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Background Workplace absenteeism increases significantly during influenza epidemics. Sick leave records may facilitate more timely detection of influenza outbreaks, as trends in increased sick leave may precede alerts issued by sentinel surveillance systems by days or weeks. Sick leave data have not been comprehensively evaluated in comparison to traditional surveillance methods. The aim of this paper is to study the performance and the feasibility of using a detection system based on sick leave data to detect influenza outbreaks. Methods Sick leave records were extracted from private French health insurance data, covering on average 209,932 companies per year across a wide range of sizes and sectors. We used linear regression to estimate the weekly number of new sick leave spells between 2016 and 2017 in 12 French regions, adjusting for trend, seasonality and worker leaves on historical data from 2010 to 2015. Outbreaks were detected using a 95%-prediction interval. This method was compared to results from the French Sentinelles network, a gold-standard primary care surveillance system currently in place. Results Using sick leave data, we detected 92% of reported influenza outbreaks between 2016 and 2017, on average 5.88 weeks prior to outbreak peaks. Compared to the existing Sentinelles model, our method had high sensitivity (89%) and positive predictive value (86%), and detected outbreaks on average 2.5 weeks earlier. Conclusion Sick leave surveillance could be a sensitive, specific and timely tool for detection of influenza outbreaks.

International audience; Background: Circulation of multidrug-resistant bacteria (MRB) in healthcare facilities is a major public health problem. These settings have been greatly impacted by the Coronavirus Disease 2019 (COVID-19) pandemic, notably due to surges in COVID-19 caseloads and the implementation of infection control measures. We sought to evaluate how such collateral impacts of COVID-19 impacted the nosocomial spread of MRB in an early pandemic context.Methods and findings: We developed a mathematical model in which Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and MRB cocirculate among patients and staff in a theoretical hospital population. Responses to COVID-19 were captured mechanistically via a range of parameters that reflect impacts of SARS-CoV-2 outbreaks on factors relevant for pathogen transmission. COVID-19 responses include both "policy responses" willingly enacted to limit SARS-CoV-2 transmission (e.g., universal masking, patient lockdown, and reinforced hand hygiene) and "caseload responses" unwillingly resulting from surges in COVID-19 caseloads (e.g., abandonment of antibiotic stewardship, disorganization of infection control programmes, and extended length of stay for COVID-19 patients). We conducted 2 main sets of model simulations, in which we quantified impacts of SARS-CoV-2 outbreaks on MRB colonization incidence and antibiotic resistance rates (the share of colonization due to antibiotic-resistant versus antibiotic-sensitive strains). The first set of simulations represents diverse MRB and nosocomial environments, accounting for high levels of heterogeneity across bacterial parameters (e.g., rates of transmission, antibiotic sensitivity, and colonization prevalence among newly admitted patients) and hospital parameters (e.g., rates of interindividual contact, antibiotic exposure, and patient admission/discharge). On average, COVID-19 control policies coincided with MRB prevention, including 28.2% [95% uncertainty interval: 2.5%, 60.2%] fewer incident cases of patient MRB colonization. Conversely, surges in COVID-19 caseloads favoured MRB transmission, resulting in a 13.8% [-3.5%, 77.0%] increase in colonization incidence and a 10.4% [0.2%, 46.9%] increase in antibiotic resistance rates in the absence of concomitant COVID-19 control policies. When COVID-19 policy responses and caseload responses were combined, MRB colonization incidence decreased by 24.2% [-7.8%, 59.3%], while resistance rates increased by 2.9% [-5.4%, 23.2%]. Impacts of COVID-19 responses varied across patients and staff and their respective routes of pathogen acquisition. The second set of simulations was tailored to specific hospital wards and nosocomial bacteria (methicillin-resistant Staphylococcus aureus, extended-spectrum beta-lactamase producing Escherichia coli). Consequences of nosocomial SARS-CoV-2 outbreaks were found to be highly context specific, with impacts depending on the specific ward and bacteria evaluated. In particular, SARS-CoV-2 outbreaks significantly impacted patient MRB colonization only in settings with high underlying risk of bacterial transmission. Yet across settings and species, antibiotic resistance burden was reduced in facilities with timelier implementation of effective COVID-19 control policies.Conclusions: Our model suggests that surges in nosocomial SARS-CoV-2 transmission generate selection for the spread of antibiotic-resistant bacteria. Timely implementation of efficient COVID-19 control measures thus has 2-fold benefits, preventing the transmission of both SARS-CoV-2 and MRB, and highlighting antibiotic resistance control as a collateral benefit of pandemic preparedness.

International audience; Pesticides, pollution de l’air, de l’eau et des aliments, changements climatiques, menaces biologiques, chimiques, radiologiques, épidémies et inégalités environnementales de santé… Les sujets d’inquiétude quant aux conséquences de la dégradation de l’environnement sur notre santé sont nombreux et ont besoin d’être compris et analysés à l’aide des connaissances scientifiques actuelles. Unique dans le paysage éditorial et scientifique francophone, cet ouvrage présente les méthodes et approches de la santé publique environnementale d’aujourd’hui. Cette 2e édition s’enrichit de nouvelles perspectives comme la démarche « Une seule santé », le concept d’exposome, et offre une vision globale des impacts sanitaires des changements climatiques. Présentant les grands défis écologiques et les inégalités socio-environnementales de notre temps, plus de 150 auteurs s’appuient sur les données les plus récentes, établissent des objectifs au gré d’exemples illustrés et d’études de cas en Europe, en Afrique et en Amérique du Nord. Alors que les programmes axés sur la santé publique, la santé environnementale, la santé au travail et les sciences de l’environnement connaissent un engouement sans précédent, cet ouvrage est une référence pour les étudiants, enseignants, chercheurs et professionnels de ces disciplines, ainsi que pour les organisations publiques et associatives dans toute la francophonie. (R.A.)

International audience; BackgroundHealthcare settings, where invasive procedures are frequently performed, may play an important role in the transmission dynamics of blood-borne pathogens when compliance with infection control precautions is suboptimal.AimsTo understand and quantify the role of hospital-based invasive procedures on hepatitis C virus (HCV) transmission.MethodsWe conducted a systematic review and meta-analysis to identify recent studies reporting association measures of HCV infection risk that are linked to iatrogenic procedures. Based on expert opinion, invasive procedures were categorised into 10 groups for which pooled measures were calculated. Finally, the relationship between pooled measures and the country-level HCV prevalence or the Healthcare Access and Quality (HAQ) index was assessed by meta-regression.ResultsWe included 71 studies in the analysis. The most frequently evaluated procedures were blood transfusion (66 measures) and surgery (43 measures). The pooled odds ratio (OR) of HCV infection varied widely, ranging from 1.46 (95% confidence interval: 1.14–1.88) for dental procedures to 3.22 (1.7–6.11) for transplantation. The OR for blood transfusion was higher for transfusions performed before 1998 (3.77, 2.42–5.88) than for those without a specified/recent date (2.20, 1.77–2.75). In procedure-specific analyses, the HCV infection risk was significantly negatively associated with the HAQ for endoscopy and positively associated with HCV prevalence for endoscopy and surgery.ConclusionsVarious invasive procedures were significantly associated with HCV infection. Our results provide a ranking of procedures in terms of HCV risk that may be used for prioritisation of infection control interventions, especially in high HCV prevalence settings.

In response to the COVID-19 pandemic, many countries have adopted a broad spectrum of containment measures, from recommendations to stay at home to quarantines of large geographic regions. As part of this response, corporations and governments alike have strongly encouraged workers to telecommute where possible. More than 3.4 billion people in 84 countries have been confined to their homes, as estimated in late March 2020, which potentially translates to many millions of workers temporarily exposed to telecommuting. Since 2000, the emergence of digital and broadband internet has facilitated the development of home telework. Despite limited research interest on its impact on occupational health, several health benefits and risks of telework have been identified in academic or grey literature (table 1) (for a review see Ref. 1). …

ObjectivesTo quantify the burden of COVID-19-related sick leave during the first pandemic wave in France, accounting for sick leaves due to symptomatic COVID-19 (‘symptomatic sick leaves’) and those due to close contact with COVID-19 cases (‘contact sick leaves’).MethodsWe combined data from a national demographic database, an occupational health survey, a social behaviour survey and a dynamic SARS-CoV-2 transmission model. Sick leave incidence from 1 March 2020 to 31 May 2020 was estimated by summing daily probabilities of symptomatic and contact sick leaves, stratified by age and administrative region.ResultsThere were an estimated 1.70M COVID-19-related sick leaves among France’s 40M working-age adults during the first pandemic wave, including 0.42M due to COVID-19 symptoms and 1.28M due to COVID-19 contacts. There was great geographical variation, with peak daily sick leave incidence ranging from 230 in Corse (Corsica) to 33 000 in Île-de-France (the greater Paris region), and greatest overall burden in regions of north-eastern France. Regional sick leave burden was generally proportional to local COVID-19 prevalence, but age-adjusted employment rates and contact behaviours also contributed. For instance, 37% of symptomatic infections occurred in Île-de-France, but 45% of sick leaves. Middle-aged workers bore disproportionately high sick leave burden, owing predominantly to greater incidence of contact sick leaves.ConclusionsFrance was heavily impacted by sick leave during the first pandemic wave, with COVID-19 contacts accounting for approximately three-quarters of COVID-19-related sick leaves. In the absence of representative sick leave registry data, local demography, employment patterns, epidemiological trends and contact behaviours can be synthesised to quantify sick leave burden and, in turn, predict economic consequences of infectious disease epidemics.

International audience

International audience; BACKGROUND:In nursing homes, the infectious risk is high, making infection control using approaches such as hand hygiene (HH) a major issue. However, the effectiveness of HH in these settings is not well documented, and HH compliance is low.METHODS:We systematically searched PubMed, Scopus, Web of Science, and Cochrane Clinical Trials for studies in nursing homes that either described a HH-related intervention or assessed HH compliance and included a measured infectious outcome. Two reviewers independently performed the study selection.RESULTS:Fifty-six studies met the inclusion criteria and were reviewed. Most were outbreak reports (39%), followed by observational studies (23%), controlled trials (23%), and before-after intervention studies (14%). Thirty-five studies (63%) reported results in favor of HH on at least one of their outcome measures; in addition, the infection control success rate was higher when at least one HH-related intervention (eg, staff education on HH, increased availability of handrub solution) was included (70% vs 30% for no intervention). However, only 25% of randomized trials concluded that HH-related interventions led to a reduction in the infectious risk.CONCLUSION:The results of this systematic review suggest that more evidence on HH effectiveness in nursing homes is needed. Future interventional studies should enhance methodologic rigor using clearly defined outcome measures, standardized reporting of findings, and a relevant HH observation tool.

The latest events such as the spread over Asia, Europe and Africa of the Highly Pathogenic Avian Influenza (HPAI) virus H5N1, the epidemic of A/H1N1pdm in 2009, the emergence of the Low Pathogenic Avian Influenza (LPAI) but zoonotic virus H7N9 in China in 2013 and the recent circulation of HPAI H5N8 in Europe, show that the permanent evolution of influenza virus in birds, humans and pigs is exposing the world to the risk of new strains with unpredictable consequences in public and animal health. In the last 10 years, a lot of efforts have been put in the improvement of capacity of animal and public health systems. However the disease is now endemic in several countries where the virus goes often undetected within the poultry population resulting in sporadic human cases and mortality. These countries are characterized by a large proportion of their population living in rural areas with poor incomes, a lack of primary care system and inefficient public or veterinary health sectors.Passive surveillance is often the only type of method feasible in poor rural settings in human and animal surveillance. With often incomplete, biased or delayed information this method will benefit from new methods of evaluation or new design concepts that could be implemented within a “One Health” framework to take into account the interfaces between human, animals and environment. We have in this thesis conceived and/or applied new methodologies for the evaluation, the design or the improvement of volunteer case-reporting of human or animal HPAI H5N1 in South-east Asia.We have first looked at different options of evaluation. We have applied stochastic scenario tree to model and assess the surveillance system of HPAI H5N1 in Thailand in backyard and free-range poultry production systems. We have estimated the sensitivity of the passive surveillance at 50% (CI95% 0.04-0.75) for a maximum detection of 3 infected farms, and showing the usefulness of this method to demonstrate freedom of disease in countries with limited resources. Thanks to participatory methods, we have involved Village Animal Health Workers (VAHWs) in their own evaluation and developed a new criteria grid, which includes local indicators of success developed and used by the VAHWs themselves.In a second part, we have considered methods to improve the design and the efficiency of passive surveillance. We have applied the grid conceived previously, to evaluate 251 VAHWs in three provinces of Cambodia. The grid allowed us to give a score to their level of activity and to analyse through logistic regression the factors influencing the most “good score”. Then we have implemented a pilot-study to test the use of SMS reporting from 112 participants from 68 villages, the objective was to detect peaks of mortality, to identify more rapidly outbreaks of infectious diseases. In a final section we have used multiple criteria decision analysis (MCDA) to map the risk of diffusion of HPAI H5N1 in poultry and in human, in order to adjust and reinforce the surveillance in the zones with greater risk of occurrence of the disease in Thailand and Cambodia.To conclude this work about tools and methods to improve surveillance systems in remote areas, we have done a comparative analysis of two challenging environments, Cambodia and Madagascar. We have done a cross analysis of the researches implemented by CIRAD (French Research Centre for International Development) in these countries during research projects implemented over the past decade. The objective was to show how new approaches for surveillance systems could be transferred between different countries with difficult socioeconomic environments and to propose new perspectives.; La propagation en Asie, Europe et Afrique du virus Influenza Aviaire hautement pathogène (IAHP) H5N1, l'épidémie de A/H1N1pdm en 2009, l'émergence de l'Influenza faiblement pathogène (IAFP), mais zoonotique, H7N9 en Chine en 2013 et la circulation récente de l'IAHP H5N8 en Europe, montrent que l'évolution permanente de ces virus chez les oiseaux, les humains et les porcs, pause un risque en santé humaine et animale au niveau mondial. Au cours des 10 dernières années, des efforts ont été fait pour renforcer les capacités en santé publique et vétérinaire. Malgré tout, le virus IAHP H5N1 reste endémique dans certains pays où il peut passer inaperçu dans les populations de volailles mais provoquent des cas humains. Ces pays sont caractérisés par une majorité de leur population vivant en zones rurales, une absence de systèmes de santé primaire et des secteurs de santé inefficaces.La surveillance passive (évènementielle) des maladies animales et humaines est souvent la seule méthode réalisable dans les milieux ruraux. Produisant une information incomplète, biaisée ou transmise avec des délais importants, elle a besoin d'être amélioré par des approches nouvelles mis en œuvre dans un cadre « One Health » prenant en compte les interfaces entre humains, animaux et environnement. Nous avons donc dans cette thèse conçu et/ou appliqué de nouvelles méthodes d'évaluation, de conception ou d'amélioration de la notification des cas d'IAHP H5N1 chez l'animal et chez l'homme en Asie du sud-est.Nous avons en premier examiné différentes alternatives d'évaluation. Nous avons appliqué des arbres de scénario (stochastique) pour modéliser et évaluer le système de surveillance de l'IAHP H5N1 en Thaïlande dans les systèmes traditionnels de productions avicoles. Nous avons estimé la sensibilité de la surveillance passive à 50 % (IC95 % 0,04-0,75) pour une détection maximale de 3 fermes infectées. Cela a montré l'utilité de cette méthode pour prouver l'absence de maladie dans les pays à ressources limitées. Par des méthodes participatives, nous avons impliqué les « agents communautaires de santé animale » dans leur propre évaluation et développé une nouvelle grille, qui comprend des indicateurs de succès utilisés par les agents eux-mêmes.Dans la seconde partie, nous avons examiné les méthodes pour améliorer la conception et l'efficacité de la surveillance passive. Nous avons appliqué la grille, pour évaluer 251 agents villageois dans trois provinces du Cambodge. La grille nous a permis de noter leur niveau d'activité et d'analyser, par régression logistique, les facteurs qui influencent l'obtention d'un score élevé. Puis, nous avons mis en place une étude pilote pour tester la déclaration par texto (SMS) auprès de 112 participants de 68 villages. L'objectif était de détecter des pics de mortalité et d'identifier plus rapidement les foyers de maladies infectieuses. Nous avons enfin utilisé l'analyse décisionnelle multicritère (MCDA) pour cartographier les risques de diffusion de l'IAHP H5N1 chez les volailles et les populations humaines en Thaïlande et au Cambodge, afin de renforcer la surveillance dans les zones à risque.En conclusion de ce travail, nous avons effectué une analyse comparative de deux environnements socio-économiques contraints : le Cambodge et Madagascar. Nous avons analysé les recherches mises en œuvre par le CIRAD (Centre Français de recherche pour le développement International) et ses partenaires dans ces 2 pays au cours de projets effectués ces 10 dernières années. L'objectif était de montrer comment de nouvelles approches pour les systèmes de surveillance peuvent être transférées entre différents pays aux contextes difficiles. A partir de cela, de nouvelles perspectives sont proposées.

Studies provide evidence that reduced nurse staffing resources are associated to an increase in health care-associated infections in intensive care units, but tools to assess the contribution of the mechanisms driving these relations are still lacking. We present an agent-based model of pathogen spread that can be used to evaluate the impact on nosocomial risk of alternative management decisions adopted to deal with transitory nurse shortage., We constructed a model simulating contact-mediated dissemination of pathogens in an intensive-care unit with explicit staffing where nurse availability could be temporarily reduced while maintaining requisites of patient care. We used the model to explore the impact of alternative management decisions adopted to deal with transitory nurse shortage under different pathogen- and institution-specific scenarios. Three alternative strategies could be adopted: increasing the workload of working nurses, hiring substitute nurses, or transferring patients to other intensive-care units. The impact of these decisions on pathogen spread was examined while varying pathogen transmissibility and severity of nurse shortage., The model-predicted changes in pathogen prevalence among patients were impacted by management decisions. Simulations showed that increasing nurse workload led to an increase in pathogen spread and that patient transfer could reduce prevalence of pathogens among patients in the intensive-care unit. The outcome of nurse substitution depended on the assumed skills of substitute nurses. Differences between predicted outcomes of each strategy became more evident with increasing transmissibility of the pathogen and with higher rates of nurse shortage., Agent-based models with explicit staff management such as the model presented may prove useful to design staff management policies that mitigate the risk of healthcare-associated infections under episodes of increased nurse shortage.

Musculoskeletal disorders (MSD) represent a major public health issue, affecting more then 40 million European workers in 2017. The overall aging of the working population is expected to increase the burden of disease, but temporal changes in exposures or diagnosis may also drive the global trends in MSD. We therefore conducted a systematic review to summarize the evidence on the role of demographic and temporal changes in the occurrence of MSD.We conducted a systematic review of articles reporting temporal trends in MSD in the general working-age population. Only articles controlling for age in the analysis were included. The risk of bias was assessed. The main indicators extracted were age-controlled time trends in MSD incidence or prevalence.Among 966 articles, 16 fulfilled the inclusion criteria, representing 23 results according to the indicators extracted. No study was found with a high risk of bias. Results presenting time trends in prevalence were found in 12 studies and incidence in 11. After controlling for age, the reported temporal trends varied, mostly between non-monotonic changes (N=12/23) and increases (N=10/23). One article also highlighted an increase among women and non-monotonic changes among men (N=1/23). Several factors other than aging were suggested to explain temporal trends in MSD, mainly trends in obesity, changing occupational exposures, and cultural factors regarding pain tolerance.This review shows that different kind of factors in addition to aging may contribute to varying or increasing trends in MSD. This review also highlighted the scarcity of evidence regarding time trends in the burden of MSD and their underlying causes.

Freshwater sports expose practitioners to pathogens in the water environment and may result in infection. In French Brittany, these infections are particularly worrying, especially since 2016 with an increase in the incidence of leptospirosis reaching 1 case per 100,000 inhabitants, which represents the highest incidence observed since 1920. We aimed to estimate the prevalence of infectious diseases related to freshwater sports practice and to identify the factors associated with these infections among freshwater sports licensees in Brittany, France. From March 18, 2019, to May 8, 2019, we interviewed freshwater sports licensees (online study) and club presidents and instructors (phone study) in Brittany. Licensee participants were 18 years old or more and practiced at least one freshwater sport in one of the 79 Brittany clubs. We used logistic regression models to study the association between our variables of interest and potential risk factors. In total, 551 licensees (20.3% of the total number of licensees) and 38 clubs (48.1%) were surveyed. Among the licensees, 29 (5.3%) reported being diagnosed with leptospirosis, of which 12 (41.3%) occurred in the last 5 years. The most reported symptoms were skin irritation/itchy skin (24.3%) and 39 individuals (7.1%) reported at least one hospitalization in their lifetime for a disease related to freshwater sports. The occurrence of leptospirosis was negatively associated with boarding from a pontoon (odds ratio (OR)=0.20, 95% confidence interval (95% CI) 0.06–0.56), practicing for less than 4 years (OR=0.17, 95% CI 0.04–0.56) compared to more than 10 years, and the occurrence of leptospirosis was positively associated with taking a soapy shower after practice (OR=4.38, 95% CI 1.90–10.51). Eskimo roll was positively associated with the occurrence of otitis and conjunctivitis (OR=3.22, 95% CI 1.82–6.03), and skin irritation/itchy skin (OR=1.66, 95% CI 0.99–2.84). Otitis, conjunctivitis, and skin irritation/itchy skin are the most commonly reported freshwater sport-related diseases in French Brittany. Despite a good level of knowledge of prevention measures, their implementation by licensees and clubs remains low. Further studies are needed to identify practices associated with infectious risk in freshwater sports.

IntroductionAlthough socioeconomic inequalities in HIV prevention, testing and treatment services have been well documented, their drivers remain poorly understood. Understanding the different pathways between socioeconomic position and HIV testing across different countries could help designing tailored programs aimed at reducing such inequalities.MethodsWe analysed data from Demographic and Health Surveys conducted between 2010 and 2018 in 18 sub-Saharan African countries (Burkina Faso, Cameroon, Côte d’Ivoire, Congo DR, Ethiopia, Guinea, Kenya, Lesotho, Liberia, Malawi, Mali, Niger, Rwanda, Senegal, Sierra Leone, Tanzania, Zambia and Zimbabwe). Using a potential outcomes framework and the product method, we decomposed the total effect linking wealth and recent (< 12 months) HIV testing into i) direct effects, and ii) indirect effects, via demand-related (related to individual’s ability to perceive need for care and inclination to seek care) or supply-related (related to individual’s ability to reach, pay for and engage in health care) mediators. Multivariable gender-specific modified Poisson models were fitted to estimate proportions mediated, while accounting for exposure-mediator interaction when present.ResultsA total of 392,044 participants were included in the analysis. Pro-rich wealth-related inequalities were observed in a majority of countries, with nine countries with high levels of inequalities among women and 15 countries among men.The indirect effects of each mediator varied greatly across countries. The proportion mediated tended to be higher for demand-related than for supply-related mediators. For instance, among women, HIV-related knowledge was estimated to mediate up to 12.1% of inequalities in Côte d’Ivoire; this proportion was up to 31.5% for positive attitudes toward people living with HIV (PLHIV) in Senegal. For the four supply-related mediators, the proportion mediated was systematically below 7%. Similar conclusions were found when repeating analyses on men for the demand-related mediators, with higher proportions mediated by positive attitudes toward PLHIV (up to 39.9% in Senegal).ConclusionsOur findings suggest that socioeconomic inequalities in HIV testing may be mediated by the demand-side more than supply-side characteristics, with important variability across countries. Overall, the important inter-country heterogeneity in pathways of socioeconomic inequalities in HIV testing illustrates that addressing inequalities requires tailored efforts as well as upstream interventions.A French version of the abstract is available upon request from the corresponding author.

International audience; Objective: To better understand the different pathways linking socioeconomic position and HIV testing uptake in 18 sub-Saharan African countries.Design: We used cross-sectional population-based surveys between 2010 and 2018.Methods: Using a potential outcomes framework and the product method, we decomposed the total effect linking wealth and recent (

This work presents an innovative epidemiological surveillance system in environmental health based on self-reported health indicators, closer to the complaints of the local population leaving around a source of environmental pollution: symptoms and loss of the quality of life. This approach is built up from a conceptual framework based on the psychometric theory and the transactional model of stress. A field application of this approach was carried out the population neighboring (n=1 495) the chemical industrial area of Salindres, Gard. This study verifies that self-reported health indicators measured with MOS SF-36 and SCL-90-R can be used to study populations exposed to multifactorial environmental risks. This study confirms that these indicators are relevant and sensitive when applied to environmental risk factors referring to the cognitive representations of risks, such as the sensorial perception of stimuli emitted by the industries. This work shows, besides, that the availability of national references for these indicators confers interpretability to these indicators, an essential quality criterion. This work discusses qualitatively the acceptability of measuring indicators of self-reported health in the population, proposes recommendations on communication for the setting of that kind of approach, and opens up avenues on management orientations., Ce travail présente un dispositif de surveillance épidémiologique novateur en santé environnementale fondée sur des évènements de santé déclarée, au plus près de la nature des plaintes exprimées par les populations : des symptômes et une dégradation de la qualité de vie. Ce dispositif est proposé à partir d’une réflexion conceptuelle reposant sur une revue de la littérature sur les théories psychométriques et le modèle transactionnel du stress et d’une application de terrain portant sur la population (n=1 495) riveraine du site industriel chimique de Salindres (Gard). Ces travaux permettent de vérifier les principales propriétés métriques d’indicateurs de santé déclarée mesurés, par les instruments MOS SF-36 et SCL-90-R, dans le cadre d’une population exposée à une pollution environnementale. Ils vérifient également l’adéquation et la sensibilité de ces indicateurs pour étudier les facteurs de risque environnementaux qui se réfèrent aux représentations cognitives des risques, comme la perception sensoriels des stimuli émis par les sites industriels. Ils montrent, en outre, que la disponibilité de références nationales portant sur la mesure de ces indicateurs leur confère un critère de qualité essentiel d’interprétation des résultats. Ces travaux apportent enfin des éléments d’appréciation de l’acceptabilité de la mesure des indicateurs de santé déclarée dans la population, des recommandations sur la communication pour la mise en œuvre d’un tel dispositif et des pistes de réflexion pour la gestion.

Kévin Jean,1,2 Ahmed Tawheed,3 Liem Binh Luong Nguyen,4 Tarek Heikal,5 Usama Eldaly,5 Neveen Elhadidy,6 Ahmed Elghaieb,7 Ahmed Aboudonia,7 Laura Tondeur,1 Amélie Dublineau,4 Arnaud Fontanet,2,4 Mohamed El-Kassas3 1Laboratoire MESuRS, Conservatoire national des arts et métiers, Paris, France; 2Unité PACRI, Institut Pasteur, Conservatoire national des arts et métiers, Paris, France; 3Endemic Medicine Department, Faculty of Medicine, Helwan University, Cairo, Egypt; 4Emerging Diseases Epidemiology Unit, Institut Pasteur, Université Paris-Cité, Paris, France; 5Medical Oncology Department, Damietta Oncology Center, Damietta, Egypt; 6Pharmaceutical Services Department, Damietta Oncology Center, Damietta, Egypt; 7Radiology Department, Damietta Oncology Center, Damietta, EgyptCorrespondence: Kévin Jean, Laboratoire MESuRS, Conservatoire national des arts et métiers, 292 rue Saint Martin, Paris, 75003, France, Email kevin.jean@lecnam.netIntroduction: We aimed to assess temporal changes in the presentation and survival of patients with hepatocellular carcinoma (HCC) in the northern Egypt region, one of the regions reporting the highest incidence of the disease globally.Methods: We conducted a monocentric retrospective study. Patients presenting at the Damietta Oncology referral center between 2007 and 2019 with a diagnosed HCC were eligible. Individual, clinical and tumor characteristics at HCC diagnosis, including the Barcelona Clinic Liver Cancer (BCLC) staging, were retrieved from medical files and patients’ final vital status was ascertained by combining various data sources. Patients were divided into 2 groups based on diagnosis period: pre- and post-2014. Survival was analysed based on Kaplan–Meier curves and differences in restricted mean survival time (RMST).Results: Data from 5097 patients (among 5210 eligible, 97.8%) were analyzed. We observed a significant trend toward HCC diagnosed at earlier stage in the post- vs pre-2014 period (BCLC stage 0/A or B: 37.2% vs 27.1%, p< 10− 3). Overall patient’s survival after the HCC diagnosis was poor, with a median of 8.1 months. The BCLC staging system performed well in predicting survival. Despite a trend toward HCC diagnosed at earlier stages, we did not observe a significant improvement in survival over time. Overall, treatments offered in this medical center were in line with international guidelines, and 16.1% of the patients who received a curative treatment had an improved survival (30.7 months in median). However, HCC recurrence was frequent among patients cured for HCC, with a median time to recurrence of 22 months.Discussion: Overall survival after HCC diagnosis in Egypt remains poor but is significantly improved by curative therapy. Despite a trend toward earlier diagnosis of HCC, we did not observe a general improvement in survival over time, which remains to be clearly understood.Keywords: hepatocellular carcinoma, liver cancer, Egypt, staging system, survival, epidemiology

ObjectiveHealthcare workers are at high risk of experiencing stress and fatigue due to the demands of their work within hospitals. Improving their physical and mental health and in turn, the quality and safety of care, requires considering factors at both individual and organizational levels. Using a multi-center prospective cohort, this study aims to identify the individual and organizational predictors of stress and fatigue of healthcare workers in several wards from university hospitals.MethodsOur cohort consist of 695 healthcare workers from 32 hospital wards drawn at random within four volunteer hospital centers in Paris-area. Three-level longitudinal analyses, accounting for repeated measures (level 1) across participants (level 2) nested within wards (level 3) and adjusted for relevant fixed and time varying confounders were performed.ResultsAt baseline, the sample was composed by 384 registered nurses, 300 auxiliary nurses and 11 midwives. According to the 3-level longitudinal models, some predictors were found in common for both stress and fatigue (low support from the hierarchy, low safety culture, overcommitment at work, presenteeism while sick…). However, specific predictors for high level of stress (negative life events, low support from the colleagues and high frequency of break cancellation) and fatigue (commuting duration, frequent use of interim staff in the ward…) were also found.ConclusionOur results may help identify at-risk healthcare workers and wards, where interventions to reduce stress and fatigue should be focused. These interventions could include manager training to favor better staff support and overall safety culture of healthcare workers.1.What is already known about this subject?Healthcare workers have high levels of perceived stress and fatigue, particularly in medical fields highly exposed to infectious risks.High occupational stress and fatigue can negatively affect healthcare workers behaviors in terms of absenteeism, and ultimately intention to leave as well as quality of care.Individual and organizational differences contribute to different perceptions and consequences of occupational stress and fatigue in healthcare workers.2.What are the new findings?The ward-level environment significantly influences the stress and fatigue of healthcare workers, in addition to individual factors and time variations.Hierarchy providing low support and with low safety culture, work overinvestment, presenteeism while sick, and working in smaller wards were identified as predictors of both high stress and fatigue of healthcare workers.Negative life events (whether personal or professional), low support from the colleagues and high frequency of break cancellation are specific predictors of high level of stress. While commuting duration, frequent use of interim staff and working in a medical ward were associated with high level of fatigue.3.How might this impact on policy or clinical practice in the foreseeable future?In this study, we can identify some areas for improvement to better prevent stress and fatigue for healthcare workers. High stress and fatigue can be reduced through mutual and specific organizational intervention strategies.

AimWe aimed to describe the characteristics of individuals infected by BA.4 or BA.5 in France in comparison to BA.1, and analyze the factors associated with hospitalization among BA.4 and BA.5 cases.MethodsA standardized questionnaire was used to collect information on confirmed and probable Omicron cases. Hospitalization risk factors among BA.4/BA.5 cases were analyzed using Poisson regression. Variables with a p-value below 0.2 in the univariate analysis and a priori confounders were included in the multivariable regression model.ResultsThe median age of the 301 cases investigated was 47 years and 97% of cases were symptomatic. The most common clinical signs were asthenia/fatigue (75.7%), cough (58.3%), fever (58.3%), headache (52.1%) and rhinorrhea (50.7%). Twelve cases were hospitalized, and 27.1% reported risk factors. No admissions to intensive care and no deaths were reported. Vaccination status was available for 292 cases, 20.9% were unvaccinated, 1.4% had received one dose, 38.3% two doses and 39.4% three doses. Cases presenting at least one risk factor were almost seventeen times more likely to be hospitalized than those with no risk factors (aRR = 16.72 [95% CI2.59–326.86]).ConclusionDespite the longer duration of and the differences in symptoms and their possible immune escape, BA.4/BA.5 Omicron sub-lineages globally showed no severe clinical presentation. The presence of at least one risk factor for severe disease significantly increased the risk of hospitalization for those infected with BA.4 or BA.5.

In response to the COVID-19 epidemic, Egypt established a unique care model based on quarantine hospitals where only externally-referred confirmed COVID-19 patients were admitted, and healthcare workers resided continuously over 1-to 2-week working shifts. While the COVID-19 risk for HCWs has been widely reported in standard healthcare settings, it has not been evaluated yet in quarantine hospitals.Here, we relied on longitudinal data, including results of routine RT-PCR tests, collected within three quarantine hospitals located in Cairo and Fayoum, Egypt. Using a model-based approach that accounts for the time-since-exposure variation in false-negative rates of RT-PCR tests, we computed the incidence of SARS-CoV-2 infection among HCWs. Over a total follow-up of 6,064 person-days (PD), we estimated an incidence rate (per 100 PD) of 1.05 (95% CrI: 0.58–1.65) at Hospital 1, 1.92 (95% CrI: 0.93–3.28) at Hospital 2 and 7.62 (95% CrI: 3.47–13.70) at Hospital 3. The probability for an HCW to be infected at the end of a shift was 13.7% (95% CrI: 7.8%–20.8%) and 23.8% (95% CrI: 12.2%–37.3%) for a 2-week shift at Hospital 1 and Hospital 2, respectively, which lies within the range of risk levels previously documented in standard healthcare settings, whereas it was >3-fold higher for a 7-day shift at Hospital 2 (42.6%, 95%CrI: 21.9%–64.4%). Our model-based estimates unveil a proportion of undiagnosed infections among HCWs of 46.4% (95% CrI: 18.8%–66.7%), 45.0% (95% CrI: 5.6%–70.8%) and 59.2% (95% CrI: 34.8%–78.8%), for Hospitals 1 to 3, respectively.The large variation in SARS-CoV-2 incidence we document here suggests that HCWs from quarantine hospitals may face a high occupational risk of infection, but that, with sufficient anticipation and infection control measures, this risk can be brought down to levels similar to those observed in standard healthcare settings.WHAT THIS PAPER ADDSWhat is already known on this topicPrevious studies conducted in standard care settings have documented that frontline healthcare workers (HCWs) face high risk of COVID-19. Whether risk levels differ in alternative care models, such as COVID-19 quarantine hospitals in Egypt where HCWs resided in the hospital days and nights for various durations, is unknown.What this study addsCOVID-19 risk for HCWs in quarantine hospitals varies substantially between facilities, from risk levels that are in the range of those documented in standard healthcare settings to levels that were approximatively 3 times higher.How this study might affect research, practice or policyWith sufficient anticipation and infection control measures, occupational COVID-19 risk for HCWs working in quarantine hospitals can be brought down to levels similar to those observed in standard healthcare settings.

BackgroundEnergy transition scenarios are prospective outlooks describing combinations of changes in socio-economic systems that are compatible with climate targets. These changes could have important health co-benefits. We aimed to quantify the health benefits of physical activity caused by active transportation on all-cause mortality in the French negaWatt scenario over the 2021-2050 period.MethodsRelying on a health impact assessment framework, we quantified the health benefits of increased walking, cycling and E-biking projected in the negaWatt scenario. The negaWatt scenario assumes increases of walking and cycling volumes of +11% and +612%, respectively, over the study period.ResultsAs compared to a scenario with no volume increase, we quantified that the negaWatt scenario would prevent 9,797 annual premature deaths in 2045 and translate into a 3-month increase of life expectancy in the general population. These health gains would generate €34 billion of economic benefits from 2045 onwards,ConclusionsIncreased physical activity implied in the negaWatt transition scenario would generate substantial public health benefits, which are comparable to the gain expected by large scale health prevention interventions.

International audience; Outbreaks of SARS-CoV-2 infection frequently occur in hospitals. Preventing nosocomial infection requires insight into hospital transmission. However, estimates of the basic reproduction number (R0) in care facilities are lacking. Analyzing a closely monitored SARS-CoV-2 outbreak in a hospital in early 2020, we estimated the patient-to-patient transmission rate and R0. We developed a model for SARS-CoV-2 nosocomial transmission that accounts for stochastic effects and undetected infections and fit it to patient test results. The model formalizes changes in testing capacity over time, and accounts for evolving PCR sensitivity at different stages of infection. R0 estimates varied considerably across wards, ranging from 3 to 15 in different wards. During the outbreak, the hospital introduced a contact precautions policy. Our results strongly support a reduction in the hospital-level R0 after this policy was implemented, from 8.7 to 1.3, corresponding to a policy efficacy of 85% and demonstrating the effectiveness of nonpharmaceutical interventions.

International audience; Colistin is a critically important antimicrobial for human medicine, and colistin-resistant Escherichia coli are commonly found in poultry and poultry products in Southeast Asia. Here, we aim at disentangling the within-farm and outside-farm drivers of colistin resistance in small-scale chicken farms of the Mekong delta of Vietnam. Nineteen Vietnamese chicken farms were followed up along a whole production cycle, during which weekly antimicrobial use data were recorded. At the beginning, middle and end of each production cycle, commensal E. coli samples from birds were collected, pooled and tested for colistin resistance. Twelve models were fitted to the data using an expectation-maximization algorithm and compared. We further tested the spatial clustering of the occurrence of resistance importations from external sources using the local Moran's I statistic. In the best model, colistin resistance in E. coli from chickens was found to be mostly affected by importations of resistance, and, to a lesser extent, by the use of antimicrobials in the last 1.73 weeks [0.00; 2.90], but not by the use of antimicrobials in day-olds, nor their colistin resistance carriage from hatchery. The occurrence of external source importations proved to be sometimes spatially clustered, suggesting a role of local environmental sources of colistin resistance.

International audience

International audience; Objectives: Socioeconomic inequalities in HIV prevention services coverage constitute important barriers to global prevention targets, especially in sub-Saharan Africa (SSA). We aimed at monitoring these inequalities from population-based survey data in 18 SSA countries between 2010 and 2018.Methods: We defined eight HIV indicators aimed at capturing uptake of HIV prevention services among adult participants. Country-specific wealth-related inequalities were measured using the Relative and Slope Index of Inequalities (RII and SII, respectively) and then pooled using random-effects meta-analyses. We compared inequalities between African regions using the Wilcoxon rank-sum test.Results: The sample consisted of 358 591 participants (66% women). Despite variability between countries and indicators, the meta-analysis revealed significant levels of relative and absolute inequalities in six out of eight indicators: HIV-related knowledge, positive attitudes toward people with HIV (PWH), condom use at last sexual intercourse, participation to prevention of mother-to-child transmission programs, medical male circumcision and recent HIV testing. The largest inequalities were reported in condom use, with condom use reported five times more among the richest versus the poorest [RII = 5.02, 95% confidence interval (CI) 2.79–9.05] and in positive attitudes toward PWH, with a 32-percentage point difference between the richest and poorest (SII = 0.32, 95% CI 0.26–0.39). Conversely, no significant inequalities were observed in multipartnership and HIV seropositivity among youth. Overall, inequalities tended to be larger in West and Central vs. East and Southern African countries.Conclusion: Despite efforts to scale-up HIV-prevention programs, socioeconomic inequalities remain substantial over the continuum of HIV primary and secondary prevention in several SSA countries.

International audience; Les avancées techniques en biologie de synthèse rendent de plus en plus accessibles la modification ou même la fabrication de virus en laboratoire. Plusieurs travaux de recherche fondés sur la synthèse de pathogènes à potentiel pandémique ont créé la polémique au cours des années 2010 et, aujourd’hui encore, l’éventualité qu’une fuite de laboratoire soit à l’origine de la pandémie de Covid-19 fait débat. En France, un vide juridique subsiste concernant la synthèse de pathogènes modifiés. Une réflexion concertée vers un encadrement légal de ce type de recherche apparaît donc nécessaire et urgent pour que la recherche continue de représenter un bénéfice, plutôt qu’un risque, pour la société.

Healthcare facilities are vulnerable to SARS-CoV-2 introductions and subsequent nosocomial outbreaks. Antigen rapid diagnostic testing (Ag-RDT) is widely used for population screening, but its health and economic benefits as a reactive response to local surges in outbreak risk are unclear. We simulate SARS-CoV-2 transmission in a long-term care hospital with varying COVID-19 containment measures in place (social distancing, face masks, vaccination). Across scenarios, nosocomial incidence is reduced by up to 40-47% (range of means) with routine symptomatic RT-PCR testing, 59-63% with the addition of a timely round of Ag-RDT screening, and 69-75% with well-timed two-round screening. For the latter, a delay of 4-5 days between the two screening rounds is optimal for transmission prevention. Screening efficacy varies depending on test sensitivity, test type, subpopulations targeted, and community incidence. Efficiency, however, varies primarily depending on underlying outbreak risk, with health-economic benefits scaling by orders of magnitude depending on the COVID-19 containment measures in place., Healthcare facilities are vulnerable to SARS-CoV-2 introductions and subsequent nosocomial outbreaks. Here, the authors simulate transmission in a long-term care facility with varying containment measures in place and evaluate reactive response with antigen rapid diagnostic testing.

ObjectiveHealthcare workers (HCWs) are at high risk of experiencing stress and fatigue due to the demands of their work within hospitals. Improving their physical and mental health and, in turn, the quality and safety of care requires considering factors at both individual and organisational/ward levels. Using a multicentre prospective cohort, this study aims to identify the individual and organisational predictors of stress and fatigue of HCWs in several wards from university hospitals.MethodsOur cohort consists of 695 HCWs from 32 hospital wards drawn at random within four volunteer hospital centres in Paris-area. Three-level longitudinal analyses, accounting for repeated measures (level 1) across participants (level 2) nested within wards (level 3) and adjusted for relevant fixed and time-varying confounders, were performed.ResultsAt baseline, the sample was composed by 384 registered nurses, 300 auxiliary nurses and 11 midwives. According to the three-level longitudinal models, some predictors were found in common for both stress and fatigue (low social support from supervisors, work overcommitment, sickness presenteeism and number of beds per ward). However, specific predictors for high level of stress (negative life events, low social support from colleagues and breaks frequently cancelled due to work overload) and fatigue (longer commuting duration, frequent use of interim staff in the ward) were also found.ConclusionOur results may help identify at-risk HCWs and wards, where interventions to reduce stress and fatigue should be focused. These interventions could include manager training to favour better staff support and overall safety culture of HCWs.

Background Carbapenemase-producing Enterobacteriaceae (CPE) cause resistant healthcare-associated infections that jeopardize healthcare systems and patient safety worldwide. The number of CPE episodes has been increasing in France since 2009, but the dynamics are still poorly understood. Objectives To use time-series modelling to describe the dynamics of CPE episodes from August 2010 to December 2016 and to forecast the evolution of CPE episodes for the 2017–20 period. Methods We used time series to analyse CPE episodes from August 2010 to November 2016 reported to the French national surveillance system. The impact of seasonality was quantified using seasonal-to-irregular ratios. Seven time-series models and three ensemble stacking models (average, convex and linear stacking) were assessed and compared with forecast CPE episodes during 2017–20. Results During 2010–16, 3559 CPE episodes were observed in France. Compared with the average yearly trend, we observed a 30% increase in the number of CPE episodes in the autumn. We noticed a 1 month lagged seasonality of non-imported episodes compared with imported episodes. Average stacking gave the best forecasts and predicted an increase during 2017–20 with a peak up to 345 CPE episodes (95% prediction interval = 124–1158, 80% prediction interval = 171–742) in September 2020. Conclusions The observed seasonality of CPE episodes sheds light on potential factors associated with the increased frequency of episodes, which need further investigation. Our model predicts that the number of CPE episodes will continue to rise in the coming years in France, mainly due to local dissemination, associated with bacterial carriage by patients in the community, which is becoming an immediate challenge with regard to outbreak control.

International audience; La pandémie du COVID-19 et le confinement instauré depuis le 17 mars 2020 plongent la population dans un isolement et une inquiétude collective sans précédent. Cette phase générera un stress post-traumatique inévitable, plus ou moins Q4 aigu selon les capacités de chacun à gérer les imprévus. Dès le retour au travail post-confinement COVID-19, les entreprises doivent faire face à une gestion particulière du stress et des troubles mentaux potentiels, dits aussi risques psychosociaux (RPS), auprès de leurs salariés. En l’absence d’actions de prévention, il serait prévisible d’observer dans le futur une inflation monotone de troubles mentaux des salariés et de la performance de l’entreprise. Les entreprises ont besoin ainsi de lignes directrices pertinentes pour orienter au mieux les plans d’action de prévention des troubles mentaux chez leurs salariés [4]. Elles doivent également évaluer le retour-surinvestissement des actions mises en place afin d’identifier les leviers d’action coût-efficaces.L’objectif de cet article est de fournir aux managers en entreprises une vision globale de la démarche à adopter en prévention des troubles mentaux, afin de réduire le lourd fardeau sanitaire et économique lié à ce phénomène, aggravé par les conséquences de la pandémie du COVID-19.

Resume Objectifs Dans le cadre de leur activite professionnelle, les sapeurs-pompiers sont exposes a de nombreux polluants, avec des consequences sanitaires significatives, comme le montrent les etudes epidemiologiques. L’objectif de ce travail etait d’evaluer quantitativement l’impact sanitaire de l’exposition aux fumees pour les sapeurs-pompiers de Paris et d’estimer les benefices potentiels d’un nouveau mode d’action permettant de modifier l’exposition, l’attaque d’attenuation. Methodes Nous avons tout d’abord etabli la liste des polluants presents dans les fumees, et estime les concentrations sur feux en France de 4 polluants majeurs. Puis nous avons determine la duree d’exposition vie entiere sans appareil respiratoire isolant dans un centre de secours parisien type. En nous appuyant sur des etudes recentes, nous avons estime comment des attaques d’attenuation modifieraient ces expositions. Enfin, nous avons utilise l’approche d’Evaluation Quantitative des Risques Sanitaires (EQRS) pour quantifier les risques associes a l’exposition aux fumees des sapeurs-pompiers de Paris, avec et sans attaques d’attenuation. Resultats L’EQRS predit un exces de risque de cancer individuel moyen de 3,7/100 000, se traduisant par un total de 0,18 cas de cancer en exces attendus chez l’ensemble des 4786 sapeurs-pompiers de Paris exposes aux fumees d’incendie. Pour les effets toxiques non cancerigenes, le quotient de danger calcule est largement superieur a 1 pour plusieurs polluants. L’attaque d’attenuation, qui conduit a une diminution des concentrations, permet de reduire le nombre de cancers en exces attendus et les quotients de danger d’environ un tiers, sans pour autant permettre de faire passer les quotients de danger en dessous de 1. Conclusions Des preconisations pour diminuer les risques sanitaires lies a l’exposition aux fumees d’incendie sont necessaires. Ces preconisations doivent etre facilement applicables et les plus simples possibles. De nouveaux modes d’extinction, tels que l’attaque d’attenuation pourraient s’averer une piste interessante.

Background Deaths due to vaccine preventable diseases cause a notable proportion of mortality worldwide. To quantify the importance of vaccination, it is necessary to estimate the burden averted through vaccination. The Vaccine Impact Modelling Consortium (VIMC) was established to estimate the health impact of vaccination. Methods We describe the methods implemented by the VIMC to estimate impact by calendar year, birth year and year of vaccination (YoV). The calendar and birth year methods estimate impact in a particular year and over the lifetime of a particular birth cohort, respectively. The YoV method estimates the impact of a particular year’s vaccination activities through the use of impact ratios which have no stratification and stratification by activity type and/or birth cohort. Furthermore, we detail an impact extrapolation (IE) method for use between coverage scenarios. We compare the methods, focusing on YoV for hepatitis B, measles and yellow fever. Results We find that the YoV methods estimate similar impact with routine vaccinations but have greater yearly variation when campaigns occur with the birth cohort stratification. The IE performs well for the YoV methods, providing a time-efficient mechanism for updates to impact estimates. Conclusions These methods provide a robust set of approaches to quantify vaccination impact; however it is vital that the area of impact estimation continues to develop in order to capture the full effect of immunisation.

International audience; The human microbiome can protect against colonization with pathogenic antibiotic-resistant bacteria (ARB), but its impacts on the spread of antibiotic resistance are poorly understood. We propose a mathematical modeling framework for ARB epidemiology formalizing within-host ARB-microbiome competition, and impacts of antibiotic consumption on microbiome function. Applied to the healthcare setting, we demonstrate a trade-off whereby antibiotics simultaneously clear bacterial pathogens and increase host susceptibility to their colonization, and compare this framework with a traditional strain-based approach. At the population level, microbiome interactions drive ARB incidence, but not resistance rates, reflecting distinct epidemiological relevance of different forces of competition. Simulating a range of public health interventions (contact precautions, antibiotic stewardship, microbiome recovery therapy) and pathogens ( Clostridioides difficile , methicillin-resistant Staphylococcus aureus , multidrug-resistant Enterobacteriaceae) highlights how species-specific within-host ecological interactions drive intervention efficacy. We find limited impact of contact precautions for Enterobacteriaceae prevention, and a promising role for microbiome-targeted interventions to limit ARB spread.

International audience

The contribution of bacteria in livestock to the global burden of antimicrobial resistance raises concerns worldwide. However, the dynamics of selection and diffusion of antimicrobial resistance in farm animals are not fully understood. Here, we used veal calf fattening farms as a model system, as they are a known reservoir of Extended Spectrum β-Lactamase-producing Escherichia coli (ESBL-EC). Longitudinal data of ESBL-EC carriage and antimicrobial use (AMU) were collected from three veal calf farms during the entire fattening process. We developed 18 agent-based mechanistic models to assess different hypotheses regarding the main drivers of ESBL-EC dynamics in calves. The models were independently fitted to the longitudinal data using Markov Chain Monte Carlo and the best model was selected. Within-farm transmission between individuals and sporadic events of contamination were found to drive ESBL-EC dynamics on farms. In the absence of AMU, the median carriage duration of ESBL-EC was estimated to be 19.6 days (95% credible interval: [12.7; 33.3]). In the best model, AMU was found to influence ESBL-EC dynamics, by affecting ESBL-EC clearance rather than acquisition. This effect of AMU was estimated to decrease gradually after the end of exposure and to disappear after 62.5 days [50.0; 76.9]. Moreover, using a simulation study, we quantified the efficacy of ESBL-EC mitigation strategies. Decreasing ESBL-EC prevalence by 50% on arrival at the fattening farm reduced prevalence at slaughter age by 33.3%. Completely eliminating the use of selective antibiotics had a strong effect on average ESBL-EC prevalence (relative reduction of 79.6%), but the effect was mild if this use was only decreased by 50% compared to baseline (relative reduction of 3.7%).

Understanding transmission routes of hospital-acquired infections (HAI) is key to improve their control. In this context, describing and analyzing dynamic inter-individual contact patterns in hospitals is essential. In this study, we used wearable sensors to detect Close Proximity Interactions (CPIs) among patients and hospital staff in a 200-bed long-term care facility over 4 months. First, the dynamic CPI data was described in terms of contact frequency and duration per individual status or activity and per ward. Second, we investigated the individual factors associated with high contact frequency or duration using generalized linear mixed-effect models to account for inter-ward heterogeneity. Hospital porters and physicians had the highest daily number of distinct contacts, making them more likely to disseminate HAI among individuals. Conversely, contact duration was highest between patients, with potential implications in terms of HAI acquisition risk. Contact patterns differed among hospital wards, reflecting varying care patterns depending on reason for hospitalization, with more frequent contacts in neurologic wards and fewer, longer contacts in geriatric wards. This study is the first to report proximity-sensing data informing on inter-individual contacts in long-term care settings. Our results should help better understand HAI spread, parameterize future mathematical models, and propose efficient control strategies.

ObjectiveTo identify the role of Staphylococcus aureus (SA) or its intracellular small-colony variant phenotype (SCV) with co-trimoxazole (CTX) or ANCA-associated vasculitis (AAV) activity.MethodsAll consecutive AAV patients with granulomatosis with polyangiitis (GPA), eosinophilic GPA or microscopic polyangiitis, followed at the French National Vasculitis Referral Center (09/2012–05/2013), and hospitalized non-AAV controls, exclusively for SA/SCV carriage comparisons, were enrolled. All had bilateral anterior nasal swab cultures. Nasal SA or SCV carriage was determined and associations with relapse(s), BVAS, ANCA-positivity, anti-staphylococcal and immunosuppressant use, were analysed ⩾4 years post-inclusion.ResultsNasal SA carriage rates did not differ among AAVs (P = 0.53): GPA (24/80; 30%), EGPA (7/28; 25%) and microscopic polyangiitis (3/11; 27.3%); and the rate was less frequent in controls than in GPA patients not taking CTX (P = 0.04). AAV patients taking CTX prophylaxis had less nasal SA carriage (8.7% vs 36.2%; P = 0.02). Nasal SA carriage or CTX use did not modify relapse rates, BVAS or ANCA-positivity at inclusion or during follow-up. Nasal SCV carriage, found in 15/207 (7.2%) patients, was similar for GPA (10/24; 41.7%), microscopic polyangiitis (2/7; 28.6%) and eosinophilic GPA (2/3; 66.7%), but higher (P = 0.02) than controls (1/14; 7.1%). SCV carriage by AAV groups did not modify relapse rates or ANCA positivity at inclusion or during follow-up; a trend towards higher BVAS was observed only for anti-PR3 ANCA patients.ConclusionNasal SA or SCV carriage was comparable among AAVs but more frequent than in controls. Nasal SA or SCV carriage and CTX use did not modify AAV relapse rates.

International audience

Background The Eliminate Yellow fever Epidemics (EYE) strategy was launched in 2017 in response to the resurgence of yellow fever in Africa and the Americas. The strategy relies on several vaccination activities, including preventive mass vaccination campaigns (PMVCs). However, to what extent PMVCs are associated with a decreased risk of outbreak has not yet been quantified. Methods and findings We used the self-controlled case series (SCCS) method to assess the association between the occurrence of yellow fever outbreaks and the implementation of PMVCs at the province level in the African endemic region. As all time-invariant confounders are implicitly controlled for in the SCCS method, this method is an alternative to classical cohort or case–control study designs when the risk of residual confounding is high, in particular confounding by indication. The locations and dates of outbreaks were identified from international epidemiological records, and information on PMVCs was provided by coordinators of vaccination activities and international funders. The study sample consisted of provinces that were both affected by an outbreak and targeted for a PMVC between 2005 and 2018. We compared the incidence of outbreaks before and after the implementation of a PMVC. The sensitivity of our estimates to a range of assumptions was explored, and the results of the SCCS method were compared to those obtained through a retrospective cohort study design. We further derived the number of yellow fever outbreaks that have been prevented by PMVCs. The study sample consisted of 33 provinces from 11 African countries. Among these, the first outbreak occurred during the pre-PMVC period in 26 (79%) provinces, and during the post-PMVC period in 7 (21%) provinces. At the province level, the post-PMVC period was associated with an 86% reduction (95% CI 66% to 94%, p < 0.001) in the risk of outbreak as compared to the pre-PMVC period. This negative association between exposure to PMVCs and outbreak was robustly observed across a range of sensitivity analyses, especially when using quantitative estimates of vaccination coverage as an alternative exposure measure, or when varying the observation period. In contrast, the results of the cohort-style analyses were highly sensitive to the choice of covariates included in the model. Based on the SCCS results, we estimated that PMVCs were associated with a 34% (95% CI 22% to 45%) reduction in the number of outbreaks in Africa from 2005 to 2018. A limitation of our study is the fact that it does not account for potential time-varying confounders, such as changing environmental drivers of yellow fever and possibly improved disease surveillance. Conclusions In this study, we provide new empirical evidence of the high preventive impact of PMVCs on yellow fever outbreaks. This study illustrates that the SCCS method can be advantageously applied at the population level in order to evaluate a public health intervention., In this cohort study, Kévin Jean and colleagues correlate lower risk of disease outbreaks with mass vaccination against yellow fever., Author summary Why was this study done? Yellow fever is a mosquito-borne, vaccine-preventable disease that may cause large urban outbreaks, especially in tropical African regions. Since 2006, preventive mass vaccination campaigns (PMVCs) have been implemented in many African provinces. These are large-scale vaccination campaigns targeting all or most age groups in a specific area. The preventive impact PMVCs may have on the risk of yellow fever outbreak has not been quantified yet. What did the researchers do and find? We used the self-controlled case series (SCCS) method to assess the association between PMVCs and outbreak risk at the province level in 34 African countries between 2005 and 2018. We compared pre- and post-PMVC periods within each province individually, thus implicitly controlling for all possible confounders that do not vary in time, especially the fact that provinces indicated for PMVCs are generally those considered at highest baseline risk of yellow fever (confounding by indication). At the province level, we estimated that implementation of PMVCs was associated with an 86% reduction (95% CI 66% to 94%) in the risk of yellow fever outbreak. A complete cohort analysis provided less reliable results than the SCCS method, likely because of confounding by indication that was not entirely controlled for by adjusting for known drivers of yellow fever. We further estimated that all PMVCs conducted between 2006 and 2018 in Africa may have reduced the total number of yellow fever outbreaks by 34% (95% CI 22% to 45%). What do these findings mean? These results provide new empirical evidence of the high preventive impact of PMVCs on yellow fever outbreaks. These results may encourage rapid rescheduling of yellow fever PMVCs that have been postponed due to the COVID-19 pandemic. The SCCS design may be advantageously applied at the population level to assess the impact of public health interventions.

Background Hospitals are suspected of playing a key role in HCV epidemic dynamics in Egypt. This work aimed at assessing HCV prevalence and associated risk factors in patients and health-care workers (HCWs) of Ain Shams University (ASU) hospitals in Cairo. Methods We included 500 patients admitted to the internal medicine or surgery hospital from February to July, 2017, as well as 50 HCWs working in these same hospitals. Participants were screened for anti-HCV antibodies and HCV RNA. A questionnaire was administered to collect data on demographic characteristics and medical/surgical history. For HCWs, questions on occupational exposures and infection control practices were also included. Results The overall prevalence of anti-HCV antibodies was 19.80% (95% CI: 16.54–23.52) among participating patients, and 8.00% (95% CI: 0.48–15.52) among participating HCWs. In HCWs, the only risk factors significantly associated with anti-HCV antibodies were age and profession, with higher prevalence in older HCWs and those working as cleaners or porters. In patients, in a multivariate logistic regression, age over 50 (aOR: 3.4 [1.9–5.8]), living outside Cairo (aOR: 2.1 [1.2–3.4]), admission for liver or gastro-intestinal complaints (aOR: 4.2 [1.8–9.9]), and history of receiving parenteral anti-schistosomiasis treatment (aOR: 2.7 [1.2–5.9]) were found associated with anti-HCV antibodies. Conclusions While HCV prevalence among patients has decreased since the last survey performed within ASU hospitals in 2008, it is still significantly higher than in the general population. These results may help better control further HCV spread within healthcare settings in Egypt by identifying at-risk patient profiles upon admission.

International audience; To date, no specific estimate of R0 for SARS-CoV-2 is available for healthcare settings. Using inter-individual contact data, we highlight that R0 estimates from the community cannot translate directly to healthcare settings, with pre-pandemic R0 values ranging 1.3-7.7 in three illustrative healthcare institutions. This has implications for nosocomial Covid-19 control.

ObjectiveThe benefit of direct-acting antivirals (DAAs) against HCV following successful treatment of hepatocellular carcinoma (HCC) remains controversial. This meta-analysis of individual patient data assessed HCC recurrence risk following DAA administration.DesignWe pooled the data of 977 consecutive patients from 21 studies of HCV-related cirrhosis and HCC, who achieved complete radiological response after surgical/locoregional treatments and received DAAs (DAA group). Recurrence or death risk was expressed as HCC recurrence or death per 100 person-years (100PY). Propensity score-matched patients from the ITA.LI.CA. cohort (n=328) served as DAA-unexposed controls (no-DAA group). Risk factors for HCC recurrence were identified using random-effects Poisson.ResultsRecurrence rate and death risk per 100PY in DAA-treated patients were 20 (95% CI 13.9 to 29.8, I2=74.6%) and 5.7 (2.5 to 15.3, I2=54.3), respectively. Predictive factors for recurrence were alpha-fetoprotein logarithm (relative risk (RR)=1.11, 95% CI 1.03 to 1.19; p=0.01, per 1 log of ng/mL), HCC recurrence history pre-DAA initiation (RR=1.11, 95% CI 1.07 to 1.16; pConclusionEffects of DAA exposure on HCC recurrence risk remain inconclusive. Active clinical and radiological follow-up of patients with HCC after HCV eradication with DAA is justified.

BackgroundYellow fever (YF) is a viral haemorrhagic fever endemic in tropical regions of Africa and South America. Current intervention policies, namely the Eliminate Yellow fever Epidemics (EYE) strategy are actioned through vaccination. However, the stockpiles and production mean that vaccination can be in short supply. As such, intervention strategies need to be optimised; one of the tools for doing this is mathematical modelling.MethodsWe fit a generalised linear model of YF reports to occurrence data available from 1987 to 2019 in Africa and South America and available serology survey data to estimate the force of infection across the continents. Then, using demographic and vaccination data, we examine the impact of interventions.FindingsWe estimate that in 2018 there were approximately 51,000 (95%CrI [31,000 - 82,000]) deaths due to YF in Africa and South America. When we examine the impact of mass vaccination campaigns in Africa, these amount to approximately 10,000 (95%CrI [6,000 - 17,000]) deaths averted in 2018 due to mass vaccination activities in Africa; this corresponds to a 47% reduction (95%CrI [10% - 77%]).InterpretationWe find that the majority, 92% (95%CrI [89% - 95%]), of global burden occurs in Africa and that mass vaccination activities have significantly reduced the current deaths per year due to YF. This methodology allows us to evaluate the effectiveness of vaccination campaigns past, present and future and illustrates the need for continued vigilance and surveillance of YF.FundingBMGF and MRC

Background High turnover among healthcare workers is an increasingly common phenomenon in hospitals worldwide, especially in intensive care units (ICUs). In addition to the serious financial consequences, this is a major concern for patient care (disrupted continuity of care, decreased quality and safety of care, increased rates of medication errors, …). Objective The goal of this article was to understand how the ICU-level nurse turnover rate may be explained from multiple covariates at individual and ICU-level, using data from 526 French registered and auxiliary nurses (RANs). Methods A cross-sectional study was conducted in ICUs of Paris-area hospitals in 2013. First, we developed a small extension of a multi-level modeling method proposed in 2007 by Croon and van Veldhoven and validated its properties using a comprehensive simulation study. Second, we applied this approach to explain RAN turnover in French ICUs. Results Based on the simulation study, the approach we proposed allows to estimate the regression coefficients with a relative bias below 7% for group-level factors and below 12% for individual-level factors. In our data, the mean observed RAN turnover rate was 0.19 per year (SD = 0.09). Based on our results, social support from colleagues and supervisors as well as long durations of experience in the profession were negatively associated with turnover. Conversely, number of children and impossibility to skip a break due to workload were significantly associated with higher rates of turnover. At ICU-level, number of beds, presence of intermediate care beds (continuous care unit) in the ICU and staff-to-patient ratio emerged as significant predictors. Conclusions The findings of this research may help decision makers within hospitals by highlighting major determinants of turnover among RANs. In addition, the new approach proposed here could prove useful to researchers faced with similar micro-macro data.

Introduction The Eliminate Yellow fever Epidemics (EYE) strategy was launched in 2017 in response to the resurgence of yellow fever in Africa and the Americas. The strategy relies on several vaccination activities, including preventive mass vaccination campaigns (PMVCs). However, by how much PMVCs are associated with a decreased risk of outbreak to occur has not yet been quantified. Methods and Findings We used the self-controlled case series (SCCS) method to assess the association between the occurrence of yellow fever outbreaks and the implementation of PMVCs at the province level in the African endemic region. As all time-invariant confounders are implicitly controlled for, the SCCS method is an alternative to classical cohort or case-control study designs when the risk of residual confounding is high, in particular confounding by indication. The location and dates of outbreaks were identified from international epidemiological records, and information on PMVCs was provided by coordinators of vaccination activities and international funders. The study sample consisted of provinces that were both affected by an outbreak and targeted for a PMVC between 2005 and 2018. We compared the relative incidence of outbreaks before and after the implementation of a PMVC. The sensitivity of our estimates to a range of assumptions was explored, and the results of the SCCS method were compared to those obtained through a retrospective cohort study design. We further derived the number of yellow fever outbreaks that have been prevented by PMVCs. The study sample consisted of 33 provinces from 11 African countries. Among these, outbreaks occurred during the pre-PMVC period in 26 (79%) provinces versus 7 (21%) occurring in the post-PMVC period. At the province level, the post-PMVC period was associated with a 86% reduction (95% Confidence interval 66% to 94%, p-value A limitation of our study is the fact that it does not account for potential time-varying confounders, such as changing environmental drivers of yellow fever or possibly improved disease surveillance. Conclusion In this study, we provide new empirical evidence of the high preventive impact of PMVCs on yellow fever outbreaks. This study illustrates that the SCCS method can be advantageously applied at the population level in order to evaluate a public health intervention. AUTHOR SUMMARY Why Was This Study Done? Yellow fever is a mosquito-borne vaccine-preventable disease that may cause large urban outbreaks, especially in tropical African regions. Since 2006, Preventive Mass Vaccination Campaigns (PMVCs) have been implemented in many African provinces. These are large scale vaccination campaigns targeting all or most age group in a specific area. The preventive impact PMVCs may have on the risk of yellow fever outbreak has not been quantified yet. What Did the Researchers Do and Find? We used the self-controlled case series (SCCS) method to assess the association between PMVCs and outbreak risk at the province level over 34 African countries between 2005 and 2018. Using this method, we compared pre- and post-PMVC period are compared within each province individually, thus controlling for all possible confounders that do not vary in time, especially the fact that provinces indicated for PMVCs are generally those considered at highest baseline risk of yellow fever (ie confounding by indication). At the province level, we estimated that implementation of PMVCs was associated with an 86% reduction (66% to 94%) in the risk of yellow fever outbreak. Results from a complete cohort analysis provided less reliable results than the SCCS method, likely because of confounding by indication that was not entirely controlled for by adjusting on known drivers of yellow fever. We further estimated that all PMVCs conducted between 2006 and 2018 in Africa may have reduced the total number of yellow fever outbreaks by 34% (22% to 45%). What Do These Findings Mean? These results provide new empirical evidence of the high preventive impact of PMVCs on yellow fever outbreaks. These results may encourage rapid re-scheduling of yellow fever PMVCs that have been postponed due to the COVID-19 pandemic. The SCCS design may be advantageously applied at the population level to assess the impact of public health interventions.

This work resulted from the MOD-COV Project (Modelling of the hOspital Dissemination of SARS-CoV-2), a collaboration between the Institut Pasteur, the Conservatoire Nationale des Arts et Métiers, and the AVIESAN/REACTing working group “Modelling SARS-CoV-2 dissemination in healthcare settings”, whose members we thank (Niccolo Buetti, Christian Brun-Buisson, Sylvie Burban, Simon Cauchemez, Guillaume Chelius, Anthony Cousien, Pascal Crepey, Vittoria Colizza, Christel Daniel, Aurélien Dinh, Pierre Frange, Eric Fleury, Antoine Fraboulet, Marie-Paule Gustin, Lidia Kardas-Sloma, Elsa Kermorvant, Jean Christophe Lucet, Chiara Poletto, Rodolphe Thiebaut, Sylvie van der Werf, Philippe Vanhems, Linda Wittkop, Jean-Ralph Zahar).We also thank the i-Bird Study Group (Anne Sophie Alvarez, Audrey Baraffe, Mariano Beiró, Inga Bertucci, Pierre-Yves Boëlle, Camille Cyncynatus, Florence Dannet, Marie Laure Delaby, Pierre Denys, Matthieu Domenech de Cellès, Eric Fleury, Antoine Fraboulet, Jean-Louis Gaillard, Boris Labrador, Jennifer Lasley, Christine Lawrence, Judith Legrand, Odile Le Minor, Caroline Ligier, Lucie Martinet, Karine Mignon, Catherine Sacleux, Jérôme Salomon, Thomas Obadia, Marie Perard, Laure Petit, Laeticia Remy, Anne Thiebaut, Damien Thomas, Philippe Tronchet, Isabelle Villain), as well as Jacob Barrett for helpful discussion.; International audience; Background: Long-term care facilities (LTCFs) are vulnerable to outbreaks of coronavirus disease 2019 (COVID-19). Timely epidemiological surveillance is essential for outbreak response, but is complicated by a high proportion of silent (non-symptomatic) infections and limited testing resources.Methods: We used a stochastic, individual-based model to simulate transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) along detailed inter-individual contact networks describing patient-staff interactions in a real LTCF setting. We simulated distribution of nasopharyngeal swabs and reverse transcriptase polymerase chain reaction (RT-PCR) tests using clinical and demographic indications and evaluated the efficacy and resource-efficiency of a range of surveillance strategies, including group testing (sample pooling) and testing cascades, which couple (i) testing for multiple indications (symptoms, admission) with (ii) random daily testing.Results: In the baseline scenario, randomly introducing a silent SARS-CoV-2 infection into a 170-bed LTCF led to large outbreaks, with a cumulative 86 (95% uncertainty interval 6-224) infections after 3 weeks of unmitigated transmission. Efficacy of symptom-based screening was limited by lags to symptom onset and silent asymptomatic and pre-symptomatic transmission. Across scenarios, testing upon admission detected just 34-66% of patients infected upon LTCF entry, and also missed potential introductions from staff. Random daily testing was more effective when targeting patients than staff, but was overall an inefficient use of limited resources. At high testing capacity (> 10 tests/100 beds/day), cascades were most effective, with a 19-36% probability of detecting outbreaks prior to any nosocomial transmission, and 26-46% prior to first onset of COVID-19 symptoms. Conversely, at low capacity (< 2 tests/100 beds/day), group testing strategies detected outbreaks earliest. Pooling randomly selected patients in a daily group test was most likely to detect outbreaks prior to first symptom onset (16-27%), while pooling patients and staff expressing any COVID-like symptoms was the most efficient means to improve surveillance given resource limitations, compared to the reference requiring only 6-9 additional tests and 11-28 additional swabs to detect outbreaks 1-6 days earlier, prior to an additional 11-22 infections.Conclusions: COVID-19 surveillance is challenged by delayed or absent clinical symptoms and imperfect diagnostic sensitivity of standard RT-PCR tests. In our analysis, group testing was the most effective and efficient COVID-19 surveillance strategy for resource-limited LTCFs. Testing cascades were even more effective given ample testing resources. Increasing testing capacity and updating surveillance protocols accordingly could facilitate earlier detection of emerging outbreaks, informing a need for urgent intervention in settings with ongoing nosocomial transmission.

At a time when sick leave is a sign of growing ill-being for workers and a cost burden for the society, the systematic digitalization and distribution of data offers great opportunities for its prevention. We have therefore taken advantage of this opportunity to develop a range of prevention tools based on statistical analysis methods. In a first part, this work proposes an analysis of the mechanisms explaining sick leave among workers. The analysis of a national survey has first identified and prioritised their main determinants using random forest. Then, an analysis of administrative data had helped to identify absence trajectories that could lead to serious sick leaves thanks to sequential analyses and multi-state modelling. In a second step, tools were developed to identify abnormal situations of sick leave at company level. A company typology was first built to produce benchmark values for companies to accurately assess their situation. Finally, an algorithm for identifying absence peaks, adapted from epidemiological surveillance models, was finally developed to automatically identify companies in difficulty.; Alors que les arrêts maladie sont le signe d’un mal-être croissant chez les salariés et qu’ils pèsent un coût certain pour la collectivité, la numérisation et le partage systématique des données offrent de belles opportunités pour leur prévention. Nous avons ainsi profité de cette opportunité pour développer un éventail d’outils de prévention basés sur des méthodes d’analyse statistique. Dans un premier temps, ces travaux de thèse proposent une analyse des mécanismes expliquant les arrêts maladie chez le salarié. L’analyse d’une enquête nationale a premièrement permis d’identifier et de hiérarchiser leurs principaux facteurs déterminants grâce à l’algorithme des forêts aléatoires. Ensuite, une analyse de données administratives a identifié des trajectoires d’absence pouvant mener à des arrêts graves grâce à des analyses séquentielles et à de la modélisation multi-état. Dans un second temps, des outils ont été développés afin d’identifier des situations anormales d’arrêt maladie à l’échelle de l’entreprise. Une typologie d’entreprise a premièrement été construite afin de produire des valeurs repère pour que les entreprises évaluent précisément leur situation. Un algorithme de détection des pics d’absence, adapté de modèles de surveillance épidémiologique, a enfin été développé pour pouvoir identifier automatiquement les entreprises en excès.

Research component of the ATLAS programmeThe ATLAS programme (2019-2021) aims to promote and deploy HIV self-testing (HIVST) in Côte d'Ivoire, Mali and Senegal and to distribute half a million HIVST through various delivery channels, targeting in particular key populations (sex workers, men who have sex with men, drug users), partners of people living with HIV (PLHIV) and patients with sexually transmitted infections. The dispensation of HIVST will be carried out in routine care, through the three countries' national AIDS strategies and in an integrated manner with existing screening policies, through eight delivery channels combining fixed and advanced strategies, primary distribution and secondary distribution. The research component presented here includes a set of observational surveys to describe, analyze and understand the social, health, epidemiological and economic effects of the introduction of HIVST in Côte d'Ivoire, Mali and Senegal to improve testing offer (accessibility, effectiveness and ethics). It is organized into 5 work packages: (i) a qualitative survey on HIVST targeted key populations, based on qualitative individual and group interviews with key implementers, members of key population communities and HIVST users; (ii) an ethnography on the integration of HIVST for screening of PLHIV’s partners in three HIV care clinics and an exploratory sub-survey on HIVST distribution in STI consultations; (iii) an anonymous telephone survey of HIVST users recruited through an invitation on HIVST kits to call a toll-free number; (iv) an economic survey of HIVST incremental costs with cost collections from a sample of HIVST dispensing sites and a time and motion study; (v) an epidemiological modelling (dynamic compartmental model) of the three countries and of the health and economic impacts of different scaling scenarios.; Volet recherche du programme ATLASLe programme ATLAS (2019-2021) vise à promouvoir et à déployer l’autodépistage du VIH (ADVIH) en Côte d’Ivoire, au Mali et au Sénégal et prévoit la distribution d’un demi millions d’autotests à travers différents canaux de dispensation, visant en particulier les populations clés (travailleuses du sexe, hommes ayant des rapports sexuels avec des hommes, usager·e·s de drogues), les partenaires des personnes vivant avec le VIH (PvVIH) et les patient·e·s atteint·e·s d’une infection sexuellement transmissible. La dispensation des kits d’ADVIH sera réalisée en soins courants, dans le cadre des stratégies nationales de lutte contre le sida des trois pays et de manière intégrée aux politiques de dépistage déjà en place, à travers huit canaux de dispensation combinant des stratégies fixes et des stratégies avancées, une distribution primaire et une distribution secondaire. Le volet recherche présenté ici comporte un ensemble d’enquêtes observationnelles visant à décrire, analyser et comprendre les effets sociaux, sanitaires, épidémiologiques et économiques de l’introduction de l’autodépistage du VIH en Côte d’Ivoire, au Mali et au Sénégal pour améliorer l’offre de dépistage (accessibilité, efficacité et éthique). Il est organisé en 5 paquets d’activités : (i) une enquête qualitative sur l’ADVIH auprès des populations clés reposant sur des entretiens qualitatifs individuels et de groupes auprès d’acteurs clés de la mise en œuvre, de membres des communautés de populations clés et d’utilisatrices et utilisateurs de l’ADVIH ; (ii) une ethnographie portant sur l’intégration de l’ADVIH pour le dépistage des partenaires de PvVIH dans trois sites de prise en charge du VIH et une sous enquête exploratoire portant sur la diffusion de l’ADVIH à travers les consultations IST ; (iii) une enquête téléphonique anonyme auprès des utilisatrices et utilisateurs de l’ADVIH recruté·e·s via une invitation à appeler un numéro vert apposée sur les kits d’ADVIH distribués ; (iv) une enquête économique des coûts incrémentiels de l’ADVIH avec une collecte des coûts auprès d’un échantillon de sites de dispensation de l’ADVIH et une étude des temps et mouvements ; (v) une modélisation épidémiologique (modèle compartimental dynamique) des trois pays et des impacts sanitaires et économiques de différents scénarios de passage à l’échelle.

Summary Background Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are typically transmitted via respiratory droplets, are leading causes of invasive diseases, including bacteraemic pneumonia and meningitis, and of secondary infections subsequent to post-viral respiratory disease. The aim of this study was to investigate the incidence of invasive disease due to these pathogens during the early months of the COVID-19 pandemic. Methods In this prospective analysis of surveillance data, laboratories in 26 countries and territories across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae, and N meningitidis from Jan 1, 2018, to May, 31, 2020, as part of the Invasive Respiratory Infection Surveillance (IRIS) Initiative. Numbers of weekly cases in 2020 were compared with corresponding data for 2018 and 2019. Data for invasive disease due to Streptococcus agalactiae, a non-respiratory pathogen, were collected from nine laboratories for comparison. The stringency of COVID-19 containment measures was quantified using the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed using Google COVID-19 Community Mobility Reports. Interrupted time-series modelling quantified changes in the incidence of invasive disease due to S pneumoniae, H influenzae, and N meningitidis in 2020 relative to when containment measures were imposed. Findings 27 laboratories from 26 countries and territories submitted data to the IRIS Initiative for S pneumoniae (62 837 total cases), 24 laboratories from 24 countries submitted data for H influenzae (7796 total cases), and 21 laboratories from 21 countries submitted data for N meningitidis (5877 total cases). All countries and territories had experienced a significant and sustained reduction in invasive diseases due to S pneumoniae, H influenzae, and N meningitidis in early 2020 (Jan 1 to May 31, 2020), coinciding with the introduction of COVID-19 containment measures in each country. By contrast, no significant changes in the incidence of invasive S agalactiae infections were observed. Similar trends were observed across most countries and territories despite differing stringency in COVID-19 control policies. The incidence of reported S pneumoniae infections decreased by 68% at 4 weeks (incidence rate ratio 0·32 [95% CI 0·27–0·37]) and 82% at 8 weeks (0·18 [0·14–0·23]) following the week in which significant changes in population movements were recorded. Interpretation The introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of S pneumoniae, H influenzae, and N meningitidis, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide. Funding Wellcome Trust (UK), Robert Koch Institute (Germany), Federal Ministry of Health (Germany), Pfizer, Merck, Health Protection Surveillance Centre (Ireland), SpID-Net project (Ireland), European Centre for Disease Prevention and Control (European Union), Horizon 2020 (European Commission), Ministry of Health (Poland), National Programme of Antibiotic Protection (Poland), Ministry of Science and Higher Education (Poland), Agencia de Salut Pública de Catalunya (Spain), Sant Joan de Deu Foundation (Spain), Knut and Alice Wallenberg Foundation (Sweden), Swedish Research Council (Sweden), Region Stockholm (Sweden), Federal Office of Public Health of Switzerland (Switzerland), and French Public Health Agency (France).

International audience; Antimicrobial resistance (AMR) has become a major threat worldwide, especially in countries with inadequate sanitation and low antibiotic regulation. However, adequately prioritizing AMR interventions in such settings requires a quantification of the relative impacts of environmental, animal, and human sources in a One-Health perspective. Here, we propose a stochastic quantitative risk assessment model for the different components at interplay in AMR selection and spread. The model computes the incidence of AMR colonization in humans from five different sources: water or food consumption, contacts with livestock, and interhuman contacts in hospitals or the community, and combines these incidences into a per-year acquisition risk. Using data from the literature and Monte-Carlo simulations, we apply the model to hypothetical Asian-like settings, focusing on resistant bacteria that may cause infections in humans. In both scenarios A, illustrative of low-income countries, and B, illustrative of high-income countries, the overall individual risk of becoming colonized with resistant bacteria at least once per year is high. However, the average predicted incidence of colonization was lower in scenario B at 0.82 (CrI [0.13, 5.1]) acquisitions/person/year, versus 1.69 (CrI [0.66, 11.13]) acquisitions/person/year for scenario A. A high percentage of population with no access to improved water on premises and a high percentage of population involved in husbandry are shown to strongly increase the AMR acquisition risk. The One-Health AMR risk assessment framework we developed may prove useful to policymakers throughout Asia, as it can easily be parameterized to realistically reproduce conditions in a given country, provided data are available.