Imperial College London

Dr Esmita Charani, PhD MSc MPharm, ESCMID Fellow

Faculty of MedicineDepartment of Infectious Disease

Senior Lead Research Pharmacist
 
 
 
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7N12Commonwealth BuildingHammersmith Campus

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Summary

 

Publications

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101 results found

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 Antimicrob Resist, Vol: 3

One of the key drivers of antibiotic resistance (ABR) and drug-resistant bacterial infections is the misuse and overuse of antibiotics in human populations. Infection management and antibiotic decision-making are multifactorial, complex processes influenced by context and involving many actors. Social constructs including race, ethnicity, gender identity and cultural and religious practices as well as migration status and geography influence health. Infection and ABR are also affected by these external drivers in individuals and populations leading to stratified health outcomes. These drivers compromise the capacity and resources of healthcare services already over-burdened with drug-resistant infections. In this review we consider the current evidence and call for a need to broaden the study of culture and power dynamics in healthcare through investigation of relative power, hierarchies and sociocultural constructs including structures, race, caste, social class and gender identity as predictors of health-providing and health-seeking behaviours. This approach will facilitate a more sustainable means of addressing the threat of ABR and identify vulnerable groups ensuring greater inclusivity in decision-making. At an individual level, investigating how social constructs and gender hierarchies impact clinical team interactions, communication and decision-making in infection management and the role of the patient and carers will support better engagement to optimize behaviours. How people of different race, class and gender identity seek, experience and provide healthcare for bacterial infections and use antibiotics needs to be better understood in order to facilitate inclusivity of marginalized groups in decision-making and policy.

Journal article

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, ISSN: 2059-7908

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

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., Int J Infect Dis, Vol: 110, Pages: 123-134

OBJECTIVE: To explore the existing evidence on patient understanding of and/or participation in infection-related care in surgical specialties. METHOD: A scoping review of the literature was conducted. PubMed, Web of Science, Scopus, and grey literature sources were searched using predefined search criteria for policies, guidelines, and studies in the English language. Data synthesis was done through content and thematic analysis to identify key themes in the included studies. RESULTS: The initial search identified 604 studies, of which 41 (36 from high-income and five from low- and middle-income countries) were included in the final review. Most of the included studies focused on measures to engage patients in infection prevention and control (IPC) activities, with few examples of antimicrobial stewardship (AMS) engagement strategies. While patient engagement interventions in infection-related care varied depending on study goals, surgical wound management was the most common intervention. AMS engagement was primarily limited to needs assessment, without follow-up to address such needs. CONCLUSION: Existing evidence highlights a gap in patient participation in infection-related care in the surgical pathway. Standardization of patient engagement strategies is challenging, particularly in the context of surgery, where several factors influence how the patient can engage and retain information. Infection-related patient engagement and participation strategies in surgery need to be inclusive and contextually fit.

Journal article

Charani E, McKee M, Ahmad R, Balasegaram M, Bonaconsa C, Merrett GB, Busse R, Carter V, Castro-Sanchez E, Franklin BD, Georgiou P, Hill-Cawthorne K, Hope W, Imanaka Y, Kambugu A, Leather AJM, Mbamalu O, McLeod M, Mendelson M, Mpundu M, Rawson TM, Ricciardi W, Rodriguez-Manzano J, Singh S, Tsioutis C, Uchea C, Zhu N, Holmes AHet al., 2021, Optimising antimicrobial use in humans-review of current evidence and an interdisciplinary consensus on key priorities for research, LANCET REGIONAL HEALTH-EUROPE, Vol: 7, ISSN: 2666-7762

Journal article

Abdulaal A, Patel A, Al-Hindawi A, Charani E, Alqahtani S, Davies G, Mughal N, Moore Let al., 2021, Clinical utility and functionality of an artificial intelligence application to predict mortality in COVID-19: a mixed methods analysis., JMIR Formative Research, Vol: 5, Pages: 1-13, ISSN: 2561-326X

BackgroundThe artificial neural network (ANN) is an increasingly important tool in the context of solving complex medical classification problems. However, one of the principal challenges in leveraging AI technology in the healthcare setting has been the relative inability to translate models into clinician workflow. Here we demonstrate the development of a COVID-19 outcome prediction application which utilises an ANN and assesses its usability in the clinical setting. MethodsUsability assessment was conducted on the application followed by a semi-structured end-user interview. Usability was specified by effectiveness, efficiency, and satisfaction measures. These data were reported with descriptive statistics. The end-user interview data were analysed using the thematic framework method, which allowed for the development of themes from the interview narratives.Participants Thirty-one Nation Health Service (NHS) physicians at a West London teaching hospital, including foundation doctors, senior house officers, registrars, and consultants.ResultsAll participants were able to complete the assessment, with a mean time to complete separate patient vignettes of 59.35 seconds (standard deviation (SD) = 10.35). Mean system usability scale (SUS) score was 91.94 (SD = 8.54), which corresponds with an adjective rating of “Excellent”. The clinicians found the application intuitive and easy to use, with the majority describing its predictions as a useful adjunct to their clinical practice. The main concern related to use of the application in isolation as opposed to in conjunction with other clinical parameters. However, most clinicians felt that the application could positively reinforce or validate their clinical judgement.ConclusionTranslating AI technologies into the clinical setting remains an important but challenging task. We demonstrate the effectiveness, efficiency, and system usability of a web application designed to predict COVID-19 patient outcomes from

Journal article

Ahmad R, Atun R, Birgand G, Castro-Sánchez E, Charani E, Ferlie E, Hussain I, Kambugu A, Labarca J, Levy Hara G, Mckee M, Mendelson M, Singh S, Varma J, Zhu J, Zingg W, Holmes Aet al., 2021, Macro level influences on strategic responses to the COVID-19 pandemic – an international survey and tool for national assessments, Journal of Global Health, Vol: 11, Pages: 1-11, ISSN: 2047-2978

Background Variation in the approaches taken to contain the SARS-CoV-2 (COVID-19) pandemic at country level has been shaped by economic and political considerations, technical capacity, and assumptions about public behaviours. To address the limited application of learning from previous pandemics, this study aimed to analyse perceived facilitators and inhibitors during the pandemic and to inform the development of an assessment tool for pandemic response planning.Methods A cross-sectional electronic survey of health and non-healthcare professionals (5 May - 5 June 2020) in six languages, with respondents recruited via email, social media and website posting. Participants were asked to score inhibitors (-10 to 0) or facilitators (0 to +10) impacting country response to COVID-19 from the following domains – Political, Economic, Sociological, Technological, Ecological, Legislative, and wider Industry (the PESTELI framework). Participants were then asked to explain their responses using free text. Descriptive and thematic analysis was followed by triangulation with the literature and expert validation to develop the assessment tool, which was then compared with four existing pandemic planning frameworks.Results 928 respondents from 66 countries (57% healthcare professionals) participated. Political and economic influences were consistently perceived as powerful negative forces and technology as a facilitator across high- and low-income countries. The 103-item tool developed for guiding rapid situational assessment for pandemic planning is comprehensive when compared to existing tools and highlights the interconnectedness of the 7 domains. Conclusions The tool developed and proposed addresses the problems associated with decision making in disciplinary silos and offers a means to refine future use of epidemic modelling.

Journal article

Zhu J, Ferlie E, Castro-Sánchez E, Birgand G, Holmes A, Atun R, Kieltyka H, Ahmad Ret al., 2021, Macro level factors influencing strategic responses to emergent pandemics: a scoping review, Journal of Global Health, Vol: 11, Pages: 1-16, ISSN: 2047-2978

Background: Strategic planning is critical for successful pandemic management. This study aimed to identify and review the scope and analytic depth of situation analyses conducted to understand their utility, and capture the documented macro-level factors impacting4pandemic management. Methods: To synthesise this disparate body of literature, we adopted a two-step search and 6review process. A systematic search of the literature was conducted to identify all studies since 2000, that have 1) employed a situation analysis;and2) examined contextual factors influencing pandemic management. The included studies are analysed using a seven-domain systems approach rom the discipline of strategic management. Findings: Nineteen studies were included in the final review ranging from single country (6) to regional, multi-country studies (13). Fourteen studies had a single disease focus, with 5 studies evaluating responses to one or more of COVID-19, Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS),Influenza A (H1N1),Ebola virus disease, and Zika virus disease pandemics. Six studies examined a single domain from political, economic, sociological, technological, ecological or wider industry(PESTELI), 5 studies examined two to four domains, and8studies examined five or more domains. Methods employed were predominantly literature reviews. The recommendations focus predominantly on addressing inhibitors in the sociological and technological domains with few recommendations articulated in the political domain. Overall, the legislative domain is least represented. Conclusions: Ex-post analysis using the seven-domain strategic management framework provides further opportunities for a planned systematic response to pandemics which remains critical as the current COVID-19 pandemic evolves.

Journal article

Rawson TM, Hernandez B, Moore L, Herrero P, Charani E, Ming D, Wilson R, Blandy O, Sriskandan S, Toumazou C, Georgiou P, Holmes Aet al., 2021, A real-world evaluation of a case-based reasoning algorithm to support antimicrobial prescribing decisions in acute care, Clinical Infectious Diseases, Vol: 72, Pages: 2103-2111, ISSN: 1058-4838

BackgroundA locally developed Case-Based Reasoning (CBR) algorithm, designed to augment antimicrobial prescribing in secondary care was evaluated.MethodsPrescribing recommendations made by a CBR algorithm were compared to decisions made by physicians in clinical practice. Comparisons were examined in two patient populations. Firstly, in patients with confirmed Escherichia coli blood stream infections (‘E.coli patients’), and secondly in ward-based patients presenting with a range of potential infections (‘ward patients’). Prescribing recommendations were compared against the Antimicrobial Spectrum Index (ASI) and the WHO Essential Medicine List Access, Watch, Reserve (AWaRe) classification system. Appropriateness of a prescription was defined as the spectrum of the prescription covering the known, or most-likely organism antimicrobial sensitivity profile.ResultsIn total, 224 patients (145 E.coli patients and 79 ward patients) were included. Mean (SD) age was 66 (18) years with 108/224 (48%) female gender. The CBR recommendations were appropriate in 202/224 (90%) compared to 186/224 (83%) in practice (OR: 1.24 95%CI:0.392-3.936;p=0.71). CBR recommendations had a smaller ASI compared to practice with a median (range) of 6 (0-13) compared to 8 (0-12) (p<0.01). CBR recommendations were more likely to be classified as Access class antimicrobials compared to physicians’ prescriptions at 110/224 (49%) vs. 79/224 (35%) (OR: 1.77 95%CI:1.212-2.588 p<0.01). Results were similar for E.coli and ward patients on subgroup analysis.ConclusionsA CBR-driven decision support system provided appropriate recommendations within a narrower spectrum compared to current clinical practice. Future work must investigate the impact of this intervention on prescribing behaviours more broadly and patient outcomes.

Journal article

Denny S, Abdolrasouli A, Elamin T, Gonzalo X, Pallett S, Charani E, Patel A, Donaldson H, Hughes S, Armstrong-James D, Moore LS, Mughal Net al., 2021, A retrospective multicenter analysis of candidaemia among COVID-19 patients during the first UK pandemic wave, Journal of Infection, Vol: 82, Pages: 276-316, ISSN: 0163-4453

Journal article

Surendran S, Castro-Sanchez E, Nampoothiri V, Joseph S, Singh S, Tarrant C, Holmes A, Charani Eet al., 2021, Indispensable yet invisible: An ethnographic study of carer roles in infection prevention in a South Indian hospital, BMJ Global Health, ISSN: 2059-7908

Objectives: We investigated the experiences and roles of patient carers in infection-related care on surgical wards in a South Indian hospital, from the perspective of healthcare workers (HCW), patients, and their carers. Methods: Ethnographic study including ward round observations (138 hours), face-to-face interviews (44 HCW, 6 patients/carers) and review of documents. Data (field notes, interview transcripts) were coded in NVivo 12 and analysed using principles of grounded theory. Data collection and analysis were iterative, recursive and continued until thematic saturation. Results: Carers play important yet unrecognised infection-related care roles. Institutional expectations of families are formalised in policies which demand that inpatients are accompanied by a relative at all times. Such intense presence embeds families in the patient care environment, as demonstrated by their high engagement in direct personal care (e.g. bathing patients) and clinical tasks (e.g. wound care). Carers actively participate in discussions on patient progress with HCWs, including post-discharge advice. Controlling the patient’s home environment carers decide on therapeutic options on patient behalf. There is a misalignment between how carers are positioned by the organisation (through policy mandates, institutional practices, and HCWs expectations), and the role that carers play in practice, resulting in their role, though indispensable, remaining invisible and unrecognised. Conclusion: Current models of patient and carer involvement in Infection Prevention and Control (IPC) are poorly aligned with settings such as India, where a wider support network has a role in patient care, reflecting the specific socio-cultural and contextual aspects of care. Culture-sensitive IPC policies which embrace the roles that patient’s families play are urgently needed.

Journal article

Pallett SJC, Denny S, Patel A, Charani E, Mughal N, Stebbing J, Davies G, Moore Let al., 2021, Point-of-care SARS-CoV-2 serological assays for enhanced case finding in a UK inpatient population., Scientific Reports, Vol: 11, Pages: 1-8, ISSN: 2045-2322

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic. Case identification is currently made by real-time polymerase chain reaction (PCR) during the acute phase and largely restricted to healthcare laboratories. Serological assays are emerging but independent validation is urgently required to assess their utility. We evaluated five different point-of-care (POC) SARS-CoV-2 antibody test kits against PCR, finding concordance across the assays (n=15). We subsequently tested 200 patients using the OrientGene COVID-19 IgG/IgM Rapid Test Cassette and find a sensitivity of 74% in the early infection period (day 5-9 post symptom onset), with 100% sensitivity not seen until day 13, demonstrating inferiority to PCR testing in the infectious period. Negative rate was 96%, but in validating the serological tests uncovered potential false-negatives from PCR testing late-presenting cases. A positive predictive value (PPV) of 37% in the general population precludes any use for general screening. Where a case definition is applied however, the PPV is substantially improved (95·4%), supporting use of serology testing in carefully targeted, high-risk populations. Larger studies in specific patient cohorts, including those with mild infection are urgently required to inform on the applicability of POC serological assays to help control the spread of SARS-CoV-2 and improve case finding of patients that may experience late complications.

Journal article

Singh S, Charani E, Devi S, Sharma A, Edathadathil F, Kumar A, Warrier A, Shareek PS, Jaykrishnan A, Ellangovan Ket al., 2021, A road-map for addressing antimicrobial resistance in low- and middle-income countries: lessons learnt from the public private participation and co-designed antimicrobial stewardship programme in the State of Kerala, India, Antimicrobial Resistance and Infection Control, Vol: 10, ISSN: 2047-2994

BackgroundThe global concern over antimicrobial resistance (AMR) is gathering pace. Low- and middle-income countries (LMICs) are at the epicentre of this growing public health threat and governmental and healthcare organizations are at different stages of implementing action plans to tackle AMR. The South Indian state of Kerala was one of the first in India to implement strategies and prioritize activities to address this public health threat.StrategiesThrough a committed and collaborative effort from all healthcare related disciplines and its professional societies from both public and private sector, the Kerala Public Private Partnership (PPP) has been able to deliver a state-wide strategy to tackle AMR A multilevel strategic leadership model and a multilevel implementation approach that included developing state-wide antibiotic clinical guidelines, a revision of post-graduate and undergraduate medical curriculum, and a training program covering all general practitioners within the state the PPP proved to be a successful model for ensuring state-wide implementation of an AMR action plan. Collaborative work of multi-professional groups ensured co-design and development of disease based clinical treatment guidelines and state-wide infection prevention policy. Knowledge exchange though international and national platforms in the form of workshops for sharing of best practices is critical to success. Capacity building at both public and private institutions included addressing practical and local solutions to the barriers e.g. good antibiotic prescription practices from primary to tertiary care facility and infection prevention at all levels.ConclusionThrough 7 years of stakeholder engagement, lobbying with government, and driving change through co-development and implementation, the PPP successfully delivered an antimicrobial stewardship plan across the state. The roadmap for the implementation of the Kerala PPP strategic AMR plan can provide learning for other state

Journal article

Nampoothiri V, Sudhir AS, Joseph MV, Mohamed Z, Menon V, Charani E, Singh Set al., 2021, Mapping the Implementation of a Clinical Pharmacist-Driven Antimicrobial Stewardship Programme at a Tertiary Care Centre in South India, ANTIBIOTICS-BASEL, Vol: 10, ISSN: 2079-6382

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, 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

Abdulaal A, Patel A, Charani E, Denny S, Alqahtani S, Davies G, Mughal N, Moore Let al., 2020, Comparison of deep learning with regression analysis in creating predictive models for SARS-CoV-2 outcomes, BMC Medical Informatics and Decision Making, Vol: 20, Pages: 1-11, ISSN: 1472-6947

Background Accurately predicting patient outcomes in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could aid patient management and allocation of healthcare resources. There are a variety of methods which can be used to develop prognostic models, ranging from logistic regression and survival analysis to more complex machine learning algorithms and deep learning. Despite several models having been created for SARS-CoV-2, most of these have been found to be highly susceptible to bias. We aimed to develop and compare two separate predictive models for death during admission with SARS-CoV-2.MethodBetween March 1 - April 24, 2020, 398 patients were identified with laboratory confirmed SARS-CoV-2 in a London teaching hospital. Data from electronic health records were extracted and used to create two predictive models using: 1) a Cox regression model and 2) an artificial neural network (ANN). Model performance profiles were assessed by validation, discrimination, and calibration.Results Both the Cox regression and ANN models achieved high accuracy (83.8%, 95% confidence interval (CI): 73.8 - 91.1 and 90.0%, 95% CI: 81.2 - 95.6, respectively). The area under the receiver operator curve (AUROC) for the ANN (92.6%, 95% CI: 91.1 - 94.1) was significantly greater than that of the Cox regression model (86.9%, 95% CI: 85.7 - 88.2), p=0.0136. Both models achieved acceptable calibration with Brier scores of 0.13 and 0.11 for the Cox model and ANN, respectively. ConclusionWe demonstrate an ANN which is non-inferior to a Cox regression model but with potential for further development such that it can learn as new data becomes available. Deep learning techniques are particularly suited to complex datasets with non-linear solutions, which make them appropriate for use in conditions with a paucity of prior knowledge. Accurate prognostic models for SARS-CoV-2 can provide benefits at the patient, departmental and organisational level.

Journal article

Charani E, Singh S, Mendelson M, Veepanattu P, Nampoothiri V, Edathadatil F, Surendran S, Bonaconsa C, Mbamalu O, Ahuja S, Sevdalis N, Tarrant C, Birgand G, Castro-SAnchez E, Ahmad R, Holmes Aet al., 2020, Building resilient and responsive research collaborations to tackle antimicrobial resistance – lessons learnt from India, South Africa and UK, International Journal of Infectious Diseases, Vol: 100, Pages: 278-282, ISSN: 1201-9712

Research, collaboration and knowledge exchange are critical to global efforts to tackle antimicrobial resistance (AMR). Different healthcare economies are faced with different challenges in implementing effective strategies to address AMR. Building effective capacity for research to inform AMR related strategies and policies AMR is recognised as an important contributor to success. Interdisciplinary, inter-sector, as well as inter-country collaboration is needed to span AMR efforts from the global to local. Developing reciprocal, long-term, partnerships between collaborators in high-income and low- and middle-income countries (LMICs) needs to be built on principles of capacity building. Using case-studies spanning local to international research collaborations to co-design, implement and evaluate strategies to tackle AMR, we evaluate and build upon the ESSENCE criteria for capacity building in LMICs. The first case-study describes the local co-design and implementation of antimicrobial stewardship in the state of Kerala in India. The second case-study describes an international research collaboration investigating AMR across surgical pathways in India, UK and South Africa. We describe the steps undertaken to develop robust, agile, and flexible antimicrobial stewardship research and implementation teams. Notably, investing in capacity building ensured that the programmes described in these case-studies were sustained through the current severe acute respiratory syndrome corona virus pandemic. Describing the strategies adopted by a local and an international collaboration to tackle AMR, we provide a model for capacity building in LMICs that can support sustainable and agile antimicrobial stewardship programmes.

Journal article

Patel A, Abdulaal A, Ariyanayagam D, Killington K, Denny SJ, Mughal N, Hughes S, Goel N, Davies GW, Moore LSP, Charani Eet al., 2020, Investigating the association between ethnicity and health outcomes in SARS-CoV-2 in a London secondary care population, PLoS One, Vol: 15, Pages: 1-12, ISSN: 1932-6203

BackgroundBlack, Asian and minority ethnic (BAME) populations are emerging as a vulnerable group in the severe acute respiratory syndrome coronavirus disease (SARS-CoV-2) pandemic. We investigated the relationship between ethnicity and health outcomes in SARS-CoV-2.Methods and findingsWe conducted a retrospective, observational analysis of SARS-CoV-2 patients across two London teaching hospitals during March 1 –April 30, 2020. Routinely collected clinical data were extracted and analysed for 645 patients who met the study inclusion criteria. Within this hospitalised cohort, the BAME population were younger relative to the white population (61.70 years, 95% CI 59.70–63.73 versus 69.3 years, 95% CI 67.17–71.43, p<0.001). When adjusted for age, sex and comorbidity, ethnicity was not a predictor for ICU admission. The mean age at death was lower in the BAME population compared to the white population (71.44 years, 95% CI 69.90–72.90 versus, 77.40 years, 95% CI 76.1–78.70 respectively, p<0.001). When adjusted for age, sex and comorbidities, Asian patients had higher odds of death (OR 1.99: 95% CI 1.22–3.25, p<0.006).ConclusionsBAME patients were more likely to be admitted younger, and to die at a younger age with SARS-CoV-2. Within the BAME cohort, Asian patients were more likely to die but despite this, there was no difference in rates of admission to ICU. The reasons for these disparities are not fully understood and need to be addressed. Investigating ethnicity as a clinical risk factor remains a high public health priority. Studies that consider ethnicity as part of the wider socio-cultural determinant of health are urgently needed.

Journal article

Pallett SJC, Rayment M, Patel A, Charani E, Denny SJ, Fitzgerald-Smith SAM, Mughal N, Jones R, Davies GW, Moore LSPet al., 2020, Serological assays for delayed SARS-CoV-2 case identification - Author's reply, The Lancet Respiratory Medicine, Vol: 8, Pages: e74-e74, ISSN: 2213-2600

Journal article

Pallett SJC, Rayment M, Patel A, Fitzgerald-Smith SAM, Denny SJ, Charani E, Mai AL, Gilmour KC, Hatcher J, Scott C, Randell P, Mughal N, Jones R, Moore LSP, Davies GWet al., 2020, Point-of-care serological assays for delayed SARS-CoV-2 case identification among health-care workers in the UK: a prospective multicentre cohort study, LANCET RESPIRATORY MEDICINE, Vol: 8, Pages: 885-894, ISSN: 2213-2600

Journal article

Abdulaal A, Patel A, Charani E, Denny S, Mughal N, Moore Let al., 2020, Prognostic modelling of COVID-19 using artificial intelligence in a UK population, Journal of Medical Internet Research, Vol: 22, Pages: 1-10, ISSN: 1438-8871

Background:The current severe acute respiratory syndrome-coronavirus disease (SARS-CoV-2) outbreak is a public health emergency which has had a significant case-fatality in the United Kingdom (UK). Whilst there appear to be several early predictors of outcome, there are no currently validated prognostic models or scoring systems applicable specifically to SARS-CoV-2 positive patients.Objective:To create a point-of-admission, mortality-risk scoring system utilising an artificial neural network (ANN).Methods:We present an ANN which can provide a patient-specific, point-of-admission mortality risk prediction to inform clinical management decisions at the earliest opportunity. The ANN analyses a set of patient features including demographics, comorbidities, smoking history and presenting symptoms and predicts patient-specific mortality risk during the current hospital admission. The model was trained and validated on data extracted from 398 patients admitted to hospital with a positive real-time reverse transcriptase polymerase chain reaction (rt-PCR) test for SARS-CoV-2.Results:Patient-specific mortality was predicted with 86.25% accuracy, with a sensitivity of 87.50% (95% CI: 61.65% to 98.45%) and specificity of 85.94% (95% CI: 74.98% to 93.36%). The positive predictive value was 60.87% (95% CI: 45.23% to 74.56%), and the negative predictive value was 96.49% (95% CI: 88.23% to 99.02%). The (AUROC) was 90.12%.Conclusions:This analysis demonstrates an adaptive ANN trained on data at a single site, which demonstrates the early utility of deep learning approaches in a rapidly evolving pandemic with no established or validated prognostic scoring systems.

Journal article

Charani E, 2020, Antimicrobial Decision-Making and Stewardship Reply, CLINICAL INFECTIOUS DISEASES, Vol: 71, Pages: 700-+, ISSN: 1058-4838

Journal article

Wathne JS, Skodvin B, Charani E, Harthug S, Blix HS, Nilsen RM, Kleppe LKS, Vukovic M, Smith Iet al., 2020, Identifying targets for antibiotic stewardship interventions through analysis of the antibiotic prescribing process in hospitals - a multicentre observational cohort study., Antimicrobial Resistance and Infection Control, Vol: 9, Pages: 114-114, ISSN: 2047-2994

BACKGROUND: In order to change antibiotic prescribing behaviour, we need to understand the prescribing process. The aim of this study was to identify targets for antibiotic stewardship interventions in hospitals through analysis of the antibiotic prescribing process from admission to discharge across five groups of infectious diseases. METHODS: We conducted a multi-centre, observational cohort study, including patients with lower respiratory tract infections, exacerbation of chronic obstructive pulmonary disease, skin- and soft tissue infections, urinary tract infections or sepsis, admitted to wards of infectious diseases, pulmonary medicine and gastroenterology at three teaching hospitals in Western Norway. Data was collected over a 5-month period and included antibiotics prescribed and administered during admission, antibiotics prescribed at discharge, length of antibiotic therapy, indication for treatment and discharge diagnoses, estimated glomerular filtration rate (eGFR) on admission, antibiotic allergies, place of initiation of therapy, admittance from an institution, patient demographics and outcome data. Primary outcome measure was antibiotic use throughout the hospital stay, analysed by WHO AWaRe-categories and adherence to guideline. Secondary outcome measures were a) antibiotic prescribing patterns by groups of diagnoses, which were analysed using descriptive statistics and b) non-adherence to the national antibiotic guidelines, analysed using multivariate logistic regression. RESULTS: Through analysis of 1235 patient admissions, we identified five key targets for antibiotic stewardship interventions in our population of hospital inpatients; 1) adherence to guideline on initiation of treatment, as this increases the use of WHO Access-group antibiotics, 2) antibiotic prescribing in the emergency room (ER), as 83.6% of antibiotic therapy was initiated there, 3) understanding prescribing for patients admitted from other institutions, as this was significantl

Journal article

Rawson TM, Moore L, Castro Sanchez E, Charani E, Davies F, Satta G, Ellington M, Holmes Aet al., 2020, COVID-19 and the potential long term impact on antimicrobial resistance, Journal of Antimicrobial Chemotherapy, Vol: 75, Pages: 1681-1684, ISSN: 0305-7453

The emergence of the SARS-CoV-2 respiratory virus has required an unprecedented response to control the spread of the infection and protect the most vulnerable within society. Whilst the pandemic has focused society on the threat of emerging infections and hand hygiene, certain infection control and antimicrobial stewardship policies may have to be relaxed. It is unclear whether the unintended consequences of these changes will have a net-positive or -negative impact on rates of antimicrobial resistance. Whilst the urgent focus must be on allaying this pandemic, sustained efforts to address the longer-term global threat of antimicrobial resistance should not be overlooked.

Journal article

Patel A, Charani E, Ariyanayagam D, Abdulaal A, Denny SJ, Mughal N, Moore LSPet al., 2020, New-onset anosmia and ageusia in adult patients diagnosed with SARS-CoV-2 infection., Clinical Microbiology and Infection, ISSN: 1198-743X

OBJECTIVES: We investigated the prevalence of anosmia and ageusia in adult patients with a laboratory-confirmed diagnosis of infection with severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2). METHODS: This was a retrospective observational analysis of patients infected with SARS-CoV-2 admitted to hospital or managed in the community and their household contacts across a London population during the period March 1st to April 1st, 2020. Symptomatology and duration were extracted from routinely collected clinical data and follow-up telephone consultations. Descriptive statistics were used. RESULTS: Of 386 patients, 141 (92 community patients, 49 discharged inpatients) were included for analysis; 77/141 (55%) reported anosmia and ageusia, nine reported only ageusia and three only anosmia. The median onset of anosmia in relation to onset of SARS-CoV-2 disease (COVID-19) symptoms (as defined by the Public Health England case definition) was 4 days (interquartile range (IQR) 5). Median duration of anosmia was 8 days (IQR 16). Median duration of COVID-19 symptoms in community patients was 10 days (IQR 8) versus 18 days (IQR 13.5) in admitted patients. As of April 1, 45 patients had ongoing COVID-19 symptoms and/or anosmia; 107/141 (76%) patients had household contacts, and of 185 non-tested household contacts 79 (43%) had COVID-19 symptoms with 46/79 (58%) reporting anosmia. Six household contacts had anosmia only. CONCLUSIONS: Over half of the positive patients reported anosmia and ageusia, suggesting that these should be added to the case definition and used to guide self-isolation protocols. This adaptation may be integral to case findings in the absence of population-level testing. Until we have successful population-level vaccination coverage, these steps remain critical in the current and future waves of this pandemic.

Journal article

Patel A, Charani E, Ariyanayagam D, Abdulaal A, Denny S, Mughal N, Moore Let al., 2020, New onset anosmia and ageusia in adult patients diagnosed with SARS-CoV-2 in a London community and secondary care population, Publisher: Elsevier BV

Background: We investigated the prevalence of anosmia and ageusia in adult patients with a laboratory confirmed diagnosis of severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2).Methods: A retrospective observational analysis was conducted amongst patients and their household contacts across a central London population diagnosed with SARS-CoV-2 and admitted to hospital or managed in the community during March 1 - April 1, 2020. Symptomatology and duration were extracted from routinely collected clinical data. Descriptive statistics were used.Findings: Of 386 patients with a laboratory diagnosis of SARS-CoV-2, 141 (92 community patients, 49 discharged inpatients) had evaluable data and were included for analysis. 77/141 (55%) reported anosmia and ageusia; nine reported only ageusia and three only anosmia. The mean duration of symptoms (as defined by the Public Health England case definition for SARS-CoV-2) was 13·1 days (0-33). The mean onset of anosmia in relation to onset of SARS-CoV-2 symptoms was 4·6 days (0-21). Duration of anosmia was 12·3 days (0-30). Duration of SARS-CoV-2 symptoms in community patients was 11·5 days (0-28) versus 16·7 days (0-33) in admitted patients. As of April 1, 45 patients had ongoing SARS-CoV-2 symptoms and/or anosmia. 107/141 (76%) patients had one or more household contacts during their isolation period. Of these, 185 non-tested household contacts, 79 (43%) had SARS-CoV-2 symptoms with 46/79 (58%) reporting anosmia. Six household contacts had anosmia only.Interpretation: More than half of SARS-CoV-2 positive patients reported anosmia and ageusia. These findings suggest anosmia and ageusia should be added to case definitions for SARS-CoV2 and guide self-isolation protocols. This adaptation may be integral to case finding in the absence of population level testing. Until a time where we have successful population level vaccination coverage, these steps remain essential both in this pa

Working paper

Duncan EM, Charani E, Clarkson JE, Francis JJ, Gillies K, Grimshaw JM, Kern WV, Lorencatto F, Marwick CA, McEwen J, Möhler R, Morris AM, Ramsay CR, Rogers Van Katwyk S, Rzewuska M, Skodvin B, Smith I, Suh KN, Davey PGet al., 2020, A behavioural approach to specifying interventions: what insights can be gained for the reporting and implementation of interventions to reduce antibiotic use in hospitals?, Journal of Antimicrobial Chemotherapy, Vol: 75, Pages: 1338-1346, ISSN: 0305-7453

BACKGROUND: Reducing unnecessary antibiotic exposure is a key strategy in reducing the development and selection of antibiotic-resistant bacteria. Hospital antimicrobial stewardship (AMS) interventions are inherently complex, often requiring multiple healthcare professionals to change multiple behaviours at multiple timepoints along the care pathway. Inaction can arise when roles and responsibilities are unclear. A behavioural perspective can offer insights to maximize the chances of successful implementation. OBJECTIVES: To apply a behavioural framework [the Target Action Context Timing Actors (TACTA) framework] to existing evidence about hospital AMS interventions to specify which key behavioural aspects of interventions are detailed. METHODS: Randomized controlled trials (RCTs) and interrupted time series (ITS) studies with a focus on reducing unnecessary exposure to antibiotics were identified from the most recent Cochrane review of interventions to improve hospital AMS. The TACTA framework was applied to published intervention reports to assess the extent to which key details were reported about what behaviour should be performed, who is responsible for doing it and when, where, how often and with whom it should be performed. RESULTS: The included studies (n = 45; 31 RCTs and 14 ITS studies with 49 outcome measures) reported what should be done, where and to whom. However, key details were missing about who should act (45%) and when (22%). Specification of who should act was missing in 79% of 15 interventions to reduce duration of treatment in continuing-care wards. CONCLUSIONS: The lack of precise specification within AMS interventions limits the generalizability and reproducibility of evidence, hampering efforts to implement AMS interventions in practice.

Journal article

Charani E, DeBarra E, Gill D, Rawson T, Gilchrist M, Naylor N, Holmes Aet al., 2019, Antibiotic prescribing in general medical and surgical specialties: a prospective cohort study, Antimicrobial Resistance and Infection Control, Vol: 8, Pages: 1-10, ISSN: 2047-2994

Background: Qualitative work has described the differences in prescribing practice across medical and surgical specialties. This study aimed to understand if specialty impacts quantitative measures of prescribing practice. Methods: We prospectively analysed the antibiotic prescribing across general medical and surgical teams for acutely admitted patients. Over a 12-month period (June 2016 – May 2017) 659 patients (362 medical, 297 surgical) were followed for the duration of their hospital stay. Antibiotic prescribing across these cohorts was assessed using Chi-squared or Wilcoxon rank-sum, depending on normality of data. The t-test was used to compare age and length of stay. A logistic regression model was used to predict escalation of antibiotic therapy. Results: Surgical patients were younger (p<0.001) with lower Charlson Comorbidity Index scores (p<0.001). Antibiotics were prescribed for 45% (162/362) medical and 55% (164/297) surgical patients. Microbiological results were available for 26% (42/164) medical and 29% (48/162) surgical patients, of which 55% (23/42) and 48% (23/48) were positive respectively. There was no difference in the spectrum of antibiotics prescribed between surgery and medicine (p=0.507). In surgery antibiotics were 1) prescribed more frequently (p=0.001); 2) for longer (p=0.016); 3) more likely to be escalated (p=0.004); 4) less likely to be compliant with local policy (p<0.001) than medicine. Conclusions: Across both specialties, microbiology investigation results are not adequately used to diagnose infections and optimise their management. There is significant variation in antibiotic decision-making (including escalation patterns) between general surgical and medical teams. Antibiotic stewardship interventions targeting surgical specialties need to go beyond surgical prophylaxis. It is critical to focus on of review the patients initiated on therapeutic antibiotics in surgical specialties to ensure that escalation and c

Journal article

Ahmad R, Zhu NJ, Leather AJM, Holmes A, Ferlie Eet al., 2019, Strengthening strategic management approaches to address antimicrobial resistance in global human health: a scoping review, BMJ Global Health, Vol: 4, ISSN: 2059-7908

Introduction: The development and implementation of national strategic plans is a critical component towards successfully addressing antimicrobial resistance (AMR). This study aimed to review the scope and analytical depth of situation analyses conducted to address AMR in human health to inform the development and implementation of national strategic plans. Methods: A systematic search of the literature was conducted to identify all studies since 2000, that have employed a situation analysis to address AMR. The included studies are analysed against frameworks for strategic analysis, primarily the PESTELI (Political, Economic, Sociological, Technological, Ecological, Legislative, Industry) framework, to understand the depth, scope and utility of current published approaches. Results: 10 studies were included in the final review ranging from single country (6) to regional-level multicountry studies (4). 8 studies carried out documentary review, and 3 of these also included stakeholder interviews. 2 studies were based on expert opinion with no data collection. No study employed the PESTELI framework. Most studies (9) included analysis of the political domain and 1 study included 6 domains of the framework. Technological and industry analyses is a notable gap. Facilitators and inhibitors within the political and legislative domains were the most frequently reported. No facilitators were reported in the economic or industry domains but featured inhibiting factors including: lack of ring-fenced funding for surveillance, perverse financial incentives, cost-shifting to patients; joint-stock drug company ownership complicating regulations. Conclusion: The PESTELI framework provides further opportunities to combat AMR using a systematic, strategic management approach, rather than a retrospective view. Future analysis of existing quantitative data with interviews of key strategic and operational stakeholders is needed to provide critical insights about where implementation eff

Journal article

Charani E, Cunnington AJ, Yousif AHA, Ahmed MS, Ahmed AEM, Babiker S, Bedri S, Buytaert W, Crawford MA, Elbashir MI, Elhag K, Elsiddig KE, Hakim N, Johnson MR, Miras AD, Swar MO, Templeton MR, Taylor-Robinson SDet al., 2019, In transition: current health challenges and priorities in Sudan, BMJ Global Health, Vol: 4:e001723, ISSN: 2059-7908

A recent symposium and workshop in Khartoum, the capital of the Republic of Sudan, brought together broad expertise from three universities to address the current burden of communicable and non-communicable diseases facing the Sudanese healthcare system. These meetings identified common challenges that impact the burden of diseases in the country, most notably gaps in data and infrastructure which are essential to inform and deliver effective interventions. Non-communicable diseases, including obesity, type 2 diabetes, renal disease and cancer are increasing dramatically, contributing to multimorbidity. At the same time, progress against communicable diseases has been slow, and the burden of chronic and endemic infections remains considerable, with parasitic diseases (such as malaria, leishmaniasis and schistosomiasis) causing substantial morbidity and mortality. Antimicrobial resistance has become a major threat throughout the healthcare system, with an emerging impact on maternal, neonatal, and paediatric populations. Meanwhile, malnutrition, micronutrient deficiency, and poor perinatal outcomes remain common and contribute to a lifelong burden of disease. These challenges echo the UN sustainable development goals and concentrating on them in a unified strategy will be necessary to address the national burden of disease. At a time when the country is going through societal and political transition, we draw focus on the country and the need for resolution of its healthcare needs.

Journal article

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