. Economic efficiency analysis approaches within SD broadly fell into two categories: as embedded sub-models or as cost calculations based on the outputs of the SD model. Embdedded sub-models within a dynamic SD framework can reveal a clear allocation of costs and benefits to periods of time, whereas cost calculations based on the SD model outputs can be useful for high-level resource allocation decisions.ConclusionsThis systematic review reveals that SD modelling is not currently used to its full potential to evaluate the technical or allocative efficiency of public sector innovations, particularly in health. The limited reporting on the experience or methodological challenges of applying allocated efficiency analyses with SD, particularly with dynamic embedded models, hampers common learning lessons to draw from and build on. Further application and comprehensive reporting of this approach would be welcome to develop the methodology further.

Journal article

Birgand G, Charani E, Ahmad R, Bonaconsa C, Mbamalu O, Nampoothri V, Surendran S, Weiser TG, Holmes A, Mendelson M, Singh Set al., 2022, Interventional research to tackle antimicrobial resistance in Low Middle Income Countries in the era of the COVID-19 pandemic: lessons in resilience from an international consortium., International Journal of Infectious Diseases, Vol: 117, ISSN: 1201-9712

This article summarizes the consequences of the COVID-19 pandemic, on an international project to tackle the antimicrobial resistance (AMR). The research leadership and process, the access to data and stakeholders were deeply disrupted by the national and international response to the pandemic, including the interruption of healthcare delivery, lockdowns, and quarantines. The key principles to deliver the research through the pandemic were mainly the high degree of interdisciplinary engagement with integrated teams, an equitable partnership across sites with capacity building and leadership training. The level of pre-existing collaboration and partnership were also keys to sustain connections and involvements throughout the pandemic. The pandemic offered opportunities for realigning research priorities. Flexibility in funding timelines and projects inputs are required to accommodate variance introduced by external factors. The current models for research collaboration and funding need to be critically evaluated and redesigned to retain the innovation which has been shown to be successful through this current experience.

Journal article

Duc MT, Thwaites CL, Van Nuil JI, McKnight J, An PL, Paton Cet al., 2022, Digital Health Policy and Programs for Hospital Care in Vietnam: Scoping Review, JOURNAL OF MEDICAL INTERNET RESEARCH, Vol: 24, ISSN: 1438-8871

Journal article

Nampoothiri V, Bonaconsa C, Bonaconsa S, Mbamalu O, Nambatya W, Ahabwe Babigumira P, Ahmad R, Castro-Sanchez E, Broom A, Szymczak J, Zingg W, Gilchrist M, Holmes A, Mendelson M, Singh S, McLeod M, Charani Eet al., 2022, What does antimicrobial stewardship look like where you are? Global narratives from participants in a massive open online course, JAC-Antimicrobial Resistance, Vol: 4, ISSN: 2632-1823

Background:Whilst antimicrobial stewardship (AMS) is being implemented globally, contextual differences exist. We describe how the use of a massive open online course (MOOC) platform provided an opportunity to gather diverse narratives on AMS from around the world.Methods:A free 3 week MOOC titled ‘Tackling antimicrobial resistance: a social science approach’ was launched in November 2019. Learners were asked specific questions about their experiences of AMS via 38 optional free-text prompts dispersed throughout the modules. Content analysis was used to identify key emerging themes from the learners’ responses in the first three runs of the MOOC.Results:Between November 2019 and July 2020, 1464 learners enrolled from 114 countries. Overall, 199 individual learners provided a total of 1097 responses to the prompts. The diverse perspectives describe unique challenges present in different contexts including ill-defined roles for pharmacists and nurses in AMS; inadequate governance and policy inconsistencies in surveillance for antibiotic consumption and antimicrobial resistance (AMR) in some countries; lack of ownership of antibiotic decision-making and buy-in from different clinical specialties; and human resource and technological constraints. Patients’ knowledge, experiences and perspectives were recognized as a valuable source of information that should be incorporated in AMS initiatives to overcome cultural barriers to the judicious use of antibiotics.Conclusions:Analysis of learner comments and reflections identified a range of enablers and barriers to AMS implementation across different healthcare economies. Common challenges to AMS implementation included the role of non-physician healthcare workers, resource limitations, gaps in knowledge of AMR, and patient engagement and involvement in AMS.

Journal article

Ahuja S, Peiffer-Smadja N, Peven K, White M, Leather AJM, Singh S, Mendelson M, Holmes A, Birgand G, Sevdalis Net al., 2022, Use of feedback data to reduce surgical site infections and optimize antibiotic use in surgery a systematic scoping review, Annals of Surgery, Vol: 275, Pages: E345-E352, ISSN: 0003-4932

Objective: Surgical site infection (SSI) prevention remains significant, particularly in the era of antimicrobial resistance. Feedback on practices and outcomes is known to be key to reduce SSI rates and optimize antibiotic usage. However, the optimal method, format and frequency of feedback for surgical teams remains unclear. The objective of the study is to understand how data from surveillance and audit are fed back in routine surgical practice.Methods: A systematic scoping review was conducted, using well-established implementation science frameworks to code the data. Two electronic health-oriented databases (MEDLINE, EMBASE) were searched to September 2019. We included studies that assessed the use of feedback as a strategy either in the prevention and management of SSI and/or in the use of antibiotics perioperatively.Results: We identified 21 studies: 17 focused on SSI rates and outcomes and 10 studies described antimicrobial stewardship for SSI (with some overlap in focus). Several interventions were reported, mostly multimodal with feedback as a component. Feedback was often provided in written format (62%), either individualized (38%) or in group (48%). Only 25% of the studies reported that feedback cascaded down to the frontline perioperative staff. In 65% of the studies, 1 to 5 implementation strategies were used while only 5% of the studies reported to have utilized more than 15 implementation strategies. Among studies reporting antibiotic usage in surgery, most (71%) discussed compliance with surgical antibiotic prophylaxis.Conclusions: Our findings highlight the need to provide feedback to all levels of perioperative care providers involved in patient care. Future research in this area should report implementation parameters in more detail.

Journal article

Ming DK, Hernandez B, Sangkaew S, Vuong NL, Lam PK, Nguyet NM, Tam DTH, Trung DT, Tien NTH, Tuan NM, Chau NVV, Tam CT, Chanh HQ, Trieu HT, Simmons CP, Wills B, Georgiou P, Holmes AH, Yacoub Set al., 2022, Applied machine learning for the risk-stratification and clinical decision support of hospitalised patients with dengue in Vietnam, PLOS Digital Health, Vol: 1, Pages: e0000005-e0000005

BackgroundIdentifying patients at risk of dengue shock syndrome (DSS) is vital for effective healthcare delivery. This can be challenging in endemic settings because of high caseloads and limited resources. Machine learning models trained using clinical data could support decision-making in this context.MethodsWe developed supervised machine learning prediction models using pooled data from adult and paediatric patients hospitalised with dengue. Individuals from 5 prospective clinical studies in Ho Chi Minh City, Vietnam conducted between 12th April 2001 and 30th January 2018 were included. The outcome was onset of dengue shock syndrome during hospitalisation. Data underwent random stratified splitting at 80:20 ratio with the former used only for model development. Ten-fold cross-validation was used for hyperparameter optimisation and confidence intervals derived from percentile bootstrapping. Optimised models were evaluated against the hold-out set.FindingsThe final dataset included 4,131 patients (477 adults and 3,654 children). DSS was experienced by 222 (5.4%) of individuals. Predictors were age, sex, weight, day of illness at hospitalisation, indices of haematocrit and platelets over first 48 hours of admission and before the onset of DSS. An artificial neural network model (ANN) model had best performance with an area under receiver operator curve (AUROC) of 0.83 (95% confidence interval [CI], 0.76–0.85) in predicting DSS. When evaluated against the independent hold-out set this calibrated model exhibited an AUROC of 0.82, specificity of 0.84, sensitivity of 0.66, positive predictive value of 0.18 and negative predictive value of 0.98.InterpretationThe study demonstrates additional insights can be obtained from basic healthcare data, when applied through a machine learning framework. The high negative predictive value could support interventions such as early discharge or ambulatory patient management in this population. Work is underway to incorporate t

Journal article

Rawson TM, Peiffer-Smadja N, Holmes A, 2022, Artificial Intelligence in Infectious Diseases, Artificial Intelligence in Medicine, Pages: 1327-1340, ISBN: 9783030645724

The management of infectious diseases lends itself to the application of artificial intelligence. The treatment of infection is complex, requiring the consideration of a large number of dynamic variables to inform decision-making. This includes considering organism, host, and drug factors in the context of local disease epidemiology and potential long-term consequences of anti-infective use, such as the development of antimicrobial resistance. The heterogeneity of clinical presentation caused by the same pathogen means that in many cases there is a paucity of data available to guide decision-making in real time, with individualized decisions made based on the individual patient and available data. Within this chapter we explore current applications of artificial intelligence in (i) the laboratory detection of microorganisms, (ii) the clinical diagnosis and management of infectious diseases, and (iii) the surveillance of infection. This chapter will not address other potential areas for the application of AI in infectious diseases that include anti-infective drug development, targeting infection prevention activity, and public health decision-making. We highlight potential future directions for AI in infectious diseases within the areas explored by this chapter and current barriers to wider adoption of such systems.

Book chapter

Borek AJ, Maitland K, McLeod M, Campbell A, Hayhoe B, Butler CC, Morrell L, Roope LSJ, Holmes A, Walker AS, Tonkin-Crine Set al., 2021, Impact of the covid-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England, Antibiotics, Vol: 10, ISSN: 2079-6382

The COVID-19 pandemic has had a profound impact on the delivery of primary care services. We aimed to identify general practitioners’ (GPs’) perceptions and experiences of how the COVID-19 pandemic influenced antibiotic prescribing and antimicrobial stewardship (AMS) in general practice in England. Twenty-four semi-structured interviews were conducted with 18 GPs at two time-points: autumn 2020 (14 interviews) and spring 2021 (10 interviews). Interviews were audio-recorded, transcribed and analysed thematically, taking a longitudinal approach. Participants reported a lower threshold for antibiotic prescribing (and fewer consultations) for respiratory infections and COVID-19 symptoms early in the pandemic, then returning to more usual (pre-pandemic) prescribing. They perceived the pandemic as having had less impact on antibiotic prescribing for urinary and skin infections. Participants perceived the changing ways of working and consulting (e.g., proportions of remote and in-person consultations) in addition to changing patient presentations and GP workloads as influencing the fluctuations in antibiotic prescribing. This was compounded by decreased engagement with, and priority of, AMS due to COVID-19-related urgent priorities. Re-engagement with AMS is needed, e.g., through reviving antibiotic prescribing feedback and targets/incentives. The pandemic disrupted, and required adaptations in, the usual ways of working and AMS. It is now important to identify opportunities, e.g., for re-organising ways of managing infections and AMS in the future.

Journal article

McLeod J, Stadler E, Wilson R, Holmes A, O'Hare Det al., 2021, Electrochemical detection of cefiderocol for therapeutic drug monitoring, Electrochemistry Communications, Vol: 133, ISSN: 1388-2481

Cefiderocol is a novel siderophore-conjugated β-lactam antibiotic which has been approved for clinical use. It has demonstrated efficacy against infections caused by Gram-negative bacteria, including carbapenem-resistant strains. Novel antibiotics are rarely brought to market and, as such, are ideal candidates for therapeutic drug monitoring which enables optimised dosing across a range of clinical scenarios whilst also reducing the chances of antimicrobial resistance. Here we demonstrate direct electrochemical detection of cefiderocol by oxidation using untreated gold and glassy carbon electrodes as well as multi-walled carbon nanotube (MWCNT)-coated glassy carbon and foamed gold electrodes. Quantification of cefiderocol in the therapeutic range is demonstrated in spiked whole human blood using MWCNT-coated pyrolytic carbon screen-printed electrodes.

Journal article

Rawson TM, Wilson RC, O'Hare D, Herrero P, Kambugu A, Lamorde M, Ellington M, Georgiou P, Cass A, Hope WW, Holmes AHet al., 2021, Optimizing antimicrobial use: challenges, advances and opportunities, NATURE REVIEWS MICROBIOLOGY, Vol: 19, Pages: 747-758, ISSN: 1740-1526

Journal article

Rawson TM, Wilson R, Moore L, Macgowan A, Lovering A, Bayliss M, Kyriakides M, Gilchrist M, Roberts J, Hope W, Holmes Aet al., 2021, Exploring the pharmacokinetics of phenoxymethylpenicillin (Penicillin-V) in adults: a healthy volunteer study, Open Forum Infectious Diseases, Vol: 8, Pages: 1-4, ISSN: 2328-8957

This healthy volunteer study aimed to explore Phenoxymethylpenicillin (Penicillin-V) pharmacokinetics (PK) to support the planning of large, dosing studies in adults. Volunteers were dosed with penicillin-V at steady state. Total and unbound penicillin-V serum concentration was determined and a base population PK model were fitted to the data.

Journal article

Boshier FAT, Venturini C, Stirrup O, Guerra-Assuncao JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, Filipe ADS, Frampton D, Glaysher S, Khan T, Kulasegara-Shylini R, Kele B, Monahan IM, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor JF, Weller SJ, Wilson-Davies E, Wade P, Williams R, Copas AJ, Cutino-Moguel T, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu TW, Nebbia G, Nastouli E, Partridge DG, Pope CF, Price JR, Robson SC, Saeed K, Shin GY, de Silva T, Snell LB, Thomson EC, Witney AA, Breuer Jet al., 2021, The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study, JOURNAL OF INFECTION, Vol: 83, Pages: 693-700, ISSN: 0163-4453

Journal article

Zhu N, Rawson T, Ahmad R, Price JR, Gilchrist M, Singh SK, Tomczyk S, Birgand G, Thamlikitkul V, Ramadan AE-S, Ahmad I, Whitfield MG, Aylin P, Holmes Aet al., 2021, A Surveillance Framework for Healthcare Associated Infections and Antimicrobial Resistance in Acute Care in the Context of COVID-19: A Rapid Literature Review and Expert Consensus

Working paper

Shafiq N, Pandey AK, Malhotra S, Holmes A, Mendelson M, Malpani R, Balasegaram M, Charani Eet al., 2021, Shortage of essential antimicrobials: a major challenge to global health security, BMJ Global Health, Vol: 6, Pages: 1-10, ISSN: 2059-7908

The lack of access to safe and effective antimicrobials for human populations is a threat to global health security and a contributor to the emergence and spread of antimicrobial resistance (AMR). The increasingly common shortages of antimicrobials are an additional threat to the emergence of AMR. While the threat of such drug shortages is most acutely experienced in low-income and middle-income settings, their consequences impact the quality and effectiveness of antimicrobials worldwide. Furthermore, there is a need for robustly conducted studies examining the impact of these increasingly prevalent shortages on patient outcomes and on the emergence and spread of AMR. In this review, we have mapped common drivers for antimicrobial shortages and propose strategies for rethinking the regulation, supply and pricing of antimicrobials to secure their sustainable access across diverse healthcare systems and to help minimise the unintended consequences of weak and ineffective supply chains. Greater government involvement in antimicrobial manufacture and supply is essential to ensure no one is left behind. Dedicated demand systems need to be developed for antimicrobials which take into consideration evolving AMR patterns, burden of diseases, pandemic events and supply and demand issues and facilitate implementation of strategies to address them. Interventions, ranging from advocacy and forecasting to public–private collaborations, new economic models and international consortia working across countries and supply chains, will help assure access to safe and effective antimicrobials to all populations around the globe and ensure that shortages no longer contribute to AMR.

Journal article

Sangkaew S, Ming D, Boonyasiri A, Honeyford K, Kalayanarooj S, Yacoub S, Dorigatti I, Holmes Aet al., 2021, Transaminases and serum albumin as early predictors of severe dengue reply, Lancet Infectious Diseases, Vol: 21, Pages: 1489-1490, ISSN: 1473-3099

Journal article

Miglietta L, Moniri A, Pennisi I, Malpartida-Cardenas K, Abbas H, Hill-Cawthorne K, Bolt F, Jauneikaite E, Davies F, Holmes A, Georgiou P, Rodriguez Manzano Jet al., 2021, Coupling machine learning and high throughput multiplex digital PCR enables accurate detection of carbapenem-resistant genes in clinical isolates, Frontiers in Molecular Biosciences, Vol: 8, Pages: 1-11, ISSN: 2296-889X

Rapid and accurate identification of patients colonised with carbapenemase-producing organisms (CPOs) is essential to adopt prompt prevention measures to reduce the risk of transmission. Recent studies have demonstrated the ability to combine machine learning (ML) algorithms with real-time digital PCR (dPCR) instruments to increase classification accuracy of multiplex PCR assays when using synthetic DNA templates. We sought to determine if this novel methodology could be applied to improve identification of the five major carbapenem-resistant genes in clinical CPO-isolates, which would represent a leap forward in the use of PCR-based data-driven diagnostics for clinical applications. We collected 3 clinical isolates (including 221 CPO-positive samples) and developed a novel 5-plex PCR assay for detection of blaIMP, blaKPC, blaNDM, blaOXA-48 and blaVIM. Combining the recently reported ML method ‘Amplification and Melting Curve Analysis’ (AMCA) with the abovementioned multiplex assay, we assessed the performance of the AMCA methodology in detecting these genes. The improved classification accuracy of AMCA relies on the usage of real-time data from a single fluorescent channel and benefits from the kinetic/thermodynamic information encoded in the thousands of amplification events produced by high throughput real-time dPCR. The 5-plex showed a lower limit of detection of 10 DNA copies per reaction for each primer set and no cross-reactivity with other carbapenemase genes. The AMCA classifier demonstrated excellentpredictive performance with 99.6% (CI 97.8-99.9%) accuracy (only one misclassified sample out of the 253, with a total of 160,041 positive amplification events), which represents a 7.9% increase (p value < 0.05) compared to conventional melting curve analysis. This work demonstrates the use of the AMCA method to increase the throughput and performance of state-of-the-art molecular diagnostic platforms, without hardware modifications and additiona

Journal article

Wan Y, Myall AC, Boonyasiri A, Bolt F, Ledda A, Mookerjee S, Weiße AY, Getino M, Turton JF, Abbas H, Prakapaite R, Sabnis A, Abdolrasoulia A, Malpartida-Cardenas K, Miglietta L, Donaldson H, Gilchrist M, Hopkins KL, Ellington MJ, Otter JA, Larrouy-Maumus G, Edwards AM, Rodriguez-Manzano J, Didelot X, Barahona M, Holmes AH, Jauneikaite E, Davies Fet al., 2021, Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both<i>bla</i><sub>IMP</sub>and<i>mcr-9</i>genes

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Carbapenemase-producing Enterobacterales (CPE) are challenging in the healthcare setting, with resistance to multiple classes of antibiotics and a high associated mortality. The incidence of CPE is rising globally, despite enhanced awareness and control efforts. This study describes an investigation of the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We carried out a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE positive patients. Genomes of IMP-encoding CPE isolates were analysed and overlayed with patient contacts to imply potential transmission events.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly<jats:italic>Klebsiella</jats:italic>spp,<jats:italic>Enterobacter</jats:italic>spp,<jats:italic>E. coli</jats:italic>), of which 86% (72/84) harboured an IncHI2 plasmid, which carried both<jats:italic>bla</jats:italic><jats:sub>IMP</jats:sub>and the mobile colistin resistance gene<jats:italic>mcr-9</jats:italic>(68/72). Phylogenetic analysis of IncHI2 plasmids identified three lineages which showed significant association with patient contact and movements between four hospital sites and across medical specialities, which had been missed on initial investigations.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-med

Journal article

Hernandez B, Herrero-Viñas P, Rawson TM, Moore LSP, Holmes A, Georgiou Pet al., 2021, Resistance trend estimation using regression analysis to enhance antimicrobial surveillance: a multi-centre study in London 2009-2016, Antibiotics, Vol: 10, Pages: 1-16, ISSN: 2079-6382

In the last years, there has been an increase of antimicrobial resistance rates around the world with the misuse and overuse of antimicrobials as one of the main leading drivers. In response to this threat, a variety of initiatives have arisen to promote the efficient use of antimicrobials. These initiatives rely on antimicrobial surveillance systems to promote appropriate prescription practices and are provided by national or global health care institutions with limited consideration of the variations within hospitals. As a consequence, physicians’ adherence to these generic guidelines is still limited. To fill this gap, this work presents an automated approach to performing local antimicrobial surveillance from microbiology data. Moreover, in addition to the commonly reported resistance rates, this work estimates secular resistance trends through regression analysis to provide a single value that effectively communicates the resistance trend to a wider audience. The methods considered for trend estimation were ordinary least squares regression, weighted least squares regression with weights inversely proportional to the number of microbiology records available and autoregressive integrated moving average. Among these, weighted least squares regression was found to be the most robust against changes in the granularity of the time series and presented the best performance. To validate the results, three case studies have been thoroughly compared with the existing literature: (i) Escherichia coli in urine cultures; (ii) Escherichia coli in blood cultures; and (iii) Staphylococcus aureus in wound cultures. The benefits of providing local rather than general antimicrobial surveillance data of a higher quality is two fold. Firstly, it has the potential to stimulate engagement among physicians to strengthen their knowledge and awareness on antimicrobial resistance which might encourage prescribers to change their prescription habits more willingly. Moreover, it pro

Journal article

Charani E, Holmes A, Bonaconsa C, Mbamalu O, Mendelson M, Surendran S, Singh S, Nampoothiri V, Boutall A, Tarrant C, Dhar P, Pennel T, Leather A, Hampton Met al., 2021, Investigating infection management and antimicrobial stewardship in surgery: a qualitative study from India and South Africa, Clinical Microbiology and Infection, Vol: 27, Pages: 1455-1464, ISSN: 1198-743X

Objectives To investigate the drivers for infection management and antimicrobial stewardship (AMS) across high infection risk surgical pathways. Methods An qualitative study, ethnographic observation of clinical practices, patient case studies, and face-to-face interviews with healthcare professionals (HCP) and patients was conducted across cardiovascular and thoracic and gastrointestinal surgical pathways in South Africa (SA) and India. Aided by Nvivo 11 software, data were coded and analysed until saturation was reached. The multiple modes of enquiry enabled cross-validation and triangulation of findings.Results Between July 2018–August 2019 data were gathered from 190 hours of non-participant observations (138 India, 72 SA); interviews with HCPs (44 India, 61 SA); patients (6 India, 8 SA), and, case studies (4 India, 2 SA). Across the surgical pathway, multiple barriers impede effective infection management and AMS. The existing, implicit roles of HCPs (including nurses, and senior surgeons) are overlooked as interventions target junior doctors, bypassing the opportunity for integrating infection-related care across the surgical team. Critically, the ownership of decisions remains with the operating surgeons and entrenched hierarchies restrict the inclusion of other HCPs in decision-making. The structural foundations to enable staff to change their behaviours and participate in infection-related surgical care is lacking.ConclusionsIdentifying the implicit existing HCPs roles in infection management is critical and will facilitate the development of effective and transparent processes across the surgical team for optimised care. Applying a framework approach that includes nurse leadership, empowering pharmacists and engaging surgical leads is essential for integrated AMS and infection-related care. Keywords: antibiotic prescribing, infection control, ethnography, low- and middle-income country, surgery

Journal article

Rodriguez-Bano J, Maria Rossolini G, Schultsz C, Tacconelli E, Murthy S, Ohmagari N, Holmes A, Bachmann T, Goossens H, Canton R, Roberts AP, Henriques-Normark B, Clancy CJ, Huttner B, Fagerstedt P, Lahiri S, Kaushic C, Hoffman SJ, Warren M, Zoubiane G, Essack S, Laxminarayan R, Plant Let al., 2021, Key considerations on the potential impacts of the COVID-19 pandemic on antimicrobial resistance research and surveillance, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 115, Pages: 1122-1129, ISSN: 0035-9203

Journal article

Charani E, Mendelson M, Ashiru-Oredope D, Hutchinson E, Kaur M, McKee M, Mpundu M, Price JR, Shafiq N, Holmes Aet al., 2021, Navigating sociocultural disparities in relation to infection and antibiotic resistance-the need for an intersectional approach, JAC-ANTIMICROBIAL RESISTANCE, Vol: 3

Journal article

Bonaconsa C, Mbamalu O, Mendelson M, Boutall A, Warden C, Rayamajhi S, Pennel T, Hampton M, Joubert I, Tarrant C, Holmes A, Charani Eet al., 2021, Visual mapping of team dynamics and communication patterns on surgical ward rounds: an ethnographic study, BMJ Quality & Safety, Vol: 30, Pages: 812-824, ISSN: 2044-5415

Background: Team dynamics influence infection prevention and management practices and implementation of antibiotic stewardship (AS). Using an innovative visual mapping approach, alongside traditional qualitative methods, we aimed to study team dynamics and flow of communication (who gets to speak, and whose voice is heard) during surgical ward rounds, and how team dynamics and communication patterns may shape decision-making in relation to infection management and AS.Materials/methods: Between May and November 2019, data were gathered through direct observations of ward rounds and face-to-face interviews with ward round participants in selected surgical specialties at a tertiary hospital in South Africa. Using a visual mapping method – sociograms – content and flow of communication and the social links between individual participants were plotted. Field notes from observations and interview transcripts were analysed using a grounded theory approach.Results: Data were gathered from 60 hours of ward round observations, including 1024 individual patient discussions; 60 sociograms, interviews with healthcare professionals (60) and patients (7). The nature of discussions about AS and IPC on ward rounds vary across specialties and are affected by the content and structure of the clinical update provided, the consultant’s leadership and interaction style, and competing priorities at the bedside. Registrars act as gatekeepers, initiating antibiotic discussions; consultants are key decision-makers. Other team members have limited input in ward round conversations, despite having recognised roles in AS and IPC. Hierarchies in teams manifest themselves on ward rounds in where staff position themselves, influencing their contribution to care. Varied leadership styles affect ward-round dynamics, in particular, whether nurses and patients are actively engaged in key decisions on infection management and antibiotic therapy, and whether actions are assigned to i

Journal article

Borek AJ, Campbell A, Dent E, Moore M, Butler CC, Holmes A, Walker AS, McLeod M, Tonkin-Crine S, STEP-UP study teamet al., 2021, Development of an intervention to support the implementation of evidence-based strategies for optimising antibiotic prescribing in general practice., Implementation Science Communications, Vol: 2, ISSN: 2662-2211

BACKGROUND: Trials show that antimicrobial stewardship (AMS) strategies, including communication skills training, point-of-care C-reactive protein testing (POC-CRPT) and delayed prescriptions, help optimise antibiotic prescribing and use in primary care. However, the use of these strategies in general practice is limited and inconsistent. We aimed to develop an intervention to enhance uptake and implementation of these strategies in primary care. METHODS: We drew on the Person-Based Approach to develop an implementation intervention in two stages. (1) Planning and design: We defined the problem in behavioural terms drawing on existing literature and conducting primary qualitative research (nine focus groups) in high-prescribing general practices. We identified 'guiding principles' with intervention objectives and key features and developed logic models representing intended mechanisms of action. (2) Developing the intervention: We created prototype intervention materials and discussed and refined these with input from 13 health professionals and 14 citizens in two sets of design workshops. We further refined the intervention materials following think-aloud interviews with 22 health professionals. RESULTS: Focus groups highlighted uncertainties about how strategies could be used. Health professionals in the workshops suggested having practice champions, brief summaries of each AMS strategy and evidence supporting the AMS strategies, and they and citizens gave examples of helpful communication strategies/phrases. Think-aloud interviews helped clarify and shorten the text and user journey of the intervention materials. The intervention comprised components to support practice-level implementation: antibiotic champions, practice meetings with slides provided, and an 'implementation support' website section, and components to support individual-level uptake: website sections on each AMS strategy (with evidence, instructions, links to electronic resources) and materi

Journal article

Ming DKY, Myall A, Hernandez B, Weisse A, Peach R, Barahona M, Rawson T, Holmes Aet al., 2021, Informing antimicrobial management in the context of COVID-19: understanding the longitudinal dynamics of C-reactive protein and procalcitonin, BMC Infectious Diseases, Vol: 21, ISSN: 1471-2334

Background:To characterise the longitudinal dynamics of C-reactive protein (CRP) and Procalcitonin (PCT) in a cohort of hospitalised patients with COVID-19 and support antimicrobial decision-making.Methods:Longitudinal CRP and PCT concentrations and trajectories of 237 hospitalised patients with COVID-19 were modelled. The dataset comprised of 2,021 data points for CRP and 284 points for PCT. Pairwise comparisons were performed between: (i) those with or without significant bacterial growth from cultures, and (ii) those who survived or died in hospital.Results:CRP concentrations were higher over time in COVID-19 patients with positive microbiology (day 9: 236 vs 123 mg/L, p < 0.0001) and in those who died (day 8: 226 vs 152 mg/L, p < 0.0001) but only after day 7 of COVID-related symptom onset. Failure for CRP to reduce in the first week of hospital admission was associated with significantly higher odds of death. PCT concentrations were higher in patients with COVID-19 and positive microbiology or in those who died, although these differences were not statistically significant.Conclusions:Both the absolute CRP concentration and the trajectory during the first week of hospital admission are important factors predicting microbiology culture positivity and outcome in patients hospitalised with COVID-19. Further work is needed to describe the role of PCT for co-infection. Understanding relationships of these biomarkers can support development of risk models and inform optimal antimicrobial strategies.

Journal article

Mbamalu O, Bonaconsa C, Nampoothiri V, Surendran S, Veepanattu P, Singh S, Dhar P, Carter V, Boutall A, Pennel T, Hampton M, Holmes A, Mendelson M, Charani Eet al., 2021, Patient understanding of and participation in infection-related care across surgical pathways: a scoping review, INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, Vol: 110, Pages: 123-134, ISSN: 1201-9712

Journal article

Lamb G, Phillips G, Charani E, Holmes A, Satta Get al., 2021, Antibiotic prescribing practices in general surgery: a mixed methods quality improvement project, INFECTION PREVENTION IN PRACTICE, Vol: 3, ISSN: 2590-0889

Journal article

Stirrup O, Boshier F, Venturini C, Guerra-Assuncao JA, Alcolea-Medina A, Beckett A, Charalampous T, da Silva Filipe A, Glaysher S, Khan T, Kulasegaran Shylini R, Kele B, Monahan I, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor J, Weller S, Wilson-Davies E, Wade P, Williams R, Copas A, Cutino-Moguel M-T, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu T, Nebbia G, Partridge D, Pope C, Price J, Robson S, Saeed K, de Silva T, Snell L, Thomson E, Witney AA, Breuer Jet al., 2021, SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study, BMJ OPEN RESPIRATORY RESEARCH, Vol: 8

Journal article

Hayhoe B, 2021, Public preferences for delayed or immediate antibiotic prescriptions in UK primary care: a choice experiment, PLoS Medicine, Vol: 18, Pages: 1-20, ISSN: 1549-1277

Delayed (or ‘back-up’) antibiotic prescription, where the patient is given a prescription but advised todelay initiating antibiotics, has been shown to be effective in reducing antibiotic use in primary care.However, this strategy is not widely used in the UK. This study aimed to identify factors influencingpreferences among the UK public for delayed prescription, and understand their relative importance,to help increase appropriate use of this prescribing option.Methods and FindingsWe conducted an online choice experiment in two UK general population samples: adults, and parentsof children under 18 years. Respondents were presented with twelve scenarios in which they, or theirchild, might need antibiotics for a respiratory tract infection, and asked to choose either an immediateor a delayed prescription. Scenarios were described by seven attributes. Data were collected betweenNovember 2018 and February 2019. Respondent preferences were modelled using mixed-effectslogistic regression.The survey was completed by 802 adults and 801 parents (75% of those who opened the survey). Thesamples reflected the UK population in age, sex, ethnicity and country of residence. The mostimportant determinant of respondent choice was symptom severity, especially for cough-relatedsymptoms. In the adult sample the probability of choosing delayed prescription was 0.53 (95% CI 0.50-0.56, p<.001) for a chesty cough and runny nose, compared to 0.30 (0.28-0.33, p<.001) for a chestycough with fever, 0.47 (0.44-0.50, p<.001) for sore throat with swollen glands and 0.37 (0.34-0.39,p<.001) for sore throat, swollen glands and fever. Respondents were less likely to choose delayedprescription with increasing duration of illness (odds ratio 0.94 (0.92-0.96, p<0.001)). Probabilities ofchoosing delayed prescription were similar for parents considering treatment for a child (44% ofchoices vs. 42% for adults, p=0.04). However, parents differed from the adult sample in showing

Journal article

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