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14 results on '"Corinne Régis"'

1. Population genomics of Corsican wildcats: Paving the way toward a new subspecies within the Felis silvestris spp. complex?

Author

Elodie Portanier, Hélène Henri, Pierre Benedetti, Frédéric Sanchis, Corinne Régis, Pascale Chevret, Marco Zedda, Adil El Filali, Sandrine Ruette, Sébastien Devillard, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecologie et évolution des populations, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE)

Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genetics, Ecology, Evolution, Behavior and Systematics
Published
2023

2. Variations in immune parameters with age in a wild rodent population and links with survival

Author

Coraline Bichet, Corinne Régis, Emmanuelle Gilot‐Fromont, Aurélie Cohas, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
immunosenescence, Marmota marmota, immune cells, Ecology, aging, [SDE]Environmental Sciences, immune remodeling, mammal, survival, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

International audience; Recent findings suggest that immune functions do not unidirectionally deteriorate with age but that a potentially adaptive remodeling, where functions of the immune system get downregulated while others get upregulated with age could also occur. Scarce in wild populations, longitudinal studies are yet necessary to properly understand the patterns and consequences of age variations of the immune system in the wild. Meanwhile, it is challenging to understand if the observed variations in immune parameters with age are due to changes at the within-individual level or to selective (dis)appearance of individuals with peculiar immune phenotypes. Thanks to a long-term and longitudinal monitoring of a wild Alpine marmot population, we aimed to understand within- and between-individual variation in the immune phenotype with age, in order to improve our knowledge about the occurrence and the evolutionary consequences of such age variations in the wild. To do so, we recorded the age-specific leukocyte concentration and leukocyte profile in repeatedly sampled dominant individuals. We then tested whether the potential changes with age were attributable to within-individual variations and/or selective (dis)appearance. Finally, we investigated if the leukocyte concentration and profiles were correlated to the probability of death at a given age. The leukocyte concentration was stable with age, but the relative number of lymphocytes decreased, while the relative number of neutrophils increased, over the course of an individual's life. Moreover, between individuals of the same age, individuals with fewer lymphocytes but more neutrophils were more likely to die. Therefore, selective disappearance seems to play a role in the age variations of the immune parameters in this population. Further investigations linking age variations in immune phenotype to individual fitness are needed to understand whether remodeling of the immune system with age could or could not be adaptive.

Published
2022

3. Short-term telomere dynamics is associated with glucocorticoid levels in wild populations of roe deer

Author

Jean-Michel Gaillard, Maryline Pellerin, Corinne Régis, Benjamin Rey, Jeanne Duhayer, Hannah Froy, Emmanuelle Gilot-Fromont, Jeffrey Carbillet, Rachael V. Wilbourn, Louise Cheynel, Jean-François Lemaître, Sylvia Pardonnet, Hélène Verheyden, François Débias, Daniel H. Nussey, Sarah L. Underwood, Rupert Palme, A. J. Mark Hewison, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), University of Veterinary Medicine [Vienna] (Vetmeduni), Institute of Evolutionary Biology [Edinburgh], School of Biological Sciences [Edinburgh], University of Edinburgh-University of Edinburgh, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), Institute of Infection, Veterinary and Ecological Sciences, Department of Anatomy Physiology and Pathology, University of Liverpool, Leahurst Campus, Cheshire CH64 7TE, UK., Office français de la biodiversité (OFB), BBSRC grant no. (BB/ L020769/1), OFB staff, ANR-15-CE32-0002,AGEX,Vieillissement sexe-spécifique en milieu naturel(2015), ANR-11-LABX-0048,ECOFECT,Dynamiques eco-évolutives des maladies infectieuses(2011), ANR-11-IDEX-0007,Avenir L.S.E.,PROJET AVENIR LYON SAINT-ETIENNE(2011), Norwegian University of Science and Technology (NTNU), Institute of Infection and Global Health [University of Liverpool, UK], University of Liverpool, Biotechnology and Biological Sciences Research Council (BBSRC) : grant no. (BB/L020769/1), and Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, UK

Subjects
Male, life history, 0106 biological sciences, Senescence, Aging, senescence, Physiology, [SDV]Life Sciences [q-bio], Zoology, capreolus capreolus, fecal glucocorticoid metabolites, Stress, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Environmental stress, stress, 03 medical and health sciences, Capreolus, biology.animal, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, Animals, Life-history, Life history, Glucocorticoids, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, Fecal glucocorticoid metabolites, Deer, aging, Stressor, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Telomere, biology.organism_classification, Roe deer, Capreolus capreolus, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Glucocorticoid, medicine.drug
Abstract

International audience; While evidence that telomere length is associated with health and mortality in humans and birds is accumulating, a large body of research is currently seeking to identify factors that modulate telomere dynamics. We tested the hypothesis that high levels of glucocorticoids in individuals under environmental stress should accelerate telomere shortening in two wild populations of roe deer (Capreolus capreolus) living in different ecological contexts. From two consecutive annual sampling sessions, we found that individuals with faster rates of telomere shortening had higher concentrations of fecal glucocorticoid metabolites, suggesting a functional link between glucocorticoid levels and telomere attrition rate. This relationship was consistent for both sexes and populations. This finding paves the way for further studies of the fitness consequences of exposure to environmental stressors in wild vertebrates.

Published
2021

4. DNA methylation as a tool to explore ageing in wild roe deer populations

Author

Sylvia Pardonnet, Emmanuelle Gilot-Fromont, Jeanne Duhayer, François Débias, Amin Haghani, Joseph A. Zoller, Caesar Z. Li, Corinne Régis, Maryline Pellerin, Steve Horvath, Jean-Michel Gaillard, Benjamin Rey, Jean-François Lemaître, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Office français de la biodiversité (OFB), David Geffen School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California-University of California, Fielding School of Public Health, Biodémographie évolutive, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Ecologie et évolution des populations, and University of California (UC)-University of California (UC)

Subjects
0106 biological sciences, Senescence, Epigenomics, Male, Aging, senescence, [SDV]Life Sciences [q-bio], growth, sex differences in lifespan, 010603 evolutionary biology, 01 natural sciences, Epigenesis, Genetic, 03 medical and health sciences, Capreolus, biology.animal, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, Animals, Epigenetics, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Deer, life-history, dNaM, Methylation, DNA Methylation, biology.organism_classification, Roe deer, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Ageing, Evolutionary biology, DNA methylation, Female, epigenetic clock, Biotechnology
Abstract

International audience; DNA methylation-based biomarkers of ageing (epigenetic clocks) promise to lead to new insights into evolutionary biology of ageing. Relatively little is known about how the natural environment affects epigenetic ageing effects in wild species. In this study, we took advantage of a unique long-term (>40 years) longitudinal monitoring of individual roe deer (Capreolus capreolus) living in two wild populations (Chizé and Trois-Fontaines, France) facing different ecological contexts, to investigate the relationship between chronological age and levels of DNA methylation (DNAm). We generated novel DNA methylation data from n = 94 blood samples, from which we extracted leucocyte DNA, using a custom methylation array (HorvathMammalMethylChip40). We present three DNA methylation-based estimators of age (DNAm or epigenetic age), which were trained in males, females, and both sexes combined. We investigated how sex differences influenced the relationship between DNAm age and chronological age using sex-specific epigenetic clocks. Our results highlight that old females may display a lower degree of biological ageing than males. Further, we identify the main sites of epigenetic alteration that have distinct ageing patterns between the two sexes. These findings open the door to promising avenues of research at the crossroads of evolutionary biology and biogerontology

Published
2021

5. Phenotypic plasticity in the invasive pest Drosophila suzukii: activity rhythms and gene expression in response to temperature

Author

Stéphane Dray, Christophe Plantamp, Hélène Henri, Gladys Mialdea, Patricia Gibert, Thibault Andrieux, Emmanuel Desouhant, Corinne Régis, CAractérisation et Suivi des Phénomènes d'Evolution de Résistance aux pesticides (CASPER), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], and Evolution, adaptation et comportement

Subjects
0106 biological sciences, Physiology, Timeless, MESH: Drosophila, 030310 physiology, [SDE.MCG]Environmental Sciences/Global Changes, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Drosophila suzukii, Melanogaster, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Circadian rhythm, Molecular Biology, Drosophila, Clock genes, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Phenotypic plasticity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Functional principal component analysis, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 15. Life on land, biology.organism_classification, CLOCK, Drosophila melanogaster, Evolutionary biology, Insect Science, Animal Science and Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Invasion biology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Supplementary information available online at http://jeb.biologists.org/lookup/doi/10.1242/jeb.199398.supplemental; International audience; Phenotypic plasticity may contribute to the invasive success of an alien species in a new environment. A highly plastic species may survive and reproduce in more diverse environments, thereby supporting establishment and colonization. We focused on plasticity in the circadian rhythm of activity, which can favour species coexistence in invasion, for the invasive species Drosophila suzukii, which is expected to be a weaker direct competitor than other Drosophila species of the resident community. We compared the circadian rhythms of the locomotor activity in adults and the expression of clock genes in response to temperature in the invasive D. suzukii and the resident Drosophila melanogaster. We showed that D. suzukii is active in a narrower range of temperatures than D. melanogaster and that the activities of the two species overlap during the day, regardless of the temperature. Both species are diurnal and exhibit rhythmic activity at dawn and dusk, with a much lower activity at dawn for D. suzukii females. Our results show that the timeless and clock genes are good candidates to explain the plastic response that is observed in relation to temperature. Overall, our results suggest that thermal phenotypic plasticity in D. suzukii activity is not sufficient to explain the invasive success of D. suzukii and call for testing other hypotheses, such as the release of competitors and/or predators.

Published
2019

6. The neutrophil to lymphocyte ratio indexes individual variation in the behavioural stress response of wild roe deer across fluctuating environmental conditions

Author

Jeanne Duhayer, Yannick Chaval, Joël Merlet, Maryline Pellerin, Jeffrey Carbillet, A. J. M. Hewison, François Débias, Typhaine Lavabre, Hélène Verheyden, Benjamin Rey, Sylvia Pardonnet, Jean-François Lemaître, Jean-Michel Gaillard, Emmanuelle Gilot-Fromont, Benoit Rannou, Corinne Régis, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Biodémographie évolutive, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Ecologie et évolution des populations, Observatoire du Mont-Blanc, Rongeurs Sauvages, Risques Sanitaires et Gestion des Populations - UR 1233 (RS2GP), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre Régional d'Exploration Fonctionnelle et Ressources Expérimentales (CREFRE), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Office National de la Chasse et de la Faune Sauvage (ONCFS), INRA, VetAgro Sup and ONCFS, and was performed in the framework of the LABEX ECOFECT (ANR-11-LABX-0048) of Universite de Lyon, within the program 'Investissements d'Avenir' (ANR-11-IDEX-0007), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Population, Zoology, Biology, Stress, 010603 evolutionary biology, 01 natural sciences, Life history theory, Capreolus, biology.animal, N:L ratio, 0501 psychology and cognitive sciences, Behaviour, Environmental conditions, 050102 behavioral science & comparative psychology, Neutrophil to lymphocyte ratio, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, 05 social sciences, biology.organism_classification, Roe deer, Habitat, Animal ecology, Capreolus capreolus, Animal Science and Zoology, Conservation biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Understanding how wild animals adapt to perturbations and their consequences for life history traits and population dynamics is a current focus of attention in ecology and conservation biology. Here, we analysed variation in the neutrophil to lymphocyte ratio (N:L ratio), a proxy of stress level, in wild roe deer Capreolus capreolus from three populations experiencing markedly different environmental conditions. We first assessed whether among-individual differences in the N:L ratio were consistent over time and across environmental contexts. We then investigated how both individual characteristics (behaviour at capture, age, sex, body mass), and environmental context (habitat and year quality) were linked to this indicator of stress level. We found moderate, but consistent, repeatability of the N:L ratio in all three populations, indicating stable among-individual differences in the way individuals cope physiologically with varying environmental conditions. In addition, we found a weak, but consistent, association between the N:L ratio and behaviour at capture in two of the three populations. Finally, the N:L ratio also varied in relation to temporal changes in environmental conditions. In particular, individuals had, on average, higher levels of stress in poor-quality years in two of the three populations. We discuss our results in relation to the coping styles framework. Significance statement Due to global change, natural populations are increasingly faced with unpredictable fluctuations of their environment. The stress response, via the release of glucocorticoids, is a key mechanism that enables individuals to cope with these variations. However, all individuals do not necessarily cope with life threatening and/or stressful situations in the same way, but as yet, the major drivers underlying variation in stress level remain unclear. We showed that the N:L ratio, reflecting baseline stress level, was repeatable and influenced by both individual and environmental factors. In particular, variation in the N:L ratio was linked to the quality of the year in terms of resource availability and, to a lesser extent, to the individual's behaviour at capture. Our study demonstrates that both environmental context and individual characteristics drive variation in the N:L ratio in a wild vertebrate population.

Published
2019

7. Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Author

Corinne Régis, Guillaume Queney, Dominique Pontier, Jean-Baptiste Pons, Lina Muselet, Cécile Kaerle, Elodie Portanier, Eric J. Petit, Damien M. de Vienne, Ondine Filippi-Codaccioni, David Fouchet, Marie-Pauline Beugin, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Ecologie et évolution des populations, Antagene - Animal Genomics Laboratory, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Lyon, ANR-11-LABX-0048, and ANR-11-IDEX-0007

Subjects
0106 biological sciences, 0301 basic medicine, Population genetics, 01 natural sciences, Haplogroup, Chiroptera, Phylogeny, education.field_of_study, biology, Reproduction, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Reproductive isolation, Mitochondrial DNA, French Guiana, Pteronotus cf, Sympatry, Genetic structure, Pteronotus cf. parnellii, Research Article, Species complex, Neotropics, Genotype, Evolution, Population, Introgression, 010603 evolutionary biology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Species Specificity, Pteronotus, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, QH359-425, otorhinolaryngologic diseases, Animals, parnellii, Microsatellite, Echolocation, Asymmetric introgression, education, Ecosystem, Ecology, Evolution, Behavior and Systematics, Cell Nucleus, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Acoustics, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Evolutionary biology, Microsatellite Repeats, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1289-8) contains supplementary material, which is available to authorized users.

Published
2018

8. Stress levels of dominants reflect underlying conflicts with subordinates in a cooperatively breeding species

Author

Coraline Bichet, Aurélie Cohas, Corinne Régis, Benjamin Rey, Sophie Lardy, Valentine Federico, Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Vogelwarte Helgoland, Institut für Vogelforschung, Work supported by the Centre National de la Recherche Scientifique (CNRS), the Earthwatch Institute, and the Rhône-Alpes region (grant 15.005146.01)., ANR-13-JSV7-0005,CMatecHoice,Choix du partenaire pour de bons gènes ou des gènes compatibles: une approche intégrative utilisant le complexe majeur d'histocompatibilité(2013), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Université Paul-Valéry - Montpellier 3 ( UM3 ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -École pratique des hautes études ( EPHE ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), ANR-13-JSV7-0005,CMatecHoice,Choix du partenaire pour de bons gènes ou des gènes compatibles: une approche intégrative utilisant le complexe majeur d'histocompatibilité ( 2013 ), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0106 biological sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, 05 social sciences, Zoology, Marmot, Neutrophils to lymphocytes ratio, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Stress level, Social rank, Marmota marmota, Dominance (ethology), Reproductive skew, Animal ecology, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, 0501 psychology and cognitive sciences, Animal Science and Zoology, 050102 behavioral science & comparative psychology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, Dominance, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Maintaining dominance status had long been considered to be less stressful than subordination. However, no consistency in stress levels of dominant and subordinate individuals has been demonstrated. Tactics used to achieve and maintain dominance could be determinant. In cooperatively breeding species, conflicts between dominants and subordinates are expected since dominant individuals tend to monopolize reproduction while subordinates seldom reproduce. Reproductive skew models predict that subordinates’ reproductive opportunities are either allotted or subject to competition with dominants. In the former case, no policing of subordinates by dominants is expected. In the latter, dominant should exert a control over the subordinates possibly leading to higher stress levels in dominants than in subordinates, which could be further elevated as the number of potential competitors in the group increases. In the present study, we aimed to test these hypotheses by assessing individual’s stress level using the neutrophils to lymphocytes ratio (N:L) in a wild cooperatively breeding rodent, the Alpine marmot (Marmota marmota). We found that dominants exhibit higher N:L ratio than subordinates and that dominants’ N:L ratio increases with the number of unrelated same-sex subordinates in the group. We conclude that controlling unrelated subordinates is stressful for dominants, as expected under tug-of-war models. These stress patterns reveal conflicting relationships between dominants and subordinates over the reproduction and social status acquisition. This study highlights the influence of the nature, strength, and direction of conflicts on stress levels. In cooperatively breeding species, reproductive skew models predict that subordinates’ reproductive opportunities are either allotted or subject to competition with dominants and, thus, can modulate the relative stress level between dominants and subordinates. In the first case, no policing of subordinates by dominants is expected, while in the second, dominant should exert a control over the subordinates which should lead to higher stress level in dominants than in subordinates, and particularly when subordinates are unrelated to the dominants. In Alpine marmots, we found that dominants exhibit higher stress level than subordinates and dominants’ stress level increased with the number of unrelated same-sex subordinates. These patterns are in agreement with the predictions of the tug-of war models of reproductive skew and indicate that controlling subordinates is costly for dominants.

Published
2018

9. Hospitalization in double-occupancy rooms and the risk of hospital-acquired influenza: a prospective cohort study

Author

P. Vanhems, Thomas Bénet, Bruno Lina, Florence Morfin, Corinne Régis, E. Munier-Marion, Service d'Hygiène, Epidémiologie et Prévention [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Laboratoire des pathogènes émergents -- Emerging Pathogens Laboratory (LPE-Fondation Mérieux), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), Adult, Male, medicine.medical_specialty, Pediatrics, double-occupancy room, 030501 epidemiology, Risk Assessment, 03 medical and health sciences, 0302 clinical medicine, Hospital-acquired infection, Epidemiology, Influenza, Human, Patients' Rooms, medicine, 80 and over, Humans, 030212 general & internal medicine, Prospective Studies, Prospective cohort study, Aged, Aged, 80 and over, Cross Infection, hospital-acquired infection, business.industry, Incidence (epidemiology), Incidence, Hazard ratio, Cohort, Influenza a, General Medicine, Middle Aged, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Confidence interval, Influenza, 3. Good health, Hospitalization, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, epidemiology, Female, 0305 other medical science, business, Human
Abstract

International audience; Hospitalization in double-occupancy rooms and the risk of hospital-acquired influenza were assessed prospectively. The incidence was 2.0 for 100 patient-days in double- vs. 0.7 in single-occupancy rooms (p 0.028). The adjusted hazard ratio of hospital-acquired influenza was 2.67 (95% confidence interval 1.05-6.76) in patients hospitalized in double- compared to single-occupancy rooms.

Published
2016

10. Factors associated with poor outcomes among adults hospitalised for influenza in France: A three-year prospective multicenter study

Author

Z. Lesieur, Pierre Tattevin, Corinne Régis, Nezha Samih-Lenzi, Florence Galtier, Martine Valette, Philippe Vanhems, D. Postil, Xavier Duval, Stéphane Jouneau, Yolande Costa, Fabrice Carrat, Bruno Lina, Corinne Merle, Odile Launay, Paul Loubet, Pierre Loulergue, Sylvie Rogez, Service des Maladies Infectieuses, Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CIC Cochin Pasteur (CIC 1417), Institut National de la Santé et de la Recherche Médicale (INSERM)-Groupe hospitalier Broca-Université Paris Descartes - Paris 5 (UPD5)-Hôtel-Dieu-Hôpital Cochin [AP-HP], F-CRIN, Innovative clinical research network in vaccinology (I-REIVAC), CIC Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-CHU Saint-Eloi-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Saint-Eloi, Service d'Hygiène, Epidémiologie et Prévention [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Laboratoire des pathogènes émergents -- Emerging Pathogens Laboratory (LPE-Fondation Mérieux), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), CIC Hôpital Bichat, Institut National de la Santé et de la Recherche Médicale (INSERM)-UFR de Médecine-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Service de pneumologie [Rennes] = Pneumology [Rennes], CHU Pontchaillou [Rennes], Service de Bactériologie, Virologie, Hygiène [CHU Limoges], CHU Limoges, Centre National de Référence Virus Influenza (Région Sud), Hospices Civils de Lyon (HCL), Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Service des maladies infectieuses et réanimation médicale [Rennes] = Infectious Disease and Intensive Care [Rennes], Fonction, structure et inactivation d'ARN bactériens, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), The study sites received funding from Sanofi Pasteur and Sanofi Pasteur MSD for the FLUVAC study. Vaccine producers had no role in the study design, data analysis, decision to publish or preparation of the manuscript., CHU Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP]-Hôtel-Dieu-Université Paris Descartes - Paris 5 (UPD5)-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Saint-Eloi, AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-UFR de Médecine, Service de Pneumologie, Rennes, Service des maladies infectieuses et réanimation médicale, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou, CHU Saint-Antoine [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu-Université Paris Descartes - Paris 5 (UPD5)-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Saint Eloi (CHRU Montpellier), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Saint Eloi (CHRU Montpellier), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-UFR de Médecine, Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Jonchère, Laurent, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre Louis d'Epidémiologie et de Santé Publique ( iPLESP ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), CIC Cochin Pasteur ( CIC 1417 ), Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Cochin [AP-HP]-Hôtel-Dieu-Université Paris Descartes - Paris 5 ( UPD5 ) -Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre Hospitalier Régional Universitaire [Montpellier] ( CHRU Montpellier ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Saint-Eloi, Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Centre International de Recherche en Infectiologie ( CIRI ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Infection, Antimicrobiens, Modélisation, Evolution ( IAME ), Université Paris Diderot - Paris 7 ( UPD7 ) -Université Paris 13 ( UP13 ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -UFR de Médecine-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Institut de recherche, santé, environnement et travail ( Irset ), Université d'Angers ( UA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -École des Hautes Études en Santé Publique [EHESP] ( EHESP ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ) -Université des Antilles ( UA ), Hospices Civils de Lyon ( HCL ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Centre d'Investigation Clinique [Rennes] ( CIC ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Hôpital Pontchaillou, Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), French National Enterovirus/Parechovirus Reference centre, Département de santé publique, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité ( CRESS (U1153 / UMR_A 1125) ), and Institut National de la Recherche Agronomique ( INRA ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM )

Subjects
0301 basic medicine, Male, Pediatrics, [SDV]Life Sciences [q-bio], Comorbidity, law.invention, chemistry.chemical_compound, 0302 clinical medicine, law, Risk Factors, Hospitalisation, 030212 general & internal medicine, Prospective Studies, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Aged, 80 and over, Mortality rate, Vaccination, Age Factors, Middle Aged, Intensive care unit, 3. Good health, [SDV] Life Sciences [q-bio], Hospitalization, Infectious Diseases, Treatment Outcome, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Population study, Female, France, Adult, Oseltamivir, medicine.medical_specialty, Adolescent, 030106 microbiology, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 03 medical and health sciences, Young Adult, Virology, Influenza, Human, medicine, Humans, Adults, Risk factor, Antiviral, Aged, Severe, [ SDV ] Life Sciences [q-bio], business.industry, medicine.disease, Survival Analysis, Influenza, Pneumonia, Epidemiologic Studies, Respiratory failure, chemistry, business
Abstract

International audience; Background: Influenza is an important cause of serious illness and death, particularly in elderly and high-risk groups. Objectives Aim of this study was to identify factors associated with poor outcomes among adults hospitalized in France for laboratory-confirmed seasonal influenza. Study design Patients hospitalized for influenza were identified in a prospective, multicenter study carried out in French hospitals during three consecutive influenza seasons (2012–2015). Influenza virus infection was confirmed by reverse transcription polymerase chain reaction. Sociodemographic and clinical variables were compared according to the virus type and subtype. Risk factors for complications, intensive care unit (ICU) admission and death were analyzed by backward stepwise logistic regression. Results The study population consisted of 566 patients, of whom 56% were older than 65 years and 82% had underlying chronic illnesses. Type A influenza viruses infected 422 patients (75%), including subtype H3N2 in 239 patients (57%). The prior vaccine coverage rate was 38%. Complications occurred in 255 patients (45%), consisting mainly of pneumonia (n = 143, 30%) and respiratory failure (n = 116, 20%). Eighty-three patients (15%) were admitted to an ICU, and the in-hospital mortality rate was 4% (n = 21). Sixty-six patients (12%) received oseltamivir. Age over 65 years was the only identified risk factor for complications. Risk factors for ICU admission were an absence of vaccination, no oseltamivir administration before admission, pre-existing chronic respiratory disease, and current smoking. Age over 65 years and ICU admission were risk factors for death. Conclusions Older individuals and patients with underlying conditions are most at risk of influenza complications. Vaccination and early oseltamivir administration, both of which are recommended for these patients, appear to reduce ICU admissions

Published
2016

11. Influenza vaccine effectiveness among healthcare workers in comparison to hospitalized patients: A 2004-2009 case-test, negative-control, prospective study

Author

Sélilah Amour, Olivier Robert, Thomas Bénet, Philippe Vanhems, Nicolas Voirin, Corinne Régis, Bruno Lina, Sylvain Roche, Yasmine Baghdadi, René Ecochard, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Virologie et pathologie humaine (VirPath), Université de Lyon-Université de Lyon, Biostatistiques santé, Département biostatistiques et modélisation pour la santé et l'environnement [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE)

Subjects
Adult, Male, 0301 basic medicine, Pediatrics, medicine.medical_specialty, Influenza vaccine, Hospitalized patients, Health Personnel, [SDV]Life Sciences [q-bio], education, 030106 microbiology, Immunology, Short Report, Negative control, Teaching hospital, 03 medical and health sciences, Immunogenicity, Vaccine, 0302 clinical medicine, Vaccination status, Influenza, Human, Health care, Flu season, Humans, Immunology and Allergy, Medicine, Prospective Studies, 030212 general & internal medicine, Hospitals, Teaching, Prospective cohort study, ComputingMilieux_MISCELLANEOUS, Pharmacology, business.industry, Vaccination, virus diseases, Middle Aged, 3. Good health, Influenza B virus, Influenza A virus, Influenza Vaccines, Case-Control Studies, Female, business
Abstract

The objective of this study was to calculate Vaccine Effectiveness (VE) in healthcare workers (HCW) and to compare VE between patients and HCW. A case-control investigation based on the prospective study was conducted between 2004 and 2009 in a teaching hospital. All HCW with influenza-like illness (ILI) from participating units (n = 24) were included, and vaccination status was characterized by interview. A total of 150 HCW presented ILI; 130 (87%) were female, 27 (18%) were positive for influenza, and 42 (28%) were vaccinated. Adjusted VE was 89% (95% CI 39 to 98). Among patients, adjusted VE was 42% (95% CI −39 to 76). The difference of VE (VEhcw - VEpat) was 46.15% (95% CI 2.41 to 144). The VE ratio (VEhcw / VEpat) was 2.09 (95% CI −1.60 to 134.17). Influenza VE differed between HCW and patients when the flu season was taken into account. This finding confirms the major impact of host determinants on influenza VE.

Published
2016

12. Influenza vaccination of healthcare workers in acute-care hospitals: a case-control study of its effect on hospital-acquired influenza among patients

Author

Bruno Lina, Corinne Régis, Brigitte Coppéré, Silene Cronenberger, Olivier Robert, Brigitte Comte, Philippe Vanhems, Nicolas Voirin, Thomas Bénet, Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon ( HCL ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Camille Jordan [Villeurbanne] ( ICJ ), École Centrale de Lyon ( ECL ), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS ), Virologie et pathologie humaine ( VirPath ), Université de Lyon-Université de Lyon, Service de médecine gériatrique, Hospices Civils de Lyon ( HCL ) -Hôpital Edouard Herriot [CHU - HCL], Service d'Hygiène, Epidémiologie et Prévention [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Hospices Civils de Lyon (HCL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut Camille Jordan (ICJ), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Virologie et pathologie humaine (VirPath), Hospices Civils de Lyon (HCL)-Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Institut Camille Jordan [Villeurbanne] (ICJ), Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, MESH : Orthomyxoviridae, [SDV]Life Sciences [q-bio], MESH : Aged, MESH : Prospective Studies, MESH: Influenza Vaccines, MESH: Aged, 80 and over, 0302 clinical medicine, Medical microbiology, Acute care, Health care, Medicine, MESH : Female, Prospective Studies, 030212 general & internal medicine, MESH : Influenza, Human, Prospective cohort study, MESH: Orthomyxoviridae, MESH: Aged, Aged, 80 and over, Cross Infection, 0303 health sciences, MESH: Middle Aged, biology, MESH: Influenza, Human, Vaccination, MESH: Nose, Healthcare worker, virus diseases, Middle Aged, MESH : Adult, MESH: Hospitals, Orthomyxoviridae, MESH: Case-Control Studies, Hospitals, 3. Good health, MESH : Hospitals, Infectious Diseases, MESH: Hemagglutination Inhibition Tests, Influenza Vaccines, Female, MESH : Nose, MESH : Cross Infection, Research Article, Adult, medicine.medical_specialty, MESH : Case-Control Studies, animal structures, Health Personnel, MESH : Male, education, Nose, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Influenza, Human, Humans, lcsh:RC109-216, MESH : Middle Aged, MESH : Aged, 80 and over, Aged, MESH: Humans, [ SDV ] Life Sciences [q-bio], 030306 microbiology, business.industry, MESH : Humans, Case-control study, MESH: Cross Infection, MESH: Adult, MESH: Vaccination, Hemagglutination Inhibition Tests, biology.organism_classification, MESH: Male, MESH: Prospective Studies, MESH : Hemagglutination Inhibition Tests, MESH : Influenza Vaccines, MESH : Vaccination, Case-Control Studies, Immunology, Emergency medicine, MESH: Health Personnel, MESH : Health Personnel, business, MESH: Female
Abstract

Background In acute-care hospitals, no evidence of a protective effect of healthcare worker (HCW) vaccination on hospital-acquired influenza (HAI) in patients has been documented. Our study objective was to ascertain the effectiveness of influenza vaccination of HCW on HAI among patients. Methods A nested case-control investigation was implemented in a prospective surveillance study of influenza-like illness (ILI) in a tertiary acute-care university hospital. Cases were patients with virologically-confirmed influenza occurring ≥ 72 h after admission, and controls were patients with ILI presenting during hospitalisation with negative influenza results after nasal swab testing. Four controls per case, matched per influenza season (2004-05, 2005-06 and 2006-07), were randomly selected. Univariate and multivariate conditional logistic regression models were fitted to assess factors associated with HAI among patients. Results In total, among 55 patients analysed, 11 (20%) had laboratory-confirmed HAI. The median HCW vaccination rate in the units was 36%. The median proportion of vaccinated HCW in these units was 11.5% for cases vs. 36.1% for the controls (P = 0.11); 2 (20%) cases and 21 (48%) controls were vaccinated against influenza in the current season (P = 0.16). The proportion of ≥ 35% vaccinated HCW in short-stay units appeared to protect against HAI among patients (odds ratio = 0.07; 95% confidence interval 0.005-0.98), independently of patient age, influenza season and potential influenza source in the units. Conclusions Our observational study indicates a shielding effect of more than 35% of vaccinated HCW on HAI among patients in acute-care units. Investigations, such as controlled clinical trials, are needed to validate the benefits of HCW vaccination on HAI incidence in patients.

Published
2012

13. High-resolution measurements of face-to-face contact patterns in a primary school

Author

Marco Quaggiotto, Philippe Vanhems, Ciro Cattuto, Corinne Régis, Alain Barrat, Nicolas Voirin, Juliette Stehlé, Wouter Van den Broeck, Lorenzo Isella, Bruno Lina, Jean-François Pinton, Centre de Physique Théorique - UMR 6207 (CPT), Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Service d'Hygiène, Epidémiologie et Prévention [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), CPT - E5 Physique statistique et systèmes complexes, Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Data Science Laboratory (ISI), ISI Foundation Institute for Scientific Interchange, Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Virologie et pathogenèse virale (VPV), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2, École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon

Subjects
FOS: Computer and information sciences, Pediatrics, Time Factors, Epidemiology, lcsh:Medicine, High resolution, Social Environment, Social and Behavioral Sciences, Quantitative Biology - Quantitative Methods, 01 natural sciences, 010305 fluids & plasmas, Developmental psychology, Face-to-face, Sociology, [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], Child, lcsh:Science, Respiratory Tract Infections, Quantitative Methods (q-bio.QM), 0303 health sciences, Schools, Multidisciplinary, [SHS.SOCIO]Humanities and Social Sciences/Sociology, Physics, 4. Education, [PHYS.PHYS.PHYS-SOC-PH]Physics [physics]/Physics [physics]/Physics and Society [physics.soc-ph], Computer Science - Social and Information Networks, 3. Good health, Infectious Diseases, Social Networks, Interdisciplinary Physics, Social Systems, Medicine, Algorithms, Research Article, Physics - Physics and Society, medicine.medical_specialty, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Infectious Disease Control, Isolation (health care), education, FOS: Physical sciences, Physics and Society (physics.soc-ph), Models, Biological, Infectious Disease Epidemiology, Statistical Mechanics, 03 medical and health sciences, Mixing patterns, Thursday, 0103 physical sciences, medicine, Humans, Social Behavior, Networks and graphs, 030304 developmental biology, Social and Information Networks (cs.SI), business.industry, Public health, lcsh:R, Social environment, Social Epidemiology, Interaction time, Computational Sociology, FOS: Biological sciences, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Infectious Disease Modeling, business
Abstract

BACKGROUND: Little quantitative information is available on the mixing patterns of children in school environments. Describing and understanding contacts between children at school would help quantify the transmission opportunities of respiratory infections and identify situations within schools where the risk of transmission is higher. We report on measurements carried out in a French school (6-12 years children), where we collected data on the time-resolved face-to-face proximity of children and teachers using a proximity-sensing infrastructure based on radio frequency identification devices. METHODS AND FINDINGS: Data on face-to-face interactions were collected on Thursday, October 1(st) and Friday, October 2(nd) 2009. We recorded 77,602 contact events between 242 individuals (232 children and 10 teachers). In this setting, each child has on average 323 contacts per day with 47 other children, leading to an average daily interaction time of 176 minutes. Most contacts are brief, but long contacts are also observed. Contacts occur mostly within each class, and each child spends on average three times more time in contact with classmates than with children of other classes. We describe the temporal evolution of the contact network and the trajectories followed by the children in the school, which constrain the contact patterns. We determine an exposure matrix aimed at informing mathematical models. This matrix exhibits a class and age structure which is very different from the homogeneous mixing hypothesis. CONCLUSIONS: We report on important properties of the contact patterns between school children that are relevant for modeling the propagation of diseases and for evaluating control measures. We discuss public health implications related to the management of schools in case of epidemics and pandemics. Our results can help define a prioritization of control measures based on preventive measures, case isolation, classes and school closures, that could reduce the disruption to education during epidemics.

Published
2011

14. Simulation of an SEIR infectious disease model on the dynamic contact network of conference attendees

Author

Ciro Cattuto, Vittoria Colizza, Wouter Van den Broeck, Lorenzo Isella, Alain Barrat, Philippe Vanhems, Jean-François Pinton, Juliette Stehlé, Nagham Khanafer, Nicolas Voirin, Corinne Régis, Centre de Physique Théorique - UMR 6207 (CPT), Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), CPT - E5 Physique statistique et systèmes complexes, Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Service d'Hygiène, Epidémiologie et Prévention [Hôpital Edouard Herriot - HCL], Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Data Science Laboratory, Institute for Scientific Interchange (ISI) Foundation, Epidémiologie des maladies infectieuses et modélisation (ESIM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Computational Epidemiology Laboratory (CERL), ISI Foundation Institute for Scientific Interchange, Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), This project was partly supported by La Société Française d'Hygiène Hospitalière and GOJO France. This study was partly supported by a grant of the Programme de Recherche, A(H1N1) co-ordinated by the Institut de Microbiologie et Maladies Infectieuses., Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2, École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and BMC, Ed.

Subjects
Physics - Physics and Society, Computer science, Population, lcsh:Medicine, FOS: Physical sciences, Physics and Society (physics.soc-ph), computer.software_genre, Quantitative Biology - Quantitative Methods, 01 natural sciences, Dynamic contact, 03 medical and health sciences, Empirical research, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 0103 physical sciences, Radio-frequency identification, 010306 general physics, education, Quantitative Methods (q-bio.QM), 030304 developmental biology, Medicine(all), 0303 health sciences, Computational model, education.field_of_study, business.industry, lcsh:R, General Medicine, 3. Good health, Homogeneous, Software deployment, Infectious disease (medical specialty), FOS: Biological sciences, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Data mining, business, computer
Abstract

Background The spread of infectious diseases crucially depends on the pattern of contacts between individuals. Knowledge of these patterns is thus essential to inform models and computational efforts. However, there are few empirical studies available that provide estimates of the number and duration of contacts between social groups. Moreover, their space and time resolutions are limited, so that data are not explicit at the person-to-person level, and the dynamic nature of the contacts is disregarded. In this study, we aimed to assess the role of data-driven dynamic contact patterns between individuals, and in particular of their temporal aspects, in shaping the spread of a simulated epidemic in the population. Methods We considered high-resolution data about face-to-face interactions between the attendees at a conference, obtained from the deployment of an infrastructure based on radiofrequency identification (RFID) devices that assessed mutual face-to-face proximity. The spread of epidemics along these interactions was simulated using an SEIR (Susceptible, Exposed, Infectious, Recovered) model, using both the dynamic network of contacts defined by the collected data, and two aggregated versions of such networks, to assess the role of the data temporal aspects. Results We show that, on the timescales considered, an aggregated network taking into account the daily duration of contacts is a good approximation to the full resolution network, whereas a homogeneous representation that retains only the topology of the contact network fails to reproduce the size of the epidemic. Conclusions These results have important implications for understanding the level of detail needed to correctly inform computational models for the study and management of real epidemics. Please see related article BMC Medicine, 2011, 9:88

Published
2011

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