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Modern Applied Statistics With S

https://dro.deakin.edu.au/eserv/DU:30146218/sharifulislam-globalburden-2020.pdf

Global Burden of Cardiovascular Diseases and Risk Factors, 1990–2019: Update From the GBD 2019 Study

Urban greening to cool towns and cities: a systematic review of the empirical evidence.

The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, oncological, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. The findings of the Rotterdam Study have been presented in over a 1,000 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.

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The Rotterdam Study: Objectives and design update

Heat is an environmental and occupational hazard. The prevention of deaths in the community caused by extreme high temperatures (heat waves) is now an issue of public health concern. The risk of heat-related mortality increases with natural aging, but persons with particular social and/or physical vulnerability are also at risk. Important differences in vulnerability exist between populations, depending on climate, culture, infrastructure (housing), and other factors. Public health measures include health promotion and heat wave warning systems, but the effectiveness of acute measures in response to heat waves has not yet been formally evaluated. Climate change will increase the frequency and the intensity of heat waves, and a range of measures, including improvements to housing, management of chronic diseases, and institutional care of the elderly and the vulnerable, will need to be developed to reduce health impacts.

https://www.annualreviews.org/doi/pdf/10.1146/annurev.publhealth.29.020907.090843

Heat Stress and Public Health: A Critical Review

Complémentarité de sources de données pour l’évaluation du dispositif VigilanS, France, 2015-2017

Objecive The study aims to evaluate the potential impact of the revision of the thesaurus used by ED physicians to code medical diagnoses, on the syndromic indicators used daily to achieve the detection objective of the French syndromic surveillance system. Introduction As part of the French syndromic surveillance system SurSaUD®, the French Public Health Agency (Sante publique France) collects daily data from the emergency department (ED) network OSCOUR® [1]. The system aims to timely identify, follow and assess the health impact of unusual or seasonal events on emergency medical activity. Individual ED data contain demographic (age, gender, residence zip code), administrative (dates of attendances and discharge, ED, etc.) and medical information (chief complaint, main and associated medical diagnoses, severity). Medical diagnoses are encoded using the ICD10 classification. Then syndromic groups are built based on these ICD10 codes for ensuring syndromic surveillance in routine. Even if ICD10 is recommended on the national guidelines for coding ED attendances, this thesaurus offers a too large variety of codes. Particularly, it includes lots of diseases that may never be observed or confirmed in ED. This variety let selection of the appropriate codes difficult for physicians in a reactive use and could discourage them to code diagnoses. In order to encourage appropriate and reactive coding practice, we decided in 2017 to produce a new diagnoses thesaurus with a limited list of ICD10 codes. Then a committee of medical and epidemiological experts was created by the Federation of regional emergency observatories (FedORU), to propose an operational thesaurus that includes relevant codes for both ED in a daily routine practice and syndromic surveillance. Methods The committee has met 10 times since 2017. Since it would have been hard to work on the complete ICD10 list, the work was based on a more limited thesaurus already used by part of French ED. Only codes, which were pertinent regarding ED activity and interest for public health alert, have been considered. The main principles that have guided the selection were to 1) keep codes related to diagnoses that physicians are able to diagnose on a clinical basis or with rapid diagnostic tests, 2) remove diagnoses providing redundant information regarding other variables (such as circumstantial information) and 3) ensure that a substitution code was kept when a removed code was frequently used or was of interest for syndromic surveillance. Among the 86 syndromic groups defined on the basis of a list of ICD10 codes selected in the complete thesaurus, 34 are daily analyzed by Sante publique France for outbreak detection and early assessment of public health events. Those 34 syndromic groups have been recalculated by considering the revised thesaurus on a three-year period (from 2015 to 2017) at national level. In order to measure the potential impact of the revised thesaurus on the syndromic groups, we have considered three evaluation measures: 1. the proportion of ICD10 codes deleted (removal rate) from the initial definition of each syndromic group, due to the limitation of the thesaurus (calculated for the 86 syndromic groups); 2. the mean difference in the daily number of attendances between the initial and the new versions of each syndromic group (calculated for the 34 syndromic groups); 3. the linear correlation coefficient between the daily numbers of attendances of the initial and the new version of each syndromic group, in order to assess if the daily fluctuations of the new syndromic group are similar to those of the initial syndromic group (calculated for the 34 syndromic groups). Results Among the 86 syndromic groups, 75 (85%) have been impacted by the revised thesaurus, which implied codes removal. Among those 75 syndromic groups, the number of ICD10 codes included in their definition has been reduced by 71% on average. This removal rate varied between 17% and 100%. Syndromic groups including initially more than 100 codes have been the most concerned by a limitation of the number of ICD10 codes. Among the 34 syndromic groups daily analyzed for outbreak detection, 32 have been impacted by code removal with a mean removal rate of 68% (0%-97%). On average, 77% of daily attendances have been retained by the new version of syndromic groups, varying from 15% to 100%. Only 3 syndromic groups have kept less than 60% of attendances: Decrease of well-being (36%), Conjunctivitis (32%) and Hypothermia (15%). On average, the correlation coefficient has been of 0.96, varying from 0.57 to 1. The lowest values have been observed for the same three syndromic groups listed above: Decrease of well-being (0.57), Conjunctivitis (0.91) and Hypothermia (0.59). 18 among the 34 syndromic groups had a correlation coefficient higher than 0.99. Conclusions The study showed that most of the syndromic groups were impacted by the revised thesaurus, which resulted in a removal of about two thirds of the ICD10 codes usually considered in daily surveillance. However, more than three quarters of attendances were still retained in the new syndromic groups. This new thesaurus was conceived to rationalize the number of diagnoses codes but a substitution code was systematically proposed to replace removed codes. Those results highlighted that a large number of codes included in the complete ICD10 thesaurus were rarely used and that the most frequent codes were kept in the revised thesaurus version. However, this study showed that a few syndromic groups were strongly impacted by the revised thesaurus and can suffer of reduced performances to detect unusual variations. Based on those results, a second round of exploration of specific parts of the complete ICD10 thesaurus will be necessary to adapt either syndromic groups or the revised thesaurus. Even if the number of attendances may be reduced due to the removal of ICD10 codes, temporal variations remain similar for the majority of syndromic groups. Syndromic surveillance system does not aim to provide exhaustive quantification of attendances for a pathology, but aims to be able to detect expected or unusual public health variations. These evaluation results correspond to the worst-case scenario assuming that ED physicians will not modify their encoding habits by using the substitution codes but keep using their current thesaurus. However, we expect that this new and simplified version will facilitate diagnosis encoding task and lead toward a better diagnosis encoding rate. Once this new thesaurus will be widely used, we can expect a substantial improvement of the quality of ED medical data and then of syndromic surveillance results. Finally, this study enhances the importance that both data providers and epidemiologists in charge of syndromic surveillance work closely, in order to improve system in shared objectives. References [1] Fouillet A, Bousquet V, Pontais I, Gallay A, Caserio-Schonemann C. The French emergency department OSCOUR network: evaluation after a 10-year existence. Online J Public Health Inform. 2015; 7(1): e74.

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Impact of a new diagnoses thesaurus on the French ED syndromic surveillance system

Meeting Abstracts from the International Burden of Disease Conference 2022

Abstract Aims Mitigation actions during the COVID-19 pandemic may impact mental health and suicide in general populations. We aimed to analyse the evolution in suicide deaths from 2020 to March 2022 in France. Methods Using free-text medical causes in death certificates, we built an algorithm, which aimed to identify suicide deaths. We measured its retrospective performances by comparing suicide deaths identified using the algorithm with deaths which had either a Tenth revision of the International Classification of Diseases (ICD-10) code for ‘intentional self-harm’ or for ‘external cause of undetermined intent’ as the underlying cause. The number of suicide deaths from January 2020 to March 2022 was then compared with the expected number estimated using a generalized additive model. The difference and the ratio between the observed and expected number of suicide deaths were calculated on the three lockdown periods and for periods between lockdowns and after the third one. The analysis was stratified by age group and gender. Results The free-text algorithm demonstrated high performances. From January 2020 to mid-2021, suicide mortality declined during France’s three lockdowns, particularly in men. During the periods between and after the two first lockdowns, suicide mortality remained comparable to the expected values, except for men over 85 years old and in 65–84 year-old age group, where a small number of excess deaths was observed in the weeks following the end of first lockdown, and for men aged 45–64 years old, where the decline continued after the second lockdown ended. After the third lockdown until March 2022, an increase in suicide mortality was observed in 18–24 year-old age group for both genders and in men aged 65–84 years old, while a decrease was observed in the 25–44 year-old age group. Conclusions This study highlighted the absence of an increase in suicide mortality during France’s COVID-19 pandemic and a substantial decline during lockdown periods, something already observed in other countries. The increase in suicide mortality observed in 18–24 year-old age group and in men aged 65–84 years old from mid-2021 to March 2022 suggests a prolonged impact of COVID-19 on mental health, also described on self-harm hospitalizations and emergency department’s attendances in France. Further studies are required to explain the factors for this change. Reactive monitoring of suicide mortality needs to be continued since mental health consequences and the increase in suicide mortality may be continued in the future with the international context.

Reactive surveillance of suicides during the COVID-19 pandemic in France, 2020 to March 2022

Abstract Background The effective reproduction number (Rt) represents the average number of secondary cases generated by an infected person. During an outbreak, near-real-time monitoring of Rt constitutes a key indicator for detecting changes in disease transmission and assessing the effectiveness of interventions. The estimation of Rt usually requires identifying infected cases in the population which is in practice challenging from available data. The purpose of this study was to compare Rt estimates for COVID-19 surveillance in France based on three data sources of different sensitivity and specificity for identifying infected cases. Methods By applying a statistical method developed by Cori et al., we estimated Rt using (1) confirmed cases identified from positive virological tests among the tested population (2) suspected cases recorded by a national network of emergency departments (3) hospital admissions for COVID-19 recorded by a national administrative system to manage hospital's organization. Results From June 2020 to March 2022, the estimates of Rt in France showed similar temporal trends regardless of the dataset. Estimates based on the daily number of confirmed cases provided an earlier signal that the two other sources, with a lag of 3 and 6 days compared to estimates based on emergency department visits and hospital admissions, respectively. Conclusions The COVID-19 experience has proven that monitoring temporal changes in Rt was a key indicator to help public health authorities controlling the outbreak in real time. Having data on infected people in the population to estimate the Rt is not straightforward in practice. As this study has shown, the opportunity of using more readily available data, provided that it is highly correlated with the spread of infection, gives a practical solution for monitoring the COVID-19 epidemic and any epidemic in general. Key messages • The effective reproduction number (Rt) is a key parameter to monitor transmission during epidemics but its estimation from available data is often a critical issue. • Based on COVID-19 experience, data sufficiently correlated with the spread of infection may be appropriate to estimate Rt and monitor its temporal trend.

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Anne Fouillet

Papers

Complémentarité de sources de données pour l’évaluation du dispositif VigilanS, France, 2015-2017

Impact of a new diagnoses thesaurus on the French ED syndromic surveillance system

Meeting Abstracts from the International Burden of Disease Conference 2022

Reactive surveillance of suicides during the COVID-19 pandemic in France, 2020 to March 2022

Monitoring the reproduction number of COVID-19 in France: estimates compared from 3 datasets