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Harmonizing population health data into OMOP common data model: a demonstration using COVID-19 sero-surveillance data from Nairobi Urban Health and Demographic Surveillance System.
Get PDFBACKGROUND: Observational health data are collected in different formats and structures, making it challenging to analyze with common tools. The Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM) is a standardized data model that can harmonize observational health data. OBJECTIVE: This paper demonstrates the use of the OMOP CDM to harmonize COVID-19 sero-surveillance data from the Nairobi Urban Health and Demographic Surveillance System (HDSS). METHODS: In this study, we extracted data from the Nairobi Urban HDSS COVID-19 sero-surveillance database and mapped it to the OMOP CDM. We used open-source Observational Health Data Sciences and Informatics (OHDSI) tools like WhiteRabbit, RabbitInAHat, and USAGI. The steps included data profiling (scanning), mapping the vocabularies using the offline USAGI and online ATHENA, and designing the extract, transform, and load (ETL) process using RabbitInAHat. The ETL process was implemented using Pentaho Data Integration community edition software and structured query language (SQL). The target OMOP CDM can now be used to analyze the prevalence of COVID-19 antibodies in the Nairobi Urban HDSS population. RESULTS: We successfully mapped the Nairobi Urban HDSS COVID-19 sero-surveillance data to the OMOP CDM. The standardized dataset included information on demographics, COVID-19 symptoms, vaccination, and COVID-19 antibody test results. CONCLUSIONS: The OMOP CDM is a valuable tool for harmonizing observational health data. Using the OMOP CDM facilitates the sharing and analysis of observational health data, leading to a better understanding of disease conditions and trends and improving evidence-based population health strategies
Diabetic foot ulcer photography study: a study within a trial to assess the reliability of two-dimensional (2D) photography for the assessment of ulcer healing in patients with diabetes-related foot ulcers-protocol paper.
Get PDFBACKGROUND: The primary endpoint in diabetes-related foot ulcer (DFU) trials is often time to healing, defined as complete re-epithelialisation with absence of drainage, requiring clinical expert assessment as the gold standard. Central blinded photograph review for confirmation of healing is increasingly being undertaken for internal validity. The Diabetic Foot Ulcer Photography study aims to determine the agreement between blinded independent review panel members for assessing ulcer healing status in patients with DFUs. METHODS AND ANALYSIS: Photographs of ulcers clinically assessed as healed or not healed across 300 participants recruited to one of two randomised controlled trials (MIDFUT and CODIFI2), will be independently reviewed by a central blinded panel consisting of four clinicians with expertise in ulcer healing assessment. Staff at recruiting sites will take photographs using a standardised camera and protocol. Photographs will be reviewed at three levels of magnification: raw image, image standardised to a measurement scale included in the photograph and standardised image with magnification permitted. Reviewers will assess the healing status and their confidence level in making a healing judgement, with reasons reported for a low confidence rating. Analysis at each level of magnification will estimate inter- and intra-rater reliability on the assessments of healing of photographs with the clinical assessment (primary) and confidence rating using multivariable logistic mixed models. Analysis of the learning curve for the assessment of healing and confidence rating will use exponential and two-phase models. ETHICS AND DISSEMINATION: Ethics approval has been granted by the National Research Ethics Service Committees (MIDFUT 17/YH/0055; CODIFI2 18-WS-0235). All participants will provide a written informed consent for photography before recruited onto the respective study. Photographs will be transferred to the trials' coordinating centre via a secure file transfer service and saved in a restricted access folder on a secure server. Results will be disseminated via publications in scientific journals and conference presentations. TRIAL REGISTRATION NUMBER: MIDFUT (ISRCTN64926597) and CODIFI2 (ISRCTN74929588)
School health and nutrition environments: A multicountry survey in five countries of sub-Saharan Africa region-Burkina Faso, Ethiopia, South Africa, Sudan, and Tanzania.
Get PDFSchools are increasingly regarded as a key setting for promoting the health, well-being, and development of children and adolescents. In this multicountry cross-sectional survey, we describe the health, nutrition, and food environments of public primary schools in five urban settings in Africa region: Ouagadougou, Burkina Faso; Addis Ababa, Ethiopia; Durban; South Africa, Khartoum, Sudan; and, Dar es Salaam, Tanzania. We evaluated the school health and nutrition (SHN) environments in three main areas: (1) the availability of health-related policies, guidelines, and school curricula, (2) the provision of health, nutrition, and water, sanitation, and hygiene (WASH) services in schools, and (3) the school food environments and eating habits of adolescents. We used stratified random sampling to recruit 79 schools from five countries. Trained fieldworkers collected standardized questionnaire data from 79 school administrators, 765 food vendors, and 4999 in-school adolescents aged 10-15 years. In our study, 24 out of 79 school administrators were aware of their school's health-related policies and guidelines while 30 schools had a specific SHN curriculum. In general, health, nutrition, and WASH services were inadequate. Possibly due to a lack of school kitchens, 14.4% of students bought snacks and unhealthy foods from food vendors. Our study indicates that schools' food and nutrition environments are insufficient to improve adolescent health and nutrition in the African region, including limited coverage of SHN policies, suboptimal facilities and nutrition services, and unregulated food environments. Schools in sub-Saharan Africa need to improve their health and nutrition environments
Neonatal mortality risk of large-for-gestational-age and macrosomic live births in 15 countries, including 115.6 million nationwide linked records, 2000-2020.
Get PDFObjective: We aimed to compare the prevalence and neonatal mortality associated with large for gestational age (LGA) and macrosomia among 115.6 million live births in 15 countries, between 2000 and 2020.
Design: Population-based, multi-country study.
Setting: National healthcare systems.
Population: Liveborn infants.
Methods: We used individual-level data identified for the Vulnerable Newborn Measurement Collaboration. We calculated the prevalence and relative risk (RR) of neonatal mortality among live births born at term + LGA (>90th centile, and also >95th and >97th centiles when the data were available) versus term + appropriate for gestational age (AGA, 10th–90th centiles) and macrosomic (≥4000, ≥4500 and ≥5000 g, regardless of gestational age) versus 2500–3999 g. INTERGROWTH 21st served as the reference population.
Main outcome measures: Prevalence and neonatal mortality risks.
Results: Large for gestational age was common (median prevalence 18.2%; interquartile range, IQR, 13.5%–22.0%), and overall was associated with a lower neonatal mortality risk compared with AGA (RR 0.83, 95% CI 0.77–0.89). Around one in ten babies were ≥4000 g (median prevalence 9.6% (IQR 6.4%–13.3%), with 1.2% (IQR 0.7%–2.0%) ≥4500 g and with 0.2% (IQR 0.1%–0.2%) ≥5000 g). Overall, macrosomia of ≥4000 g was not associated with increased neonatal mortality risk (RR 0.80, 95% CI 0.69–0.94); however, a higher risk was observed for birthweights of ≥4500 g (RR 1.52, 95% CI 1.10–2.11) and ≥5000 g (RR 4.54, 95% CI 2.58–7.99), compared with birthweights of 2500–3999 g, with the highest risk observed in the first 7 days of life.
Conclusions: In this population, birthweight of ≥4500 g was the most useful marker for early mortality risk in big babies and could be used to guide clinical management decisions
Synergies between food biodiversity, processing levels, and the EAT-Lancet diet for nutrient adequacy and environmental sustainability: a multiobjective optimization using the European Prospective Investigation into Cancer and Nutrition cohort.
No full textBACKGROUND: Diets have become increasingly monotonous and high in ultraprocessed foods (UPFs), contributing to poor health outcomes and environmental degradation. Although sustainable diets, food biodiversity, and food processing levels have each been linked to nutritional and environmental outcomes, their combined impact has not been assessed. OBJECTIVES: This study aims to examine whether food biodiversity, intakes of UPFs, and adherence to the EAT-Lancet diet can simultaneously optimize nutrient adequacy while reducing environmental impacts. METHODS: Using data from 368,733 adults in the European Prospective Investigation into Cancer and Nutrition, we assessed associations and interactions between dietary species richness (DSR) (disaggregated into DSRPlant and DSRAnimal), food processing levels (Nova categories; % g/d), and adherence to EAT-Lancet recommendations [healthy reference diet (HRD) score; 0-140 points] with the Probability of Adequate Nutrient Intake Diet (PANDiet) score, dietary greenhouse gas emissions (GHGe; kg CO2-eq/d), and land use (m2/d). Regression models subsequently informed multiobjective optimization to identify optimal dietary patterns balancing nutritional and environmental outcomes. RESULTS: Compared with observed diets, optimal diets showed a mean HRD score increase of 13.91 (95% confidence interval: 13.89, 13.93) points; DSRPlant increased by mean of 1.36 (1.35, 1.37) species, and a mean substitution of 12.44 (12.40, 12.49) percentage points of UPFs with unprocessed or minimally processed foods. Correspondingly, the mean PANDiet score increased by 4.12 (4.10, 4.14) percentage points, whereas GHGe and land use reduced by 1.07 (1.05, 1.09) kg CO2-eq/d and 1.43 (1.41, 1.45) m2/d, respectively. CONCLUSIONS: Diets that adhere to the EAT-Lancet diet, are more biodiverse, and prioritize unprocessed and minimally processed foods over UPFs, have the potential to synergistically enhance nutrient adequacy while minimizing environmental impacts. These findings suggest that moderate improvements across multiple dietary dimensions simultaneously can achieve meaningful gains in both nutritional adequacy and environmental sustainability
Economic evaluation of next-generation sequencing technologies in pediatric patient groups with confirmed or possible rare diseases: A systematic literature review.
No full textPURPOSE: Next-generation sequencing (NGS) can accelerate the diagnosis of rare diseases (RDs). Economic evaluations assess the costs and benefits of new technologies and can help inform policy decisions on upscaled adoption into clinical practice. This review synthesizes current evidence on the economic evaluation of NGS for diagnosing RDs in pediatrics.
METHODS: Seven databases were consulted to identify full economic evaluations of NGS technologies used in the RD screening pathway for pediatric populations. Eligible studies were conducted in Organization for Economic Co-operation and Development or European Union member countries published between January 2015 and May 2024.
RESULTS: Of the 25 studies, most found NGS to be cost-effective compared with standard diagnostic methods, especially when used early in the diagnostic pathway. There remains significant variability in study methodology (including study perspective and lack of long-term cost considerations), which limits comparability of evidence. There has also been limited evaluation of NGS screening in healthy or asymptomatic populations (eg, newborn screening).
CONCLUSION: Although evidence shows that NGS technologies are generally cost-effective when used to screen for RD in pediatrics, there is a need for standardized approaches to contribute robust evidence that can be used to effectively support health care policy in this area
National Reporting of Bowel Cancer Care by the National Bowel Cancer Audit (NBOCA) Supports Hospital Teams to Improve care and Outcomes.
No full textThere are substantial international disparities in the care and outcomes of patients diagnosed with colorectal cancer (CRC) [1, 2]. When compared to other high-income countries, the UK has one of the poorest survival rates [3-5]. The UK’s poorer performance [6] cannot be fully explained by a more advanced stage distribution and may instead reflect deficits in access to optimal treatment [3].
Variation in the quality of CRC care directly impacts patient outcomes, including survival and quality of life. The NBOCA Quality Improvement (QI) plan [7], aims to quantify and address unwarranted variation in England and Wales. The plan prioritises ten performance indicators (Table 1), which are the foundation of the annual NBOCA State of the Nation report. In collaboration with key stakeholders, including the NBOCA Patient and Public Involvement Forum and the Clinical Advisory Group [8], performance indicators are selected based on three properties: measurable so feedback can be credible, actionable so feedback can translate into change, and improvable so actions have the desired effect on patient care [7]. Performance indicators are regularly reviewed, and new indicators are developed to ensure they remain clinically impactful. Although indicators such as resection margin and lymph node count are clinically important, poor data completeness in national datasets means they are currently not reliably measurable.
Each performance indicator has a local target for National Health Service (NHS) providers. Local targets are selected following review of national guidelines, and a consensus process with the NBOCA Clinical Advisory Group. Where local targets are consistently achieved, they are revised to stimulate continued quality improvement. Through public reporting of the ten performance indicators [9], NBOCA measures compliance of NHS providers with evidence-based standards, promotes best practice in the delivery of CRC services, and supports NHS units to identify areas for improvement
Body mass index and tuberculosis risk: an updated systematic literature review and dose-response meta-analysis.
Get PDFBACKGROUND:
The relationship between nutritional status and tuberculosis is critically important but poorly understood. We extended a 2009 review characterizing the relationship between body mass index (BMI) and tuberculosis risk.
METHODS:
We systematically searched for new studies published between 2009 and 2024 investigating BMI and tuberculosis risk in adults. We extracted estimates of risk in BMI categories, used resampling to assign a median BMI 'dose' within each category, and included these in one-stage dose-response meta-analyses, stratifying results by population group and country tuberculosis burden. We fitted linear models for comparability with the 2009 review and restricted cubic spline models to investigate nonlinear relationships and piecewise linear models.
RESULTS:
Our analyses showed an inverse dose-response relationship between BMI and tuberculosis risk across all populations in the full underweight to obese range (15.0-35.0 kg/m2). The spline and piecewise linear models showed a nonlinear relationship-in 22 general-population cohorts (n = 24 921 531), there was a steep per-unit reduction in risk for BMI of <25.0 kg/m2 [18.0%, 95% confidence interval (CI): 16.4-19.6], which decreased more gradually for BMI of ≥25.0 kg/m2 (6.9%, 95% CI: 4.6-9.2). In 18 cohorts of people with HIV (n = 162 609), the reduction was 15.3% for BMI of <23.0 kg/m2 (95% CI: 13.1-17.5) and 2.6% (95% CI: -3.1-7.9) for BMI of ≥23.0 kg/m2. In three cohorts of people with diabetes (n = 1 118 424), the reduction was 20.5% for BMI of <24.0 kg/m2 (95% CI: 18.4-22.6) and 13.4% (95% CI: 3.9-22.0) for BMI of ≥24.0 kg/m2. Based on the global BMI distribution, we estimated a relative risk of tuberculosis associated with undernutrition (BMI < 18.5 kg/m2) of 5.0 (95% CI: 4.2-5.9).
CONCLUSIONS:
Our results highlight the independent importance of nutritional status as a driver of the tuberculosis epidemic
The development of a global research agenda and individual participant data platform for visceral leishmaniasis: challenges and future opportunities.
Get PDFBACKGROUND: Visceral leishmaniasis (VL) is one of the neglected tropical diseases (NTDs) listed by the World Health Organization (WHO). The disease is currently in the elimination phase in the Indian subcontinent (ISC) and being targeted for elimination by 2030 in East Africa (EA). Maintaining the necessary financial and political commitments to achieve and sustain the current elimination efforts remains challenging. As with other NTDs, VL research is constrained by limited funding, and drug development has relied largely on partnerships between not-for-profit organisations and the pharmaceutical industry. Conducting robust clinical studies remains difficult, and therapeutic innovations have been limited. However, re-use of existing data offers an untapped opportunity to generate new evidence.
METHODS: We describe the process of developing a global VL research agenda and the establishment of an individual participant data (IPD) platform at the Infectious Diseases Data Observatory (IDDO). Key steps included a systematic scoping review of VL clinical trials, consultations with the Scientific Advisory Committee, expert and public reviews, and implementation of an equitable governance framework to harmonise and share IPD.
RESULTS: The VL research agenda, finalised in 2019, identified priority methodological and clinical questions suited to IPD analyses. The IDDO VL platform currently hosts harmonised data from nearly 15,000 patients across more than 50 studies (VL and post-kala-azar dermal leishmaniasis, PKDL). The platform is an inclusive resource guided by an equitable governance framework and provides a critical asset to support new evidence generation and can serve as a historical data to support accelerated drug development.
CONCLUSIONS: The development of a global VL research agenda has provided an inventory of priority research questions of public health importance. A shared IPD platform aligned with this agenda was developed to complement ongoing global efforts. In addition, such a platform can accelerate secondary evidence generation, support methodological innovation and inform future trial designs and policy. Sustained collaboration and investment are needed to maximise the scientific and public health value of data re-use in VL and PKDL
The acquisition of rmpADC can increase virulence of classical Klebsiella pneumoniae in the absence of other hypervirulence-associated genes.
Get PDFKlebsiella pneumoniae is one of the most common causes of nosocomial infections, and the rise of drug-resistant K. pneumoniae strains is complicating treatment and contributing to a mounting global health crisis. K. pneumoniae has two pathotypes: classical (cKp) and hypervirulent (hvKp). CKp typically causes opportunistic infections in immunocompromised individuals in healthcare settings and often is multi-drug resistant. HvKp can be community-acquired and cause high-mortality infections in immunocompetent individuals. Concerningly, antibiotic-resistant cKp strains with hypervirulence-associated genes and traits have recently emerged. Determining if and how hv-associated genes contribute to increased virulence of cKp strains is essential to addressing this growing threat. The rmpADC operon is an hv-associated locus that confers hypermucoviscosity (HMV), a key virulence phenotype, and rmp genes are often found in convergent strains. In this study, we aimed to determine if the rmp genes alone could increase the virulence of cKp strains in the absence of other hv-associated genes. We introduced genetically distinct rmp loci from different lineages into a broad array of cKp isolates and found that, while many isolates became HMV positive, only a subset of these strains showed an increase in virulence in a mouse model of pneumonia. Sequence type and capsule type were not predictive of how rmp acquisition impacted the clinical isolates. Our results indicate that HMV is likely necessary but not sufficient for hypervirulence and that rmp sequence can influence virulence potential in cKp strains.IMPORTANCEKlebsiella pneumoniae is a global pathogen, and gene exchange between hypervirulent (hvKp) and classical (cKp) strains is a rising threat. It is essential to understand how hvKp genes impact virulence phenotypes and identify the cKp strain backgrounds most amenable to enhanced virulence. Hypermucoviscosity (HMV) is a critical virulence factor in hypervirulent K. pneumoniae, conferred by the rmpADC locus. The rmp genes are encoded on mobile genetic elements and have been detected in convergent antibiotic-resistant K. pneumoniae strains of concern. In this study, we explored the impact of rmp acquisition in a broad set of classical clinical isolates. We observed that HMV appears necessary, but not sufficient, for increased virulence. Sequence type, capsule type, and HMV capacity could not predict which classical isolates gain an rmp-dependent colonization benefit. These insights increase our understanding of the distinctions between cKp and hvKp and further our ability to identify and treat new strains of concern