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

Author

Coraline Bichet, Corinne Régis, Emmanuelle Gilot‐Fromont, and Aurélie Cohas

Subjects
aging, immune cells, immune remodeling, immunosenescence, mammal, Marmota marmota, Ecology, QH540-549.5
Abstract

Abstract 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
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2. Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates

Author

Rylan Shearn, Alison E Wright, Sylvain Mousset, Corinne Régis, Simon Penel, Jean-François Lemaitre, Guillaume Douay, Brigitte Crouau-Roy, Emilie Lecompte, and Gabriel AB Marais

Subjects
sex chromosomes, recombination suppression, sexual dimorphism, sexually antagonistic mutations, primates, lemurs, Medicine, Science, Biology (General), QH301-705.5
Abstract

Sex chromosomes are typically comprised of a non-recombining region and a recombining pseudoautosomal region. Accurately quantifying the relative size of these regions is critical for sex-chromosome biology both from a functional and evolutionary perspective. The evolution of the pseudoautosomal boundary (PAB) is well documented in haplorrhines (apes and monkeys) but not in strepsirrhines (lemurs and lorises). Here, we studied the PAB of seven species representing the main strepsirrhine lineages by sequencing a male and a female genome in each species and using sex differences in coverage to identify the PAB. We found that during primate evolution, the PAB has remained unchanged in strepsirrhines whereas several recombination suppression events moved the PAB and shortened the pseudoautosomal region in haplorrhines. Strepsirrhines are well known to have much lower sexual dimorphism than haplorrhines. We suggest that mutations with antagonistic effects between males and females have driven recombination suppression and PAB evolution in haplorrhines

Published
2020
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4. Estimating potential infection transmission routes in hospital wards using wearable proximity sensors.

Author

Philippe Vanhems, Alain Barrat, Ciro Cattuto, Jean-François Pinton, Nagham Khanafer, Corinne Régis, Byeul-a Kim, Brigitte Comte, and Nicolas Voirin

Subjects
Medicine, Science
Abstract

BACKGROUND: Contacts between patients, patients and health care workers (HCWs) and among HCWs represent one of the important routes of transmission of hospital-acquired infections (HAI). A detailed description and quantification of contacts in hospitals provides key information for HAIs epidemiology and for the design and validation of control measures. METHODS AND FINDINGS: We used wearable sensors to detect close-range interactions ("contacts") between individuals in the geriatric unit of a university hospital. Contact events were measured with a spatial resolution of about 1.5 meters and a temporal resolution of 20 seconds. The study included 46 HCWs and 29 patients and lasted for 4 days and 4 nights. 14,037 contacts were recorded overall, 94.1% of which during daytime. The number and duration of contacts varied between mornings, afternoons and nights, and contact matrices describing the mixing patterns between HCW and patients were built for each time period. Contact patterns were qualitatively similar from one day to the next. 38% of the contacts occurred between pairs of HCWs and 6 HCWs accounted for 42% of all the contacts including at least one patient, suggesting a population of individuals who could potentially act as super-spreaders. CONCLUSIONS: Wearable sensors represent a novel tool for the measurement of contact patterns in hospitals. The collected data can provide information on important aspects that impact the spreading patterns of infectious diseases, such as the strong heterogeneity of contact numbers and durations across individuals, the variability in the number of contacts during a day, and the fraction of repeated contacts across days. This variability is however associated with a marked statistical stability of contact and mixing patterns across days. Our results highlight the need for such measurement efforts in order to correctly inform mathematical models of HAIs and use them to inform the design and evaluation of prevention strategies.

Published
2013
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5. High-resolution measurements of face-to-face contact patterns in a primary school.

Author

Juliette Stehlé, Nicolas Voirin, Alain Barrat, Ciro Cattuto, Lorenzo Isella, Jean-François Pinton, Marco Quaggiotto, Wouter Van den Broeck, Corinne Régis, Bruno Lina, and Philippe Vanhems

Subjects
Medicine, Science
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
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6. Microsatellites and mitochondrial evidence of multiple introductions of the invasive raccoon Procyon lotor in France

Author

Jérémy Larroque, Pascale Chevret, Juliette Berger, Sandrine Ruette, Tim Adriaens, Koen Van Den Berge, Vinciane Schockert, François Léger, Géraldine Veron, Cécile Kaerle, Corinne Régis, Manon Gautrelet, Jean-François Maillard, and Sébastien Devillard

Subjects
Ecology, Ecology, Evolution, Behavior and Systematics
Abstract

Raccoons (Procyon lotor) are worldwide invaders, due to deliberate or accidental releases, and their impacts exceed hundred of billions of Euros in Europe only. In France, raccoons have currently established three separate, expanding populations. Identifying the current spatial genetic structure, dispersal events and phylogeography of these populations is needed to infer the invasion history and identify management units. We used wild and captive individuals sampled in France and Belgium to characterize the genetic diversity and current population genetic structure of French raccoon populations and identify potential genetic connectivity with the Belgium population using both mitochondrial DNA and microsatellite loci. Results confirm that French populations are the result of at least three independent introductions. While the three populations display low genetic diversity and sign of recent bottleneck, they are still expanding, suggesting that in addition to their ecological plasticity, the remaining genetic diversity is sufficient to successfully adapt to their new environment and allow a quick colonization. Particular attention must be given to the North-Eastern population, which shows genetic admixture with the Belgium population, as admixed individuals may exhibit hybrid vigor facilitating their expansion. The comparison of captive and wild individuals did not allow to identify a potential captive origin of the wild populations. The current regulation in France allowing captivity in zoos without enforcement to tighten the biosecurity of detention facilities might dampen any management measure as few introduced founders might be enough to create new populations.

Published
2023

7. 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

8. Changes in immune phenotype with age impaired survival: a longitudinal approach in Alpine marmots

Author

Coraline Bichet, Aurélie Cohas, Corinne Régis, and Gilet-Fromont E

Subjects
Text mining, business.industry, Immunology, Biology, business, Immune phenotype
Abstract

Recent findings suggest that immunosenescence should not be considered as a unidirectional deterioration, and that the remodeling of the immune system with age could also be adaptive. Longitudinal studies on immunosenescence in wild populations are scarce, and therefore, processes like selective disappearance cannot be easily torn apart from senescence. Using a long-term and longitudinal monitoring of a wild population of Alpine marmots, 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 consequence of immunosenescence in the wild. We tested, once controlled for a potential selective disappearance, whether individuals’ immune function only decreases as they age, as expected from the disposable soma theory, or whether remodelling of the immune system does occur. Therefore, we recorded the age-specific leukocyte concentration and counts in repeatedly sampled dominant individuals and we tested the potential changes with age as well as their association with survival probabilities. The overall leukocyte concentration was stable with age, but the lymphocyte count decreased, while the neutrophil count increased, over the course of an individual’s life. The leukocyte counts also predicted survival: at a given age, individuals with fewer lymphocytes but more neutrophils were more likely to die. Longitudinal studies, like the present one, are required to properly understand the patterns and consequences of immunosenescence in the wild.

Published
2021

9. 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

10. 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

11. Epigenetic clock and DNA methylation studies of roe deer in the wild

Author

Corinne Régis, Emmanuelle Gilot-Fromont, Joseph A. Zoller, Steve Horvath, Amin Haghani, Maryline Pellerin, Jean-François Lemaître, Jean-Michel Gaillard, Benjamin Rey, Caesar Z. Li, Biodémographie évolutive, 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), and Ecologie et évolution des populations

Subjects
0106 biological sciences, 0303 health sciences, education.field_of_study, [SDV]Life Sciences [q-bio], Population, dNaM, Methylation, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Roe deer, 03 medical and health sciences, Capreolus, Biomarkers of aging, Evolutionary biology, biology.animal, DNA methylation, Epigenetics, education, 030304 developmental biology
Abstract

DNA methylation-based biomarkers of aging (epigenetic clocks) promise to lead to new insights in the evolutionary biology of ageing. Relatively little is known about how the natural environment affects epigenetic aging 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=90 blood samples 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 through the use of sex-specific epigenetic clocks. Our results highlight that both populations and sex influence the epigenetic age, with the bias toward a stronger male average age acceleration (i.e. differences between epigenetic age and chronological ages) particularly pronounced in the population facing harsh environmental conditions. Further, we identify the main sites of epigenetic alteration that have distinct aging patterns across the two sexes. These findings open the door to promising avenues of research at the crossroad of evolutionary biology and biogerontology.

Published
2020

12. 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

13. Phenotypic plasticity in the invasive pest

Author

Christophe, Plantamp, Hélène, Henri, Thibault, Andrieux, Corinne, Régis, Gladys, Mialdea, Stéphane, Dray, Patricia, Gibert, and Emmanuel, Desouhant

Subjects
Temperature, Animals, CLOCK Proteins, Drosophila Proteins, Gene Expression, Drosophila, Adaptation, Physiological, Locomotion, Circadian Rhythm
Abstract

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

Published
2019

14. Does host socio-spatial behavior lead to a fine-scale spatial genetic structure in its associated parasites?

Author

Patricia Michel, Daniel Maillard, Elodie Portanier, Mathieu Garel, Hélène Henri, Elizabeth Redman, Sébastien Devillard, Marie-Thérèse Poirel, Corinne Régis, Christian Itty, Jeanne Duhayer, Gilles Bourgoin, 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
Male, 0106 biological sciences, Veterinary (miscellaneous), nematode, Population, Population genetics, Animals, Wild, Environment, 010603 evolutionary biology, 01 natural sciences, Host-Parasite Interactions, Gene flow, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Animals, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RC109-216, education, 030304 developmental biology, Life Cycle Stages, 0303 health sciences, education.field_of_study, Sheep, Behavior, Animal, biology, Host (biology), Genetic Variation, population genetics, mouflon, biology.organism_classification, host-parasite co-structure, Mouflon, haemonchus contortus, Genetics, Population, Infectious Diseases, ovis gmelini musimon × ovis sp, Evolutionary biology, Insect Science, Genetic structure, Biological dispersal, Female, Haemonchus, Animal Science and Zoology, Parasitology, France, Research Article, Microsatellite Repeats, Haemonchus contortus
Abstract

Gastro-intestinal nematodes, especially Haemonchus contortus, are widespread pathogenic parasites of small ruminants. Studying their spatial genetic structure is as important as studying host genetic structure to fully understand host-parasite interactions and transmission patterns. For parasites having a simple life cycle (e.g., monoxenous parasites), gene flow and spatial genetic structure are expected to strongly rely on the socio-spatial behavior of their hosts. Based on five microsatellite loci, we tested this hypothesis for H. contortus sampled in a wild Mediterranean mouflon population (Ovis gmelini musimon × Ovis sp.) in which species- and environment-related characteristics have been found to generate socio-spatial units. We nevertheless found that their parasites had no spatial genetic structure, suggesting that mouflon behavior was not enough to limit parasite dispersal in this study area and/or that other ecological and biological factors were involved in this process, for example other hosts, the parasite life cycle, or the study area history.Le comportement socio-spatial de l’hôte conduit-il à une structure génétique à fine échelle de ses parasites ?Les nématodes gastro-intestinaux, et plus particulièrement Haemonchus contortus, sont cosmopolites et pathogènes chez les petits ruminants. Étudier leur structure génétique spatiale est aussi important que d’étudier celle des hôtes pour pleinement comprendre les interactions hôtes-parasites et les processus de transmission. Pour les parasites ayant des cycles de vie simples (par exemple, les parasites monoxènes), on s’attend à ce que les flux de gènes et la structure génétique spatiale dépendent fortement du comportement socio-spatial de leurs hôtes. En utilisant cinq loci microsatellites, nous avons testé cette hypothèse pour des H. contortus échantillonnés dans une population sauvage de mouflons méditerranéens (Ovis gmelini musimon × Ovis sp.) dans laquelle les caractéristiques de l’espèce et de l’environnement génèrent des unités socio-spatiales. Nous avons néanmoins mis en évidence que leurs parasites ne présentent pas de structure génétique spatiale, ce qui suggère que le comportement des mouflons ne restreint pas la dispersion des parasites dans cette aire d’étude et/ou que d’autres facteurs biologiques et écologiques tels que d’autres hôtes, le cycle de vie du parasite, ou l’histoire de l’aire d’étude jouent un rôle dans ce processus.

Published
2019

15. 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

16. Evolution of Hepatitis B Virus Receptor NTCP Reveals Differential Pathogenicities and Species Specificities of Hepadnaviruses in Primates, Rodents, and Bats

Author

Jean-Baptiste Pons, Dominique Pontier, François-Loïc Cosset, Lucie Etienne, Barthélémy Ngoubangoye, Stéphanie Jacquet, Corinne Régis, Ariel de Bernardo, 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 International de Recherches Médicales de Franceville (CIRMF), Virologie humaine, École normale supérieure - Lyon (ENS Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), 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), mulet-marquis, odile, Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), École normale supérieure de Lyon (ENS de Lyon)-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), and Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI)

Subjects
Primates, Hepatitis B virus, Rodent, Immunology, Organic Anion Transporters, Sodium-Dependent, Rodentia, medicine.disease_cause, Microbiology, Host Specificity, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Orthohepadnavirus, Viral envelope, Species Specificity, Viral Envelope Proteins, biology.animal, Chiroptera, Virology, medicine, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Animals, Humans, Primate, Receptor, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, biology, Symporters, Host (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Virus Internalization, biology.organism_classification, Hepatitis B, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genetic Diversity and Evolution, Insect Science, Hepadnavirus, 030217 neurology & neurosurgery, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Human hepatitis B virus (HBV) is a global health problem, affecting more than 250 million people worldwide. HBV-like viruses, named orthohepadnaviruses, also naturally infect nonhuman primates, rodents, and bats, but their pathogenicity and evolutionary history are unclear. Here, we determined the evolutionary history of the HBV receptors NTCP and GPC5 over millions of years of primate, rodent, and bat evolution. We use this as a proxy to understand the pathogenicity of orthohepadnaviruses in mammalian hosts and to determine the implications for species specificity. We found that NTCP, but not GPC5, has evolved under positive selection in primates (27 species), rodents (18 species), and bats (21 species) although at distinct residues. Notably, the positively selected codons map to the HBV-binding sites in primate NTCP, suggesting past genetic “arms races” with pathogenic orthohepadnaviruses. In rodents, the positively selected codons fall outside and within the presumed HBV-binding sites, which may contribute to the restricted circulation of rodent orthohepadnaviruses. In contrast, the presumed HBV-binding motifs in bat NTCP are conserved, and none of the positively selected codons map to this region. This suggests that orthohepadnaviruses may bind to different surfaces in bat NTCP. Alternatively, the patterns may reflect adaptive changes associated with metabolism rather than pathogens. Overall, our findings further point to NTCP as a naturally occurring genetic barrier for cross-species transmissions in primates, which may contribute to the narrow host range of HBV. In contrast, this constraint seems less important in bats, which may correspond to greater orthohepadnavirus circulation and diversity. IMPORTANCE Chronic infection with hepatitis B virus (HBV) is a major cause of liver disease and cancer in humans. Mammalian HBV-like viruses are also found in nonhuman primates, rodents, and bats. As for most viruses, HBV requires a successful interaction with a host receptor for replication. Cellular receptors are thus key determinants of host susceptibility as well as specificity. One hallmark of pathogenic virus-host relationships is the reciprocal evolution of host receptor and viral envelope proteins, as a result of their antagonistic interaction over time. The dynamics of these so-called “evolutionary arms races” can leave signatures of adaptive selection, which in turn reveal the evolutionary history of the virus-host interaction as well as viral pathogenicity and the genetic determinants of species specificity. Here, we show how HBV-like viruses have shaped the evolutionary history of their mammalian host receptor, as a result of their ancient pathogenicity, and decipher the genetic determinants of cross-species transmissions.

Published
2018
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17. 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

18. Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates

Author

Brigitte Crouau-Roy, Simon Penel, Rylan Shearn, Sylvain Mousset, Guillaume Douay, Jean-François Lemaître, Alison E. Wright, Gabriel A. B. Marais, Corinne Régis, and Emilie Lecompte

Subjects
0106 biological sciences, 0303 health sciences, Evolution of sexual reproduction, biology, Pseudoautosomal region, Lemur, Chromosome, 010603 evolutionary biology, 01 natural sciences, Genome, Sexual dimorphism, 03 medical and health sciences, Evolutionary biology, biology.animal, Gene, Recombination, 030304 developmental biology
Abstract

Sex chromosomes are typically comprised of a non-recombining region and a recombining pseudoautosomal region. Accurately quantifying the relative size of these regions is critical for sex chromosome biology both from a functional (i.e. number of sex-linked genes) and evolutionary perspective (i.e. extent of Y degeneration and X-Y heteromorphy). The evolution of the pseudoautosomal boundary (PAB) - the limit between the recombining and the non-recombining regions of the sex chromosomes - is well documented in haplorrhines (apes and monkeys) but not in strepsirrhines (lemurs and lorises), which represent almost 30% of all primates. Here we studied the PAB of seven species representing the main strepsirrhine lineages by sequencing a male and a female genome in each species and using sex differences in coverage to identify the PAB. We found that during primate evolution, the PAB has remained unchanged in strepsirrhines whereas several recombination suppression events moved the PAB and shortened the pseudoautosomal region in haplorrhines. Strepsirrhines are well known to have much lower sexual dimorphism than haplorrhines. We suggest that mutations with antagonistic effects between males and females have driven recombination suppression and PAB evolution in haplorrhines. Our work supports the view that sexually antagonistic mutations have influenced the evolution of sex chromosomes in primates.

Published
2018

19. 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

20. Routes of transmission during a nosocomial influenza A(H3N2) outbreak among geriatric patients and healthcare workers

Author

Philippe Vanhems, Jean-Sébastien Casalegno, Corinne Régis, Thomas Bénet, D. Eibach, M. Bouscambert, B.-A. Kim, Bruno Lina, Brigitte Comte, 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
Male, [SDV]Life Sciences [q-bio], Attack rate, Hemagglutinin Glycoproteins, Influenza Virus, Disease Outbreaks, 0302 clinical medicine, Hygiene, Surveys and Questionnaires, Acute care, Epidemiology, Cluster Analysis, Medicine, 030212 general & internal medicine, Phylogeny, media_common, Aged, 80 and over, Cross Infection, Molecular Epidemiology, 0303 health sciences, biology, Transmission (medicine), virus diseases, General Medicine, Middle Aged, 3. Good health, Infectious Diseases, RNA, Viral, Female, France, Adult, Microbiology (medical), medicine.medical_specialty, Genotype, Isolation (health care), media_common.quotation_subject, Neuraminidase, Viral Proteins, Young Adult, 03 medical and health sciences, Influenza, Human, Humans, Aged, 030306 microbiology, business.industry, Influenza A Virus, H3N2 Subtype, Outbreak, Sequence Analysis, DNA, Virology, Emergency medicine, biology.protein, business
Abstract

Summary Background Influenza presents a life-threatening infection for hospitalized geriatric patients, who might be nosocomially infected via healthcare workers (HCWs), other patients or visitors. In the 2011/2012 influenza season an influenza A(H3N2) outbreak occurred in the geriatric department at the Hopital Edouard Herriot, Lyon. Aim To clarify the transmission chain for this influenza A(H3N2) outbreak by sequence analysis and to identify preventive measures. Methods Laboratory testing of patients with influenza-like illness in the acute care geriatric department revealed 22 cases of influenza between 19th February and 15th March 2012. Incidences for patients and HCWs were calculated and possible epidemiological links were analysed using a questionnaire. Neuraminidase and haemagglutinin genes of culture-positive samples and community influenza samples were sequenced and clustered to detect patients with identical viral strains. Findings Sixteen patients and six HCWs were affected, resulting in an attack rate of 24% and 11% respectively. Six nosocomial infections were recorded. The sequence analysis confirmed three independent influenza clusters on three different sections of the geriatric ward. For at least two clusters, an HCW source was determined. Conclusion Epidemiological and microbiological results confirm influenza transmission from HCWs to patients. A higher vaccination rate, isolation measures and better hand hygiene are recommended in order to prevent outbreaks in future influenza seasons.

Published
2014

21. Detection of hospital outbreaks of influenza-like illness based on excess of incidence rates compared to the community

Author

Brigitte Coppéré, Vanessa Escuret, Brigitte Comte, Bruno Lina, Philippe Vanhems, Corinne Régis, René Ecochard, Marine Giard, Thomas Bénet, Sylvain Roche, and Nicolas Voirin

Subjects
Pediatrics, medicine.medical_specialty, Epidemiology, Hospitalized patients, Viral infection, Disease Outbreaks, Influenza, Human, medicine, Humans, Prospective Studies, Cross Infection, Influenza-like illness, business.industry, Incidence, Health Policy, Public Health, Environmental and Occupational Health, virus diseases, Outbreak, University hospital, Hospitals, respiratory tract diseases, Community-Acquired Infections, Infectious Diseases, Population Surveillance, France, business
Abstract

The risk of nosocomial influenza-like illness (noso-ILI) compared with that of community-acquired ILI was calculated during 3 influenza seasons (2004-2007) at a 1100-bed university hospital with a total of 21,519 hospitalized patients. Outbreaks of noso-ILI occurred in each season, although a protective effect against noso-ILI was also identified for other wards.

Published
2014

22. 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

23. 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

24. 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

25. Influenza vaccine effectiveness among adult patients in a University of Lyon hospital (2004–2009)

Author

Brigitte Coppéré, Bruno Lina, Sélilah Amour, Corinne Régis, Brigitte Comte, Philippe Vanhems, Nicolas Voirin, M. Bouscambert-Duchamp, Silène Pires-Cronenberger, 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 ), 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 ), 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], 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), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Virologie et pathologie humaine (VirPath), Hospices Civils de Lyon (HCL)-Hôpital Edouard Herriot [CHU - HCL], and Hospices Civils de Lyon (HCL)

Subjects
Male, Hospitalized patients, [SDV]Life Sciences [q-bio], MESH : Aged, MESH : Prospective Studies, Hospitals, University, MESH: Influenza Vaccines, MESH: Aged, 80 and over, 0302 clinical medicine, Medicine, MESH : Female, Prospective Studies, MESH : Influenza, Human, 030212 general & internal medicine, Aged, 80 and over, MESH: Aged, 0303 health sciences, MESH: Middle Aged, MESH: Influenza, Human, virus diseases, Middle Aged, MESH : Adult, MESH: Case-Control Studies, 3. Good health, Infectious Diseases, Influenza Vaccines, Molecular Medicine, Female, France, Adult, MESH : Case-Control Studies, medicine.medical_specialty, Influenza vaccine, MESH : Male, Virus, 03 medical and health sciences, Age groups, Internal medicine, Influenza, Human, Flu season, Humans, MESH : Middle Aged, MESH : France, MESH : Aged, 80 and over, MESH : Hospitals, University, Aged, 030304 developmental biology, MESH: Hospitals, University, MESH: Humans, [ SDV ] Life Sciences [q-bio], General Veterinary, General Immunology and Microbiology, Adult patients, business.industry, MESH : Humans, Public Health, Environmental and Occupational Health, MESH: Adult, MESH: Male, MESH: Prospective Studies, MESH : Influenza Vaccines, Confidence interval, MESH: France, Case-Control Studies, Immunology, business, MESH: Female
Abstract

International audience; The aim of this study was to estimate influenza vaccine effectiveness (IVE) against laboratory-confirmed influenza among hospitalized patients. A case-control investigation was based on the prospective surveillance of influenza-like illness (ILI) during five flu seasons. We compared influenza-positive cases and influenza-negative controls. Unadjusted overall IVE was 62% (95% confidence interval 24% to 81%). We found that IVE was lower during the 2004-05 flu season (11%; 95% CI -232% to 76%) when the vaccine and circulating viruses were mismatched. Expansion of the study to other hospitals could provide IVE estimates earlier in the season, for different age groups and emerging virus strains.

Published
2012

26. Contacts between health care workers and patients in a short-stay geriatric unit during the peak of a seasonal influenza epidemic compared with a nonepidemic period

Author

Thomas Bénet, Nagham Khanafer, Nadia Oussaid, Corinne Régis, Brigitte Comte, Philippe Vanhems, Adélaïde Vincent, Nicolas Voirin, and Géraldine Martin-Gaujard

Subjects
Cross infection, medicine.medical_specialty, Pediatrics, Patients, Epidemiology, Health Services for the Aged, Health Personnel, 030501 epidemiology, Seasonal influenza, Hospitals, University, 03 medical and health sciences, Health personnel, 0302 clinical medicine, Health care, Influenza, Human, medicine, Disease Transmission, Infectious, Humans, 030212 general & internal medicine, Contact duration, Intensive care medicine, Contact number, Epidemics, Cross Infection, business.industry, Health Policy, Public Health, Environmental and Occupational Health, University hospital, Infectious Diseases, Short stay, 0305 other medical science, business, Behavior Observation Techniques
Abstract

Background Patterns of contacts between health care workers and patients during seasonal epidemics are unknown. Our study objective was to compare the number and duration of contacts between health care workers and patients during a nonepidemic period versus a community influenza epidemic, and to identify supercontactors. Methods Our observational study was conducted in a short-stay geriatric unit of a university hospital. Contacts between individuals were recorded by active radio frequency identification devices. Contact patterns were compared between 2 periods according to contact number and duration. Each care period lasted 5 days in the nonepidemic and influenza epidemic periods. Results The study included 21 medical doctors, 43 nurses, and 56 patients. In total, 3,200 contacts (61.4%; 152,700 seconds) were recorded during the nonepidemic period, with 2,013 contacts (38.6%; 92,740 seconds) in the epidemic period ( P = .007). More cumulative contacts occurred during the nonepidemic period between nurses and patients (n = 2,638 [82%] vs n = 1,599 [79%]), but not between patients (n = 56 [18%] vs n = 414 [21%]). Contact duration between nurses and patients lasted longer during the nonepidemic period ( P = .04). During the epidemic period, 6 nurses (15%) considered to be supercontactors accounted for 44.3% of the total number of contacts with patients. Conclusion The pattern of contacts between individuals differed according to the presence or not of the community influenza peak that might have influenced the risk of nosocomial influenza.

Published
2015

27. Combining high-resolution contact data with virological data to investigate influenza transmission in a tertiary care hospital

Author

Byeul-a Kim, Nagham Khanafer, Alain Barrat, Brigitte Comte, Jean-Sébastien Casalegno, Cécile Payet, Bruno Lina, Corinne Régis, Philippe Vanhems, Ciro Cattuto, Nicolas Voirin, CPT - E5 Physique statistique et systèmes complexes, Centre de Physique Théorique - UMR 7332 (CPT), and 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)

Subjects
Microbiology (medical), Adult, Male, medicine.medical_specialty, Infectious Disease Transmission, Patient-to-Professional, Epidemiology, MEDLINE, medicine.disease_cause, Real-Time Polymerase Chain Reaction, Infectious Disease Transmission, Professional-to-Patient, Tertiary Care Centers, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Health care, Influenza, Human, medicine, Influenza A virus, Humans, 030212 general & internal medicine, Intensive care medicine, Phylogeny, 030304 developmental biology, Aged, Aged, 80 and over, 0303 health sciences, Cross Infection, Transmission (medicine), Infectious disease transmission, business.industry, Influenza A Virus, H3N2 Subtype, Influenza transmission, Tertiary care hospital, Middle Aged, 3. Good health, Influenza B virus, Infectious Diseases, Emergency medicine, Observational study, Female, Contact Tracing, business
Abstract

OBJECTIVEContact patterns and microbiological data contribute to a detailed understanding of infectious disease transmission. We explored the automated collection of high-resolution contact data by wearable sensors combined with virological data to investigate influenza transmission among patients and healthcare workers in a geriatric unit.DESIGNProof-of-concept observational study. Detailed information on contact patterns were collected by wearable sensors over 12 days. Systematic nasopharyngeal swabs were taken, analyzed for influenza A and B viruses by real-time polymerase chain reaction, and cultured for phylogenetic analysis.SETTINGAn acute-care geriatric unit in a tertiary care hospital.PARTICIPANTSPatients, nurses, and medical doctors.RESULTSA total of 18,765 contacts were recorded among 37 patients, 32 nurses, and 15 medical doctors. Most contacts occurred between nurses or between a nurse and a patient. Fifteen individuals had influenza A (H3N2). Among these, 11 study participants were positive at the beginning of the study or at admission, and 3 patients and 1 nurse acquired laboratory-confirmed influenza during the study. Infectious medical doctors and nurses were identified as potential sources of hospital-acquired influenza (HA-Flu) for patients, and infectious patients were identified as likely sources for nurses. Only 1 potential transmission between nurses was observed.CONCLUSIONSCombining high-resolution contact data and virological data allowed us to identify a potential transmission route in each possible case of HA-Flu. This promising method should be applied for longer periods in larger populations, with more complete use of phylogenetic analyses, for a better understanding of influenza transmission dynamics in a hospital setting.Infect Control Hosp Epidemiol 2015;00(0): 1–7

Published
2015

28. The risk of hospital-acquired GB virus C infection: a pilot case–control study

Author

D. Yzèbe, C. Del Signore, J. Fabry, M.A. Trabaud, Nicolas Voirin, C. Trepo, Corinne Régis, and Philippe Vanhems

Subjects
Adult, Male, Risk, Microbiology (medical), medicine.medical_specialty, Hepatitis, Viral, Human, Hepatitis C virus, GB virus C, Pilot Projects, medicine.disease_cause, Virus, Flaviviridae, Internal medicine, Bronchoscopy, medicine, Humans, Risk factor, Substance Abuse, Intravenous, Aged, Cross Infection, biology, business.industry, Case-control study, General Medicine, Odds ratio, Flaviviridae Infections, Middle Aged, biology.organism_classification, Infectious Diseases, Case-Control Studies, Cohort, Immunology, Female, business
Abstract

The risk of hospital-acquired infection with GB virus C (GBV-C) was explored among 42 patients. The factors independently associated with detection of GBV-C RNA in serum were bronchoscopic examination [adjusted odds ratio (OR)=18.1 (95% confidence interval 1.3-255.3), P=0.03] and a history of illicit drug use [OR=14.5 (1.0-218.7), P=0.05]. In this cohort of patients, invasive procedures appear to be associated with GBV-C infection but not with hepatitis C virus (HCV) infection.

Published
2003

29. Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors

Author

Nagham Khanafer, Nicolas Voirin, Jean-François Pinton, Ciro Cattuto, Alain Barrat, Philippe Vanhems, Corinne Régis, Byeul-a Kim, Brigitte Comte, 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), CPT - E5 Physique statistique et systèmes complexes, Centre de Physique Théorique - UMR 7332 (CPT), 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, Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), 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, 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), Service de médecine gériatrique, Hospices Civils de Lyon (HCL)-Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
Pediatrics, Wearable computer, lcsh:Medicine, 01 natural sciences, Quantitative Biology - Quantitative Methods, 010305 fluids & plasmas, law.invention, 0302 clinical medicine, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Proximity sensor, Medicine, Infection transmission, 030212 general & internal medicine, Longitudinal Studies, lcsh:Science, Quantitative Methods (q-bio.QM), Geriatrics, 0303 health sciences, education.field_of_study, Cross Infection, Multidisciplinary, General Medicine, University hospital, 3. Good health, Transmission (mechanics), Medical emergency, General Agricultural and Biological Sciences, Research Article, medicine.medical_specialty, Physics - Physics and Society, Science, Population, FOS: Physical sciences, Physics and Society (physics.soc-ph), Communicable Diseases, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0103 physical sciences, Patients' Rooms, Disease Transmission, Infectious, Humans, 010306 general physics, education, 030304 developmental biology, business.industry, lcsh:R, Correction, medicine.disease, FOS: Biological sciences, Communicable disease transmission, Communicable Disease Control, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract

BACKGROUND: Contacts between patients, patients and health care workers (HCWs) and among HCWs represent one of the important routes of transmission of hospital-acquired infections (HAI). A detailed description and quantification of contacts in hospitals provides key information for HAIs epidemiology and for the design and validation of control measures. METHODS AND FINDINGS: We used wearable sensors to detect close-range interactions ("contacts") between individuals in the geriatric unit of a university hospital. Contact events were measured with a spatial resolution of about 1.5 meters and a temporal resolution of 20 seconds. The study included 46 HCWs and 29 patients and lasted for 4 days and 4 nights. 14,037 contacts were recorded overall, 94.1% of which during daytime. The number and duration of contacts varied between mornings, afternoons and nights, and contact matrices describing the mixing patterns between HCW and patients were built for each time period. Contact patterns were qualitatively similar from one day to the next. 38% of the contacts occurred between pairs of HCWs and 6 HCWs accounted for 42% of all the contacts including at least one patient, suggesting a population of individuals who could potentially act as super-spreaders. CONCLUSIONS: Wearable sensors represent a novel tool for the measurement of contact patterns in hospitals. The collected data can provide information on important aspects that impact the spreading patterns of infectious diseases, such as the strong heterogeneity of contact numbers and durations across individuals, the variability in the number of contacts during a day, and the fraction of repeated contacts across days. This variability is however associated with a marked statistical stability of contact and mixing patterns across days. Our results highlight the need for such measurement efforts in order to correctly inform mathematical models of HAIs and use them to inform the design and evaluation of prevention strategies.

Published
2013
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30. O023: Combining electronic contacts data and virological data for studying the transmission of infections at hospital

Author

J-F Pinton, Nicolas Voirin, Ciro Cattuto, Cécile Payet, Alain Barrat, Nagham Khanafer, Corinne Régis, Philippe Vanhems, Brigitte Comte, B-A Kim, and Bruno Lina

Subjects
Microbiology (medical), medicine.medical_specialty, Hospital setting, business.industry, education, Public Health, Environmental and Occupational Health, virus diseases, Influenza transmission, Bioinformatics, law.invention, Infectious Diseases, Transmission (mechanics), Medical microbiology, law, Statistical analyses, Emergency medicine, medicine, Oral Presentation, Pharmacology (medical), business
Abstract

HCWs. Among these persons with a high number of contacts, 3 (60%) patients and 1 (10%) HCW had con- firmed influenza. Among those with a lower number of contacts, 7 (22%) patients and 4 (11%) HCWs had con- firmed influenza. Further statistical analyses are ongoing to assess the relationship between the number and dura- tion of contacts and the risk of influenza transmission. Conclusion Collecting contacts data in the hospital setting and com- bining this information with virological data could be an interesting approach to study the transmission of HAIs. We identified patients and HCWs with a high number of contacts, who could be considered as potential super- spreaders of infections. This is key information that may help to implement prevention and control measures.

Published
2013

31. Five years of hospital based surveillance of influenza-like illness and influenza in a short-stay geriatric unit

Author

Corinne Régis, Brigitte Comte, Vanessa Escuret, Bruno Lina, Nicolas Voirin, Olivier Robert, Philippe Vanhems, Byeul-a Kim, 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), 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), Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), 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), Service de médecine gériatrique, centre hospitalier Lyon Sud, Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Laboratoire des pathogènes émergents -- Emerging Pathogens Laboratory (LPE-Fondation Mérieux), 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
Male, medicine.medical_specialty, Time Factors, Fever, Health Services for the Aged, [SDV]Life Sciences [q-bio], Short Report, Context (language use), General Biochemistry, Genetics and Molecular Biology, Influenza, Human, medicine, Sore throat, Humans, Prospective Studies, Prospective cohort study, Aged, Medicine(all), Geriatrics, Aged, 80 and over, Influenza-like illness, Cross Infection, Surveillance, Biochemistry, Genetics and Molecular Biology(all), business.industry, Outbreak, virus diseases, Pharyngitis, General Medicine, medicine.disease, Influenza, 3. Good health, respiratory tract diseases, Hospitalization, Short stay, Cough, Population Surveillance, Emergency medicine, Female, Medical emergency, medicine.symptom, Geriatrics, Surveillance, business, Hospital-acquired
Abstract

Background Data on influenza in the healthcare setting are often based on retrospective investigations of outbreaks and a few studies described influenza during several consecutive seasons. The aim of the present work is to report data on influenza like illness (ILI) and influenza from 5-year prospective surveillance in a short-stay geriatrics unit. Findings A short stay geriatrics unit underwent 5 years of ILI surveillance from November 2004 to March 2009, with the aim of describing ILI in a non-outbreak context. The study was proposed to patients who presented ILI, defined as fever >37.8°C or cough or sore throat. Among 1,353 admitted patients, 115 presented an ILI, and 34 had hospital-acquired ILI (HA-ILI). Influenza was confirmed in 23 patients, 13 of whom had been vaccinated. Overall attack rates were 2.78% and 0.02% for HA-ILI and HA-confirmed influenza respectively, during the 5 seasons. Conclusions This 5-year surveillance study supports the notion that influenza infections are common in hospitals, mostly impacting the elderly hospitalized in short-stay units. It highlights the need for appropriate control measures to prevent HA-ILI in geriatric units and protect elderly patients.

Published
2013

32. 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

33. 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

34. 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

35. Risk of Influenza-Like Illness in an Acute Health Care Setting During Community Influenza Epidemics in 2004-2005, 2005-2006, and 2006-2007

Author

Nicolas Voirin, Christine Gorain, Bruno Lina, Fatiha Najioullah, Marine Giard, Béatrice Barret, Sandra David, Philippe Vanhems, Silène Pires-Cronenberger, René Ecochard, Bernard Hirschel, Sylvain Roche, Brigitte Comte, Vanessa Escuret, Marie-Noelle Crozet, Laurence Pollissard, and Corinne Régis

Subjects
Adult, Male, Risk, medicine.medical_specialty, Pediatrics, 03 medical and health sciences, 0302 clinical medicine, Residence Characteristics, Influenza, Human, Health care, Epidemiology, Internal Medicine, medicine, Humans, Prospective Studies, 030212 general & internal medicine, Risk factor, Epidemics, Prospective cohort study, Aged, Aged, 80 and over, Cross Infection, 0303 health sciences, Influenza-like illness, 030306 microbiology, business.industry, Transmission (medicine), Public health, virus diseases, Middle Aged, respiratory tract diseases, 3. Good health, Relative risk, Acute Disease, Emergency medicine, Female, business
Abstract

Background The person-to-person transmission of influenza-like illness (ILI) and influenza has been described mostly in long-term care units. Studies in acute hospital settings are rare and mostly retrospective. Methods We prospectively estimated the relative risk (RR) of hospital-acquired (HA) ILI during hospitalization according to in-hospital exposures to contagious individuals. Surveillance of ILI and laboratory-confirmed influenza was undertaken at Edouard Herriot Hospital (1100 beds) during 3 influenza seasons. A total of 21 519 patients and 2153 health care workers (HCWs) from 2004 to 2007 were included. The RR of HA-ILI in patients was calculated according to exposure to other contagious patients and HCWs. Results For patients exposed to at least 1 contagious HCW compared with those with no documented exposure in the hospital, the RR of HA-ILI was 5.48 (95% confidence interval [CI], 2.09-14.37); for patients exposed to at least 1 contagious patient, the RR was 17.96 (95% CI, 10.07-32.03); and for patients exposed to at least 1 contagious patient and 1 contagious HCW, the RR was 34.75 (95% CI, 17.70-68.25). Conclusions Hospitalized patients exposed to potentially infectious patients and HCWs with ILI inside the hospital are at greater risk for HA-ILI. Such results identify priorities regarding preventive measures for seasonal or pandemic influenza.

Published
2011

36. Quelles alternatives à la fermeture des écoles pour la transmission de la grippe ?

Author

Bruno Lina, Cécile Payet, Corinne Régis, Philippe Vanhems, Nicolas Voirin, and Jean-François Pinton

Subjects
Epidemiology, Public Health, Environmental and Occupational Health
Abstract

Introduction La vaccination des enfants et la fermeture des ecoles sont des interventions recommandees pour controler la propagation de la grippe, mais leur association ne semble pas offrir un gain cumule pour le controle de la transmission. Notre objectif etait d’evaluer l’impact de l’ajournement temporaire des enfants, associe a la vaccination, comme strategie alternative a la fermeture des ecoles. Methodes Un modele stochastique individu-centre a ete utilise pour simuler la propagation de la grippe dans une ecole au moyen de donnees detaillees de contact recueillies aupres de 242 enfants equipes de capteurs RFID. Vingt et un scenarios, combinant differentes frequences d’ajournement et strategies de vaccination, ont ete etudies. Resultats En l’absence d’ajournement et de vaccination, un taux d’attaque de 55 % (134/242) etait calcule, dont 90 % des cas resultant de transmission intra-ecole. En l’absence de vaccination, un ajournement effectue trois fois par jour aboutissait a un taux d’attaque de 25 % (73 cas evites). Cet effet etait superieur ou similaire a certains scenarios bases sur la vaccination, mais avec un ajournement moins frequent. La vaccination des enfants semblait contributive en cas d’identification insuffisante des cas. Discussion Malgre les limites de la modelisation, ce travail indique que la plupart des cas resulte d’une transmission intra-ecole et que l’ajournement temporaire des enfants symptomatiques peut etre une mesure de prevention utile, facilement utilisable dans les ecoles, pour ralentir la phase precoce des epidemies. Plus generalement, des mesures de prevention non pharmacologiques, au niveau de la classe ou des enfants, pourraient offrir des perspectives alternatives a la fermeture des ecoles.

Published
2014

37. Prevalence of primary resistance to zidovudine and lamivudine in drug-naive human immunodeficiency virus type-1 infected patients: high proportion of reverse transcriptase codon 215 mutant in circulating lymphocytes and free virus

Author

Christian Trepo, Jill Detmer, Karine Leriche‐Guerin, Jacques Ritter, Mary-Anne Trabaud, Corinne Régis, Isabelle Bordes, Janice A. Kolberg, and Laurent Cotte

Subjects
Anti-HIV Agents, viruses, Mutant, HIV Infections, Biology, Polymerase Chain Reaction, Virus, Zidovudine, Proviruses, Virology, medicine, Humans, Lymphocytes, Codon, Lamivudine, Nucleic Acid Hybridization, Drug Resistance, Microbial, biochemical phenomena, metabolism, and nutrition, Provirus, Viral Load, Resistance mutation, Reverse transcriptase, HIV Reverse Transcriptase, Infectious Diseases, DNA, Viral, HIV-1, RNA, Viral, Reverse Transcriptase Inhibitors, Viral load, medicine.drug
Abstract

The presence of primary zidovudine (AZT)-resistance (mutation T215Y/F) or lamivudine (3TC)-resistance (mutation M184V) was evaluated in 90 drug-naive patients infected with human immunodeficiency virus type-1 (HIV-1) between 1987 and 1997. The proportion of mutant strains in proviral samples or plasma viral samples was determined using a differential hybridization assay. Mutation T215Y/F was found in five (5.6%) patients infected between 1994 and 1997, whereas none of these patients harbored the mutation M184V. The T215Y/F mutation was present in the virus and/or provirus and persisted for at least two years. In one patient, the mutant provirus was associated with only wild-type free virus. Four of these patients were followed, and two were treated subsequently to a regimen containing AZT but with low response. The persistence of primary resistance mutations might depend on the proportion of these mutations at the time of infection, although mutant provirus might not give rise to replicating variants.

Published
2000

38. P14.19 Nosocomial Transmission of Influenza During Seasons 2004-2005 and 2005-2006 at Edouard Herriot University Hospital, Lyon, France

Author

C. Gorain, Corinne Régis, Marie-Noelle Crozet, B. Una, F. Najioullah, P. Debeaudrap, L. Pollissard, Philippe Vanhems, S. Cronenberger, D. Floret, Brigitte Comte, and B. Barret

Subjects
Microbiology (medical), medicine.medical_specialty, Infectious Diseases, business.industry, Nosocomial transmission, medicine, General Medicine, Medical emergency, University hospital, Intensive care medicine, medicine.disease, business
Published
2006

39. Using wearable electronic sensors for assessing contacts between individuals in various environments

Author

Alain Barrat, Philippe Vanhems, W. van den Broeck, J Stehlé, Ciro Cattuto, Marco Quaggiotto, Bruno Lina, Nicolas Voirin, Corinne Régis, J-F Pinton, Nagham Khanafer, and Lorenzo Isella

Subjects
Average duration, Pathology, medicine.medical_specialty, animal structures, business.industry, Hospital setting, health care facilities, manpower, and services, education, lcsh:R, virus diseases, Wearable computer, lcsh:Medicine, General Medicine, Contact network, medicine.disease, General Biochemistry, Genetics and Molecular Biology, Health care, medicine, Oral Presentation, lcsh:Q, Medical emergency, business, lcsh:Science
Abstract

Transmission of hospital acquired infections (HAI) is mainly based on contacts between patients, patients and health care workers (HCWs) and between HCWs. Description and quantification of contacts at hospital are key information for HAIs epidemiology and implementing control measures.

Published
2011

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

Author

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien M. de Vienne, Elodie Portanier, David Fouchet, Cecile Kaerle, Lina Muselet, Guillaume Queney, Eric J. Petit, Corinne Regis, Jean-Baptiste Pons, and Dominique Pontier

Subjects
Pteronotus cf. parnellii, Microsatellite, Mitochondrial DNA, Phylogeny, Echolocation, Population genetics, Evolution, QH359-425
Abstract

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.

Published
2018
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