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Journal articleArinaminpathy N, Reed C, Biggerstaff M, et al., 2024,
Estimating community-wide indirect effects of influenza vaccination: triangulation using mathematical models and bias analysis.
, Am J EpidemiolUnderstanding whether influenza vaccine promotion strategies produce community-wide indirect effects is important for establishing vaccine coverage targets and optimizing vaccine delivery. Empirical epidemiologic studies and mathematical models have been used to estimate indirect effects of vaccines but rarely for the same estimand in the same dataset. Using these approaches together could be a powerful tool for triangulation in infectious disease epidemiology because each approach is subject to distinct sources of bias. We triangulated evidence about indirect effects from a school-located influenza vaccination program using two approaches: a difference-in-difference (DID) analysis, and an age-structured, deterministic, compartmental model. The estimated indirect effect was substantially lower in the mathematical model than in the DID analysis (2.1% (95% Bayesian credible intervals 0.4 - 4.4%) vs. 22.3% (95% CI 7.6% - 37.1%)). To explore reasons for differing estimates, we used sensitivity analyses and probabilistic bias analyses. When we constrained model parameters such that projections matched the DID analysis, results only aligned with the DID analysis with substantially lower pre-existing immunity among school-age children and older adults. Conversely, DID estimates corrected for potential bias only aligned with mathematical model estimates under differential outcome misclassification. We discuss how triangulation using empirical and mathematical modelling approaches could strengthen future studies.
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Journal articleGrenfell P, Elmes J, Stuart R, et al., 2024,
East London Project: a participatory mixed-method evaluation on how removing enforcement could affect sex workers' safety, health and access to services in East London.
, Public Health Res (Southampt), Pages: 1-53BACKGROUND: Sex workers' risk of violence and ill-health is shaped by their work environments, community and structural factors, including criminalisation. AIM: We evaluated the impact of removing police enforcement on sex workers' safety, health and access to services. DESIGN: Mixed-methods participatory study comprising qualitative research, a prospective cohort study, mathematical modelling and routine data collation. SETTING: Three boroughs in London, UK. PARTICIPANTS: People aged ≥ 18 years, who provided in-person sexual services. INTERVENTIONS: Simulated removal of police enforcement. OUTCOMES: Primary - recent or past experience of sexual, physical or emotional violence. Secondary - depression/anxiety symptoms, physical health, chlamydia/gonorrhoea, and service access. RESULTS: A combination of enforcement by police, local authorities and immigration, being denied justice when reporting violence, and linked cuts to specialist health and support services created harmful conditions for sex workers. This disproportionately affected cisgender and transgender women who work on the streets, use drugs, are migrants and/or women of colour. Among women (n = 197), street-based sex workers experienced higher levels than indoor sex workers of recent violence from clients (73% vs. 36%), police (42% vs. 7%) and others (67% vs. 17%); homelessness (65% vs. 7%); anxiety and depression (71% vs 35%); physical ill-health (57% vs 31%); and recent law enforcement (87% vs. 9%). For street-based sex workers, recent arrest was associated with violence from others (adjusted odds ratio (AOR)) 2.77, 95% confidence interval (CI) 1.11 to 6.94). Displacement by police was associated with client violence (AOR 4.35; 95% CI 1.36 to 13.90) as were financial difficulties (AOR 4.66; CI 1.64 to 13.24). Among indoor sex workers, unstable residency (AOR 3.19; 95% CI 1.36 to 7.49) and financial difficulties (AOR 3.66; 95% CI 1.64 to 8.18) contributed to risk of client violence. Among all g
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Journal articleMenkir TF, Citarella BW, Sigfrid L, et al., 2024,
Modeling the relative influence of socio-demographic variables on post-acute COVID-19 quality of life.
, medRxivIMPORTANCE: Post-acute sequelae of SARS-CoV-2, referred to as "long COVID", are a globally pervasive threat. While their many clinical determinants are commonly considered, their plausible social correlates are often overlooked. OBJECTIVE: To compare social and clinical predictors of differences in quality of life (QoL) with long COVID. Additionally, to measure how much adjusted associations between social factors and long COVID-associated quality of life are unexplained by important clinical intermediates. DESIGN SETTING AND PARTICIPANTS: Data from the ISARIC long COVID multi-country prospective cohort study. Subjects from Norway, the United Kingdom (UK), and Russia, aged 16 and above, with confirmed acute SARS-CoV-2 infection reporting >= 1 long COVID-associated symptoms 1+ month following infection. EXPOSURE: The social exposures considered were educational attainment (Norway), employment status (UK and Russia), and female vs male sex (all countries). MAIN OUTCOME AND MEASURES: Quality of life-adjusted days, or QALDs, with long COVID. RESULTS: This cohort study included a total of 3891 participants. In all three countries, educational attainment, employment status, and female sex were important predictors of long COVID QALDs. Furthermore, a majority of the estimated relationships between each of these social correlates and long COVID QALDs could not be attributed to key long COVID-predicting comorbidities. In Norway, 90% (95% CI: 77%, 100%) of the adjusted association between the top two quintiles of educational attainment and long COVID QALDs was not explained by clinical intermediates. The same was true for 86% (73%, 100%) and 93% (80%,100%) of the adjusted associations between full-time employment and long COVID QALDs in the United Kingdom (UK) and Russia. Additionally, 77% (46%,100%) and 73% (52%, 94%) of the adjusted associations between female sex and long COVID QALDs in Norway and the UK were unexplained by the clinical mediators. CONCLUSIONS
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Journal articleGrant R, Rubin M, Abbas M, et al., 2024,
Expanding the use of mathematical modeling in healthcare epidemiology and infection prevention and control.
, Infect Control Hosp Epidemiol, Pages: 1-6During the coronavirus disease 2019 pandemic, mathematical modeling has been widely used to understand epidemiological burden, trends, and transmission dynamics, to facilitate policy decisions, and, to a lesser extent, to evaluate infection prevention and control (IPC) measures. This review highlights the added value of using conventional epidemiology and modeling approaches to address the complexity of healthcare-associated infections (HAI) and antimicrobial resistance. It demonstrates how epidemiological surveillance data and modeling can be used to infer transmission dynamics in healthcare settings and to forecast healthcare impact, how modeling can be used to improve the validity of interpretation of epidemiological surveillance data, how modeling can be used to estimate the impact of IPC interventions, and how modeling can be used to guide IPC and antimicrobial treatment and stewardship decision-making. There are several priority areas for expanding the use of modeling in healthcare epidemiology and IPC. Importantly, modeling should be viewed as complementary to conventional healthcare epidemiological approaches, and this requires collaboration and active coordination between IPC, healthcare epidemiology, and mathematical modeling groups.
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Journal articleMerson L, Duque S, Garcia-Gallo E, et al., 2024,
Optimising Clinical Epidemiology in Disease Outbreaks: Analysis of ISARIC-WHO COVID-19 Case Report Form Utilisation
, Epidemiologia, Vol: 5, Pages: 557-580Standardised forms for capturing clinical data promote consistency in data collection and analysis across research sites, enabling faster, higher-quality evidence generation. ISARIC and the World Health Organization have developed case report forms (CRFs) for the clinical characterisation of several infectious disease outbreaks. To improve the design and quality of future forms, we analysed the inclusion and completion rates of the 243 fields on the ISARIC-WHO COVID-19 CRF. Data from 42 diverse collaborations, covering 1886 hospitals and 950,064 patients, were analysed. A mean of 129.6 fields (53%) were included in the adapted CRFs implemented across the sites. Consistent patterns of field inclusion and completion aligned with globally recognised research priorities in outbreaks of novel infectious diseases. Outcome status was the most highly included (95.2%) and completed (89.8%) field, followed by admission demographics (79.1% and 91.6%), comorbidities (77.9% and 79.0%), signs and symptoms (68.9% and 78.4%), and vitals (70.3% and 69.1%). Mean field completion was higher in severe patients (70.2%) than in all patients (61.6%). The results reveal how clinical characterisation CRFs can be streamlined to reduce data collection time, including the modularisation of CRFs, to offer a choice of data volume collection and the separation of critical care interventions. This data-driven approach to designing CRFs enhances the efficiency of data collection to inform patient care and public health response.
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Journal articleGifford H, Rhodes J, Farrer RA, 2024,
The diverse genomes of Candida auris
, The Lancet Microbe, Vol: 5- Cite
- Citations: 1
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Journal articleKucharski A, Cori A, 2024,
Inference of epidemic dynamics in the COVID-19 era and beyond
, Epidemics: the journal of infectious disease dynamics, Vol: 48, ISSN: 1755-4365The COVID-19 pandemic demonstrated the key role that epidemiology and modelling play in analysing infectious threats and supporting decision making in real-time. Motivated by the unprecedented volume and breadth of data generated during the pandemic, we review modern opportunities for analysis to address questions that emerge during a major modern epidemic. Following the broad chronology of insights required — from understanding initial dynamics to retrospective evaluation of interventions, we describe the theoretical foundations of each approach and the underlying intuition. Through a series of case studies, we illustrate real life applications, and discuss implications for future work.
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Journal articleYang Q, Park SW, Saad-Roy CM, et al., 2024,
Assessing population-level target product profiles of universal human influenza A vaccines
, EPIDEMICS, Vol: 48, ISSN: 1755-4365 -
Journal articleKruger M, van Elsland SL, Davidson A, et al., 2024,
Outcome of retinoblastoma after implementation of national retinoblastoma treatment guidelines in South Africa
, JCO Global Oncology, Vol: 10, ISSN: 2687-8941PurposeRetinoblastoma, a curable childhood cancer, has been identified as a tracer cancer in the WHO Global Initiative for Childhood Cancer. To document the outcomes of children with retinoblastoma in South Africa, treated as per the first prospective standard national treatment guidelines for childhood cancer in South Africa.Patients and MethodsAll children diagnosed with retinoblastoma between 2012 and 2016 in five South African pediatric oncology units were treated with a standard treatment on the basis of the International Society of Pediatric Oncology-Pediatric Oncology in Developing Countries guidelines for high-income settings. Treatment included focal therapy with/without chemotherapy, or enucleation with/without chemotherapy, and orbital radiotherapy, depending on enucleated eye histology. The end point was survival at 24 months, using Kaplan-Meier curves with log-rank (Mantel-Cox) and chi-square (χ2) tests with respective P values reported.ResultsA total of 178 children were included in the study; 68% presented with unilateral disease. The median age was 27 months (range 0-118 months) with a male:female ratio of 1:0.75. The overall survival was 79% at 24 months with significant association with stage at diagnosis (P < .001) and older age over 2 years as opposed to younger than 2 years (P < .001). Causes of death were disease progression/relapses in 90% (34 of 38) and unknown in 2% (1 of 38), whereas treatment abandonment was 1.7% (3 of 178).ConclusionEfficacy with national treatment guidelines was confirmed, and feasibility of implementing standard national childhood cancer treatment guidelines was documented, involving multidisciplinary teams in South Africa. Outcome was significantly associated with stage at diagnosis and age.
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Journal articleUzzell CB, Gray E, Rigby J, et al., 2024,
Environmental surveillance for Salmonella Typhi in rivers and wastewater from an informal sewage network in Blantyre, Malawi
, PLoS Neglected Tropical Diseases, Vol: 18, ISSN: 1935-2727Environmental surveillance for Salmonella Typhi may provide information on the community-level dynamics of typhoid fever in resource poor regions experiencing high disease burden. Many knowledge gaps concerning the feasibility of ES remain, especially in areas lacking formal sewage systems. We implemented protocols for S. Typhi ES, including site selection and catchment population estimation, sample concentration and testing using qPCR for S. Typhi specific gene targets. Between May 2021 and May 2022, we collected grab samples and Moore swabs from 43 sites in Blantyre, Malawi. Catchment characteristics, water quality, and human faecal contamination (qPCR for Bacteroides HF183) were also recorded. Their association with S. Typhi detection was investigated using a logistic mixed-effects regression analysis. Prevalence of S. Typhi in ES samples was 2.1% (1.1–4.0%) and 3.9% (1.9–7.9%) for grab and Moore swab samples, respectively. HF183 was associated S. Typhi positivity, with a unit increase in log genome copies/microlitre increasing the odds of detection of S. Typhi by 1.56 (95% CI: 1.29–1.89) and 1.33 (1.10–1.61) in Moore swabs and grab samples, respectively. The location and timing of S. Typhi detection through ES was not associated with the incidence of typhoid fever reported in associated catchment populations. During this period of relatively low typhoid fever incidence, wastewater surveillance continued to detect S. Typhi in human sewage and wastewater suggesting that ES using natural river systems can be a sensitive indicator of transmission.
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