14 results on '"Ana Maria Burguiere"'
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2. Evaluation of High-Throughput Sequencing for Identifying Known and Unknown Viruses in Biological Samples
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Valérie Caro, Fabien Dorange, Justine Cheval, Ana Maria Burguiere, Nicolas Dumey, Claude Jean Manuguerra, Ghislaine Guigon, Kevin Pariente, Nicolas Berthet, Lionel Frangeul, Marc Eloit, Marc Lecuit, Claudine Rousseaux, Ivan Moszer, Hervé Bourhy, Sylvain Brisse, Virginie Sauvage, Laurent Dacheux, Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Institut Pasteur [Paris] (IP), Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Dynamique des Lyssavirus et Adaptation à l'Hôte (DyLAH), Texcell, Epidémiologie et Physiopathologie des Virus Oncogènes (EPVO (UMR_3569 / U-Pasteur_3)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Microorganismes et Barrières de l'Hôte (Equipe avenir), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de Virologie - Department of Virology, Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), The platform Genotyping of Pathogens and Public Health is supported in part by the Institut de Veille Sanitaire (Saint-Maurice, France). This study was mainly supported by Programme Transversal de Recherche (PATHODISC 301) from the Institut Pasteur (France) and by grants from region Ile de France., Institut Pasteur [Paris], Cellule d'Intervention Biologique d'Urgence (CIBU), Dynamique des Lyssavirus et Adaptation à l'Hôte, Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Microorganismes et Barrières de l'Hôte, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], and Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA)
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Microbiology (medical) ,Genetics ,0303 health sciences ,Contig ,030306 microbiology ,[SDV]Life Sciences [q-bio] ,Nucleic acid sequence ,Sequence assembly ,DNA ,Biology ,Genome ,DNA sequencing ,Deep sequencing ,03 medical and health sciences ,Sequencing ,viruses ,Identifying ,Illumina dye sequencing ,030304 developmental biology ,Reference genome - Abstract
High-throughput sequencing furnishes a large number of short sequence reads from uncloned DNA and has rapidly become a major tool for identifying viruses in biological samples, and in particular when the target sequence is undefined. In this study, we assessed the analytical sensitivity of a pipeline for detection of viruses in biological samples based on either the Roche-454 genome sequencer or Illumina genome analyzer platforms. We sequenced biological samples artificially spiked with a wide range of viruses with genomes composed of single or double-stranded DNA or RNA, including linear or circular single-stranded DNA. Viruses were added at a very low concentration most often corresponding to 3 or 0.8 times the validated level of detection of quantitative reverse transcriptase PCRs (RT-PCRs). For the viruses represented, or resembling those represented, in public nucleotide sequence databases, we show that the higher output of Illumina is associated with a much greater sensitivity, approaching that of optimized quantitative (RT-)PCRs. In this blind study, identification of viruses was achieved without incorrect identification. Nevertheless, at these low concentrations, the number of reads generated by the Illumina platform was too small to facilitate assembly of contigs without the use of a reference sequence, thus precluding detection of unknown viruses. When the virus load was sufficiently high, de novo assembly permitted the generation of long contigs corresponding to nearly full-length genomes and thus should facilitate the identification of novel viruses.
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- 2011
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3. Rouxiella chamberiensis gen. nov., sp. nov., a member of the family Enterobacteriaceae isolated from parenteral nutrition bags
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Clément Andonian, Meriadeg Ar Gouilh, Véronique Vincent, Mathias Vandenbogaert, Michel Perraud, Valérie Caro, Anne Le Flèche-Matéos, Ana Maria Burguiere, Yolande Arnoux, Fabienne Lomprez, Jean-Claude Manuguerra, Laure Diancourt, Marion Levast, and Jean-Michel Thiberge
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DNA, Bacterial ,Parenteral Nutrition ,Molecular Sequence Data ,Carbohydrates ,Yersinia ,Microbiology ,Serratia ,Rouxiella chamberiensis ,Aesculin ,chemistry.chemical_compound ,Enterobacteriaceae ,RNA, Ribosomal, 16S ,Raffinose ,Melibiose ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Base Composition ,biology ,Nucleic Acid Hybridization ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,16S ribosomal RNA ,Bacterial Typing Techniques ,Type species ,chemistry ,Genes, Bacterial ,Equipment Contamination ,France ,Multilocus Sequence Typing - Abstract
Parenteral nutrition bags for newborns were found contaminated by a previously undescribed member of the family Enterobacteriaceae . The six isolates studied by rrs gene (encoding 16S rRNA) sequence analysis and multi-locus sequence analysis (MLSA) formed a discrete branch close to the genera Ewingella , Rahnella , Yersinia , Hafnia and Serratia . Phenotypically, the new taxon was distinct from these five genera. The new taxon gave positive results in Voges–Proskauer, Simmons citrate and o-nitrophenyl-β-galactoside hydrolysis tests; fermented d-glucose, d-mannitol, l-rhamnose, melibiose, l-arabinose and d-xylose; hydrolysed aesculin; and did not ferment maltose, trehalose, raffinose, d-sorbitol, sucrose or cellobiose. Tests for motility, gas production, urease, gelatinase and nitrate reduction were also negative. All isolates failed to grow at 37 °C. The DNA G+C content of strain 130333T was 53 mol%. On the basis of data obtained in this study, the six isolates represent a novel species of a new genus in the family Enterobacteriaceae , named Rouxiella chamberiensis gen. nov., sp. nov. The type strain of the type species is 130333T ( = CIP 110714T = DSM 28324T).
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- 2015
4. Identification of the First Human Gyrovirus, a Virus Related to Chicken Anemia Virus
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Virginie Sauvage, Valérie Caro, Vincent Foulongne, Meriadeg Ar Gouilh, Marc Lecuit, Justine Cheval, Marc Eloit, Jennifer Richardson, Kevin Pariente, Olivier Dereure, Jean Claude Manuguerra, Ana Maria Burguiere, Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris], PathoQuest, Laboratoire de Virologie, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Service de Dermatologie, Microorganismes et Barrières de l'Hôte (Equipe avenir), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Génotypage des Eucaryotes (Plate-Forme), Région Ile de France, Programme Hospitalier de Recherche Clinique of the Montpellier University Hospital, Eloit, Marc, Cellule d'Intervention Biologique d'Urgence (CIBU), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA), Microorganismes et Barrières de l'Hôte, Institut Pasteur [Paris] (IP), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)
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[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Anemia ,maladie contagieuse ,Molecular Sequence Data ,Immunology ,poulet ,virus ,Biology ,Polymerase Chain Reaction ,Microbiology ,Virus ,law.invention ,Open Reading Frames ,03 medical and health sciences ,Gyrovirus ,law ,Virology ,medicine ,Humans ,Amino Acid Sequence ,cellule cancereuse ,Polymerase chain reaction ,Feces ,030304 developmental biology ,anémie ,0303 health sciences ,Base Sequence ,Sequence Homology, Amino Acid ,030306 microbiology ,medicine.disease ,biology.organism_classification ,3. Good health ,Open reading frame ,Genetic Diversity and Evolution ,Apoptosis ,Insect Science ,Cancer cell ,Capsid Proteins ,Bronchoalveolar Lavage Fluid ,Chicken anemia virus - Abstract
We have identified in a skin swab sample from a healthy donor a new virus that we have named human gyrovirus (HGyV) because of its similarity to the chicken anemia virus (CAV), the only previously known member of the Gyrovirus genus. In particular, this virus encodes a homolog of the CAV apoptin, a protein that selectively induces apoptosis in cancer cells. By PCR screening, HGyV was found in 5 of 115 other nonlesional skin specimens but in 0 of 92 bronchoalveolar lavages or nasopharyngeal aspirates and in 0 of 92 fecal samples.
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- 2011
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5. A Member of a New Picornaviridae Genus Is Shed in Pig Feces
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Kevin Pariente, Marc Eloit, Virginie Sauvage, Jean-Claude Manuguerra, Justine Cheval, Erika Muth, Meriadeg Ar Gouilh, Ana Maria Burguiere, Valérie Caro, Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris], PathoQuest, Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Département de Virologie - Department of Virology, Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), This study was mainly supported by Programme Transversal de Recherche (PATHODISC 301) of the Institut Pasteur (Paris, France) and by grants from region Ile de France, Cellule d'Intervention Biologique d'Urgence (CIBU), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Pasteur [Paris] (IP), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
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Male ,[SDV]Life Sciences [q-bio] ,animal diseases ,New Picornaviridae Genus ,Immunology ,Molecular Sequence Data ,Sus scrofa ,Picornaviridae ,Parechovirus ,Genome, Viral ,Microbiology ,Genome ,Virus ,Pig Feces ,03 medical and health sciences ,Feces ,Virology ,Animals ,Amino Acid Sequence ,Viral shedding ,Phylogeny ,030304 developmental biology ,0303 health sciences ,biology ,Base Sequence ,Sequence Homology, Amino Acid ,030306 microbiology ,Genetic Variation ,biology.organism_classification ,Virus Shedding ,Open reading frame ,Genetic Diversity and Evolution ,Insect Science ,DNA, Viral ,Herd ,Metagenome ,Capsid Proteins ,Female - Abstract
During a study of the fecal microbiomes from two healthy piglets using high-throughput sequencing (HTS), we identified a viral genome containing an open reading frame encoding a predicted polyprotein of 2,133 amino acids. This novel viral genome displayed the typical organization of picornaviruses, containing three structural proteins (VP0, VP3, and VP1), followed by seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3C pro , and 3D pol ). Given its particular relationship with Parechovirus , we propose to name it “Pasivirus” for Pa recho si ster clade virus, with “Swine pasivirus 1” (SPaV1) as the type species. Fecal samples collected at an industrial farm from healthy sows and piglets from the same herd (25 and 75, respectively) with ages ranging from 4 to 28 weeks were analyzed for the presence of SPaV1 by one-step reverse transcription (RT)-PCR targeting a 3D region of 151 bp. SPaV1 was detected in fecal samples from 51/75 healthy piglets (68% of the animals) and in none of the 25 fecal samples from healthy sows, indicating that SPaV1 circulates through enteric infection of healthy piglets. We propose that SPaV1 represents the first member of a novel Picornaviridae genus related to parechoviruses.
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- 2012
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6. Recurrent Breast Abscesses due to Corynebacterium kroppenstedtii, a Human Pathogen Uncommon in Caucasian Women
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Yolande Arnoux, Fabienne Lomprez, Nicolas Berthet, India Leclercq, Anne Le Flèche-Matéos, Ana Maria Burguiere, Jean-Claude Manuguerra, Anne-Sophie Le Guern, Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris], Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre Médical de l'Institut Pasteur (CMIP), This programme was supported by the Programme Transversal de Recherche (PTR DEVA n° 246) financed by Institut Pasteur (Paris, France) and from the sponsorship of Fondation Total-Institut Pasteur. They thank Grégory Jouvion (Unité d’Histophathologie humaine et modèles animaux, Institut Pasteur) for some translation concerning histology and Philippe Riegel (Université Louis Pasteur, Hôpitaux Universitaires de Strasbourg) for his clinical experience. They also thank the Platform of Genotyping of Pathogens and Public Health (PF8) at Institut Pasteur for using the Affymetrix station and Meriadeg Le Gouil for his photography assistance., Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Centre Médical de l'Institut Pasteur
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0303 health sciences ,Pathology ,medicine.medical_specialty ,business.industry ,[SDV]Life Sciences [q-bio] ,Case Report ,Human pathogen ,General Medicine ,Case presentation ,Granulomatous mastitis ,medicine.disease ,Dermatology ,3. Good health ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,0302 clinical medicine ,030220 oncology & carcinogenesis ,medicine ,Etiology ,Sputum ,lcsh:RC109-216 ,medicine.symptom ,business ,030304 developmental biology ,Corynebacterium kroppenstedtii - Abstract
Background.Corynebacterium kroppenstedtii(Ck) was first described in 1998 from human sputum. Contrary to what is observed in ethnic groups such as Maori,Ckis rarely isolated from breast abscesses and granulomatous mastitis in Caucasian women.Case Presentation. We herein report a case of recurrent breast abscesses in a 46-year-old Caucasian woman.Conclusion. In the case of recurrent breast abscesses, even in Caucasian women, the possible involvement ofCkshould be investigated. The current lack of such investigations, probably due to the difficulty to detectCk, may cause the underestimation of such an aetiology.
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- 2012
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7. Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing
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Vincent Foulongne, Virginie Sauvage, Olivier Dereure, Charles Hebert, Meriadeg Ar Gouilh, Justine Cheval, Jean-Claude Manuguerra, Kevin Pariente, Valérie Caro, Ana Maria Burguiere, Michel Segondy, Marc Eloit, Université Montpellier 1 (UM1), Dept Dermatol, University of Dresden Medical School, Institut Pasteur [Paris], PathoQuest, Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut de Veille Sanitaire (Saint-Maurice, France), region Ile de France, Montpellier University Hospital [AOI 2008, UF8425], Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris] (IP), Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and Département de Virologie - Department of Virology
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Bacterial Diseases ,Viral Diseases ,Flora ,MERKEL CELL POLYOMAVIRUS ,SAMPLES ,viruses ,[SDV]Life Sciences [q-bio] ,lcsh:Medicine ,Merkel cell polyomavirus ,Human skin ,Dermatologic Pathology ,MOLECULAR ANALYSIS ,PSORIATIC LESIONS ,Bacteriophages ,lcsh:Science ,Papillomaviridae ,Phylogeny ,Skin ,Circoviridae ,Genetics ,0303 health sciences ,Multidisciplinary ,biology ,Merkel cell carcinoma ,High-Throughput Nucleotide Sequencing ,Bacterial Pathogens ,3. Good health ,GENOMIC CHARACTERIZATION ,Infectious Diseases ,CIRCOVIRUSES ,Medicine ,BACTERIAL BIOTA ,Polyomaviridae ,Research Article ,Skin Infections ,CARCINOMA ,Dermatology ,Genome, Viral ,Microbiology ,Microbial Ecology ,03 medical and health sciences ,Virology ,medicine ,Humans ,CUTANEOUS HUMAN PAPILLOMAVIRUSES ,Human virome ,HEALTHY SKIN ,Microbiome ,Biology ,030304 developmental biology ,Bacteria ,030306 microbiology ,lcsh:R ,DNA Viruses ,biology.organism_classification ,medicine.disease ,Metagenome ,lcsh:Q ,Circovirus ,Genome, Bacterial - Abstract
International audience; The human skin is a complex ecosystem that hosts a heterogeneous flora. Until recently, the diversity of the cutaneous microbiota was mainly investigated for bacteria through culture based assays subsequently confirmed by molecular techniques. There are now many evidences that viruses represent a significant part of the cutaneous flora as demonstrated by the asymptomatic carriage of beta and gamma-human papillomaviruses on the healthy skin. Furthermore, it has been recently suggested that some representatives of the Polyomavirus genus might share a similar feature. In the present study, the cutaneous virome of the surface of the normal-appearing skin from five healthy individuals and one patient with Merkel cell carcinoma was investigated through a high throughput metagenomic sequencing approach in an attempt to provide a thorough description of the cutaneous flora, with a particular focus on its viral component. The results emphasize the high diversity of the viral cutaneous flora with multiple polyomaviruses, papillomaviruses and circoviruses being detected on normal-appearing skin. Moreover, this approach resulted in the identification of new Papillomavirus and Circovirus genomes and confirmed a very low level of genetic diversity within human polyomavirus species. Although viruses are generally considered as pathogen agents, our findings support the existence of a complex viral flora present at the surface of healthy-appearing human skin in various individuals. The dynamics and anatomical variations of this skin virome and its variations according to pathological conditions remain to be further studied. The potential involvement of these viruses, alone or in combination, in skin proliferative disorders and oncogenesis is another crucial issue to be elucidated.
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- 2012
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8. Persistence of the 2009 Pandemic Influenza A (H1N1) Virus in Water and on Non-Porous Surface
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Anthony Pinon, Christophe Batéjat, India Leclercq, Amélie Dublineau, Jean-Claude Manuguerra, Ana Maria Burguiere, Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris] (IP), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Université Sorbonne Paris Cité (USPC), This study was supported by the European Union funded RIVERS program (Sixth Framework Program SSP-5-B-INFLUENZA 04 405: Resistance of Influenza Viruses in Environmental Reservoirs and Systems: http://cordis.europa.eu/fp6). The authors are grateful to BNP-Paribas and its foundation (http://mecenat.bnpparibas.com/) for their financial support., and European Project: 38057,RIVERS
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Viral Diseases ,viruses ,[SDV]Life Sciences [q-bio] ,010501 environmental sciences ,medicine.disease_cause ,Global Health ,01 natural sciences ,Persistence (computer science) ,MESH: Dogs ,Influenza A Virus, H1N1 Subtype ,Emerging Viral Diseases ,MESH: Reverse Transcriptase Polymerase Chain Reaction ,Pandemic ,Influenza A virus ,MESH: Animals ,MESH: Orthomyxoviridae Infections ,MESH: Microbial Viability ,Infectivity ,0303 health sciences ,Multidisciplinary ,MESH: Kinetics ,Reverse Transcriptase Polymerase Chain Reaction ,MESH: Influenza, Human ,Temperature ,MESH: Temperature ,3. Good health ,Viral Persistence and Latency ,MESH: Glass ,Infectious Diseases ,Medicine ,MESH: Genome, Viral ,Water Microbiology ,Porosity ,Research Article ,MESH: Pandemics ,Infectious Disease Control ,Surface Properties ,Science ,Temperature salinity diagrams ,Genome, Viral ,Biology ,Microbiology ,Virus ,Cell Line ,MESH: Influenza A Virus, H1N1 Subtype ,03 medical and health sciences ,Dogs ,MESH: Porosity ,Orthomyxoviridae Infections ,Virology ,Microbial Control ,Influenza, Human ,medicine ,MESH: Water ,Animals ,Humans ,Pandemics ,Microbial Pathogens ,0105 earth and related environmental sciences ,MESH: Surface Properties ,Microbial Viability ,MESH: Humans ,030306 microbiology ,Water ,Influenza A virus subtype H5N1 ,Viral Replication ,Influenza ,MESH: Cell Line ,Salinity ,Kinetics ,Virulence Factors and Mechanisms ,Glass ,Viral Transmission and Infection - Abstract
International audience; Knowledge of influenza A virus survival in different environmental conditions is a key element for the implementation of hygiene and personal protection measures by health authorities. As it is dependent on virus isolates even within the same subtype, we studied the survival of the 2009 H1N1 pandemic (H1N1pdm) virus in water and on non-porous surface. The H1N1pdm virus was subjected to various environmental parameters over time and tested for infectivity. In water, at low and medium salinity levels and 4°C, virus survived at least 200 days. Increasing temperature and salinity had a strong negative effect on the survival of the virus which remained infectious no more than 1 day at 35°C and 270 parts per thousand (ppt) of salt. Based on modeled data, the H1N1pdm virus retained its infectivity on smooth non-porous surface for at least 7 days at 35°C and up to 66 days at 4°C. The H1N1pdm virus has thus the ability to persist in water and on glass surface for extended periods of time, even at 35°C. Additional experiments suggest that external viral structures in direct contact with the environment are mostly involved in loss of virus infectivity.
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- 2011
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9. Massively parallel pathogen identification using high-density microarrays
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Giulia C. Kennedy, Ana Maria Burguiere, Walter Lee, Hervé Bourhy, Philip Dickinson, Gilberte Coralie, Laurent Dacheux, Nicolas Berthet, Christopher Davies, Stewart T. Cole, Christophe Batéjat, Anita K. Reinhardt, Ingrid Filliol, Tatiana Vallaeys, Iain G. Old, Yaron Turpaz, Beate Heym, Shenglan Zhang, Katherine A. Kong, Jean Claude Manuguerra, Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Institut Pasteur [Paris] (IP), Affymetrix, Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Hôpital Ambroise Paré [AP-HP], Dynamique des Lyssavirus et Adaptation à l'Hôte (DyLAH), Génétique Moléculaire Bactérienne, This study was supported by Grant No. UC1 AI062613 (Kennedy) from the National Institute of Allergy and Infectious Diseases, National Institutes of Health. We thank A. Baldwin, S. Brisse, E. Carniel, J.-Y. Coppée, J.-M. Fournier, P. Glaser, P. Grimont, M. Mock, M. Popoff, O. Chesneau, P. Courvalin, P. Despres, C. LeBouguenec, B. Regnault, M.-L. Quilici and their staff for helpful suggestions and for providing nucleic acids from various bacteria and viruses. Vesicular stomatitis virus was a gift from Danielle Blondel, Unité Mixte de Virologie Moléculaire et Structurale, UMR 2472, CNRS, 91198 Gif sur Yvette Cedex, France. We thank C. Drosten (Bernhard Nocht Institute, Hamburg, Germany) for kindly making primer sequences and plasmids available for this study. We thank Guoliang Xing, Gangwu Mei, Brant Wong and Michael Mittman for assistance in array design., and Institut Pasteur [Paris]
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DNA, Bacterial ,Microarray ,MESH: Bacterial Infections ,[SDV]Life Sciences [q-bio] ,Molecular Sequence Data ,Virulence ,Bioengineering ,Biology ,MESH: Base Sequence ,Applied Microbiology and Biotechnology ,Biochemistry ,MESH: Viruses ,03 medical and health sciences ,Antibiotic resistance ,MESH: Drug Resistance, Bacterial ,Drug Resistance, Bacterial ,Drug Resistance, Viral ,Humans ,Genotyping ,Pathogen ,Research Articles ,030304 developmental biology ,Oligonucleotide Array Sequence Analysis ,Genetics ,0303 health sciences ,MESH: Drug Resistance, Viral ,MESH: Humans ,MESH: Molecular Sequence Data ,Bacteria ,Base Sequence ,030306 microbiology ,Bacterial Infections ,biology.organism_classification ,MESH: DNA, Bacterial ,MESH: DNA, Viral ,MESH: Bacteria ,MESH: Virus Diseases ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Virus Diseases ,MESH: Oligonucleotide Array Sequence Analysis ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,DNA, Viral ,Viruses ,Monkeypox virus ,Identification (biology) ,DNA microarray ,Biotechnology - Abstract
International audience; Identification of microbial pathogens in clinical specimens is still performed by phenotypic methods that are often slow and cumbersome, despite the availability of more comprehensive genotyping technologies. We present an approach based on whole-genome amplification and resequencing microarrays for unbiased pathogen detection. This 10 h process identifies a broad spectrum of bacterial and viral species and predicts antibiotic resistance and pathogenicity and virulence profiles. We successfully identify a variety of bacteria and viruses, both in isolation and in complex mixtures, and the high specificity of the microarray distinguishes between different pathogens that cause diseases with overlapping symptoms. The resequencing approach also allows identification of organisms whose sequences are not tiled on the array, greatly expanding the repertoire of identifiable organisms and their variants. We identify organisms by hybridization of their DNA in as little as 1-4 h. Using this method, we identified Monkeypox virus and drug-resistant Staphylococcus aureus in a skin lesion taken from a child suspected of an orthopoxvirus infection, despite poor transport conditions of the sample, and a vast excess of human DNA. Our results suggest this technology could be applied in a clinical setting to test for numerous pathogens in a rapid, sensitive and unbiased manner.
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- 2011
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10. Human polyomavirus related to African green monkey lymphotropic polyomavirus
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Jean-Claude Manuguerra, Olivier Dereure, Jennifer Richardson, Meriadeg Ar Gouilh, Virginie Sauvage, Valérie Caro, Ana Maria Burguiere, Marc Eloit, Justine Cheval, Kevin Pariente, Marc Lecuit, Vincent Foulongne, Institut Pasteur [Paris] (IP), Institut National de la Santé et de la Recherche Médicale (INSERM), Université Montpellier 2 - Sciences et Techniques (UM2), PathoQuest, Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Paris Descartes - Paris 5 (UPD5), The project 'Genotyping of Pathogens and Public Health' was supported in part by the Institut de Veille Sanitaire, Saint-Maurice, France. This study was supported in part by grants from region Ile de France and the Programme Hospitalier de Recherche Clinique of the Montpellier University Hospital (AOI 2008, Protocole UF8425)., Institut Pasteur [Paris], and École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
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Male ,Skin Neoplasms ,Tumor Virus Infections ,Epidemiology ,viruses ,[SDV]Life Sciences [q-bio] ,lcsh:Medicine ,Human skin ,Polymerase Chain Reaction ,Merkel Cells ,shedding ,Chlorocebus aethiops ,infections ,high-throughput nucleotide sequencing ,expedited ,Phylogeny ,Aged, 80 and over ,0303 health sciences ,integumentary system ,Merkel cell carcinoma ,food and beverages ,high-throughput sequencing ,Middle Aged ,3. Good health ,Infectious Diseases ,medicine.anatomical_structure ,skin virome ,human polyomavirus ,Female ,Merkel cell ,Adult ,Microbiology (medical) ,skin ,Molecular Sequence Data ,polyomavirus ,Merkel cell carcinoma patients ,Biology ,Virus ,lcsh:Infectious and parasitic diseases ,Young Adult ,03 medical and health sciences ,medicine ,Animals ,Humans ,lcsh:RC109-216 ,Human virome ,Aged ,030304 developmental biology ,Polyomavirus Infections ,030306 microbiology ,Research ,lcsh:R ,African green monkey lymphotrophic virus ,Sequence Analysis, DNA ,medicine.disease ,Virology ,Carcinoma, Merkel Cell ,DNA, Viral ,Immunology ,African Green Monkey - Abstract
TOC summary: This virus is shed at the human skin surface., While studying the virome of the skin surface of a patient with a Merkel cell carcinoma (MCC) by using unbiased, high-throughput sequencing, we identified a human polyomavirus nearly identical to human polyomavirus 9, a virus recently reported in blood and urine of renal transplantion patients and closely related to the African green monkey lymphotropic polyomavirus. Specific PCR analysis further identified this virus in 2/8 patients with MCC but in only 1/111 controls without MCC. This virus was shed for >20 months by the MCC index patient and was on the skin of the spouse of the index patient. These results provide information on the viral ecology of human skin and raise new questions regarding the pathology of virus-associated skin disorders.
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- 2011
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11. Heat inactivation of the <scp>M</scp> iddle <scp>E</scp> ast respiratory syndrome coronavirus
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India Leclercq, Ana Maria Burguiere, Jean Claude Manuguerra, Christophe Batéjat, Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris] (IP), The research leading to these results has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement N° 278433-PREDEMICS. We are also grateful to BNP-Paribas and its foundation (http://www.mecenat.bnpparibas.com/) for their financial support., We also thank Gilberte Coralie, Frederic Fichenick and Claudine Rousseaux for helping., and European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011)
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Pulmonary and Respiratory Medicine ,Hot Temperature ,Epidemiology ,Middle East respiratory syndrome coronavirus ,[SDV]Life Sciences [q-bio] ,viruses ,Biology ,medicine.disease_cause ,Microbiology ,MERS-CoV ,03 medical and health sciences ,Biosafety ,medicine ,Humans ,inactivation ,030304 developmental biology ,Infectivity ,0303 health sciences ,030306 microbiology ,Public Health, Environmental and Occupational Health ,virus diseases ,Short Articles ,Heat ,Virology ,Disinfection ,Heat inactivation ,Titer ,Infectious Diseases ,Middle East Respiratory Syndrome Coronavirus ,Vero cell ,Cell culture supernatant ,Coronavirus Infections - Abstract
International audience; The culture supernatants of the emerging Middle East respiratory syndrome coronavirus (MERS-CoV) were submitted to three temperatures over time and tested for infectivity by TCID50 method on Vero E6 cells. At 56°C, almost 25 minutes were necessary to reduce the initial titre by 4 log10 . Increasing temperature to 65°C had a strong negative effect on viral infectivity as virucidy dropped significantly to 1 minute. On the contrary, no significant decrease in titre was observed after 2 hours at 25°C. These data might be useful in establishing biosafety measures in laboratories against MERS-CoV.
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- 2014
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12. High-density resequencing DNA microarrays in public health emergencies
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Amélie Dublineau, Antoine Gessain, Jean-Claude Manuguerra, India Leclercq, Claudia Filippone, Sayuri Shigematsu, Ana Maria Burguiere, Nicolas Berthet, Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]
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medicine.medical_specialty ,Genes, Viral ,Biomedical Engineering ,High density ,Bioengineering ,Biology ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,Influenza A Virus, H1N1 Subtype ,High-Throughput Screening Assays ,Influenza, Human ,medicine ,Humans ,ComputingMilieux_MISCELLANEOUS ,Phylogeny ,030304 developmental biology ,Oligonucleotide Array Sequence Analysis ,Genetics ,0303 health sciences ,030306 microbiology ,Public health ,Sequence Analysis, DNA ,United States ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Molecular Medicine ,RNA, Viral ,DNA microarray ,Centers for Disease Control and Prevention, U.S ,Emergencies ,Biotechnology - Abstract
International audience
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- 2010
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13. Evolution of H5N1 avian influenza viruses in Asia
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Rebecca Garten, Yanbing Li, Nguyen Hong Diep, John Wood, Robert G. Webster, Le Quynh Mai, Nguyen Tien Dung, Hua Ian Chen, Alice Crosier, Masaji Mase, San Sorn, David E. Swayne, Haan Woo Sung, Maryse Tardy-Panit, Victoria Gregory, Saliha Azebi, Chun Kang, Masatsugu Obuchi, Jill Banks, Takehiko Saito, Frédérique Cuvelier, David L. Suarez, La Morris Loftin, Keiji Fukuda, Niranjan Bhat, Scott A. Harper, Erica Spackman, Rick A. Bright, Masaki Imai, Jean Thierry Aubin, Stéphanie Desvaux, James Robertson, Catherine K. Smith, Takato Odagiri, Jean Claude Manuguerra, Klaus Stöhr, Stephen Lindstom, Michael L. Perdue, Julia Desheva, Richard J. Webby, Wenging Zhang, Diane J. Hulse, Jan Mabry, Jean Marc Reynes, Marek J. Slomka, A. Hay, Sylvie van der Werf, Philippe Buchy, Doan Nguyen, Nancy J. Cox, Lindsay Edwards, Ai Ninomiya, Ian Brown, A. R. Douglas, Timothy M. Uyeki, Sirenda Vong, Phan Van Tu, Claudine Rousseaux, Shigeyuki Itamura, Jae Hong Kim, Malik Peiris, Margaret McCarron, Guohua Deng, Alexander Klimov, Elena A. Govorkova, Ruben O. Donis, Scott F. Dowell, Amanda Balish, Xiyan Xu, Yi Pu Lin, Samadhan Jadhao, Nguyen Thi Hong Hanh, Erich Hoffmann, Phuong Song Lien, Peter K.C. Cheng, Marie-Jo Medina, Patricia Jeannin, Masato Tashiro, Jackie Katz, Yumi Matsuoka, Aaron Curns, James Mark Simmerman, Pranee Thawatsupha, Somchai Sangkitporn, Ana Maria Burguiere, Alan W. Hampson, Guan Yi, Taronna R. Maines, Chang-Won Lee, Terrence M. Tumpey, Wilina Lim, Yong Kuk Kwon, Michael W. Shaw, Institut Pasteur [Paris], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur d'Ho Chi Minh Ville, Research at St. Jude Hospital was supported in part by grant AI95357 from the National Institutes of Health., and Institut Pasteur [Paris] (IP)
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Avian ,Epidemiology ,Adamantane ,Hemagglutinin Glycoproteins, Influenza Virus ,medicine.disease_cause ,Poultry ,MESH: Influenza Vaccines ,MESH: Poultry ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,Influenza A Virus ,MESH: Animals ,MESH: Genetic Variation ,MESH: Phylogeny ,Phylogeny ,MESH: Evolution, Molecular ,0303 health sciences ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,MESH: Asia ,MESH: Influenza, Human ,MESH: Hemagglutinin Glycoproteins, Influenza Virus ,MESH: Chickens ,virus diseases ,NA protein ,MESH: Neuraminidase ,virology ,3. Good health ,Phenotype ,Infectious Diseases ,Influenza Vaccines ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Human mortality from H5N1 ,molecular Evolution ,Microbiology (medical) ,MESH: Antiviral Agents ,Asia ,MESH: Influenza A Virus, H5N1 Subtype ,Neuraminidase ,Biology ,MESH: Poultry Diseases ,MESH: Phenotype ,Antiviral Agents ,H5N1 genetic structure ,Evolution, Molecular ,03 medical and health sciences ,Oseltamivir ,MESH: Influenza in Birds ,Influenza, Human ,medicine ,Animals ,Humans ,hemagglutinin ,M2 protein ,Poultry Diseases ,030304 developmental biology ,MESH: Humans ,[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,Influenza A Virus, H5N1 Subtype ,030306 microbiology ,Research ,Genetic Variation ,Virology ,Influenza ,Influenza A virus subtype H5N1 ,Influenza in Birds ,Chickens - Abstract
Human infections were from a virus clade undergoing antigenic drift that showed resistance to adamantanes but sensitivity to neuraminidase inhibitors., An outbreak of highly pathogenic avian influenza A (H5N1) has recently spread to poultry in 9 Asian countries. H5N1 infections have caused >52 human deaths in Vietnam, Thailand, and Cambodia from January 2004 to April 2005. Genomic analyses of H5N1 isolates from birds and humans showed 2 distinct clades with a nonoverlapping geographic distribution. All the viral genes were of avian influenza origin, which indicates absence of reassortment with human influenza viruses. All human H5N1 isolates tested belonged to a single clade and were resistant to the adamantane drugs but sensitive to neuraminidase inhibitors. Most H5N1 isolates from humans were antigenically homogeneous and distinct from avian viruses circulating before the end of 2003. Some 2005 isolates showed evidence of antigenic drift. An updated nonpathogenic H5N1 reference virus, lacking the polybasic cleavage site in the hemagglutinin gene, was produced by reverse genetics in anticipation of the possible need to vaccinate humans.
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- 2005
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14. Persistence of the 2009 pandemic influenza A (H1N1) virus in water and on non-porous surface.
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Amélie Dublineau, Christophe Batéjat, Anthony Pinon, Ana Maria Burguière, India Leclercq, and Jean-Claude Manuguerra
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Medicine ,Science - Abstract
Knowledge of influenza A virus survival in different environmental conditions is a key element for the implementation of hygiene and personal protection measures by health authorities. As it is dependent on virus isolates even within the same subtype, we studied the survival of the 2009 H1N1 pandemic (H1N1pdm) virus in water and on non-porous surface. The H1N1pdm virus was subjected to various environmental parameters over time and tested for infectivity. In water, at low and medium salinity levels and 4°C, virus survived at least 200 days. Increasing temperature and salinity had a strong negative effect on the survival of the virus which remained infectious no more than 1 day at 35°C and 270 parts per thousand (ppt) of salt. Based on modeled data, the H1N1pdm virus retained its infectivity on smooth non-porous surface for at least 7 days at 35°C and up to 66 days at 4°C. The H1N1pdm virus has thus the ability to persist in water and on glass surface for extended periods of time, even at 35°C. Additional experiments suggest that external viral structures in direct contact with the environment are mostly involved in loss of virus infectivity.
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- 2011
- Full Text
- View/download PDF
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