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1. A Homozygous Missense Variant in PPP1R1B/DARPP‐32 Is Associated With Generalized Complex Dystonia

Author

Anne Molitor, Gaoqun Zhang, Bruno Rinaldi, Sepand Rastegar, Muhammad Umair, Seiamak Bahram, Sylvie Friant, Mathieu Anheim, Sylvain Mayeur, Benoit Lhermitte, Stefan T. Arold, Amjad Khan, Béatrice Lannes, Raphael Carapito, Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), GENOMAX [plateforme], Fédération Hospitalo-Universitaire OMICARE, Fédération Hospitalo-Universitaire (OMICARE), Centre de Recherche d’Immunologie et d’Hématologie [Strasbourg], LabEx Transplantex [Strasbourg], Université de Strasbourg (UNISTRA), Fédération de Médecine Translationnelle de Strasbourg (FMTS), CHU Strasbourg, Karlsruher Institut für Technologie (KIT), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), King Saud Bin Abdulaziz University for Health Sciences [Riyadh] (KSAU-HS), Centurion University of Technology and Management [India], King Abdullah University of Science and Technology (KAUST), Centre de Biologie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Nouvel Hôpital Civil de Strasbourg, Les Hôpitaux Universitaires de Strasbourg (HUS), univOAK, Archive ouverte, Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)

Subjects
Dopamine and cAMP-Regulated Phosphoprotein 32, autosomal recessive generalized dystonia, Movement disorders, Substantia nigra, Sciences du Vivant [q-bio]/Médecine humaine et pathologie, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, 03 medical and health sciences, 0302 clinical medicine, medicine, Missense mutation, Animals, Humans, Generalized epilepsy, Zebrafish, Exome sequencing, PPP1R1B, 030304 developmental biology, Dystonia, Genetics, 0303 health sciences, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, biology, Homozygote, medicine.disease, biology.organism_classification, 3. Good health, DARPP-32, Neurology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Dystonic Disorders, Neurology (clinical), medicine.symptom, exome sequencing, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Background: The dystonias are a heterogeneous group of hyperkinetic disorders characterized by sustained or intermittent muscle contractions that cause abnormal movements and/or postures. Although more than 200 causal genes are known, many cases of primary dystonia have no clear genetic cause.Objectives: To identify the causal gene in a consanguineous family with three siblings affected by a complex persistent generalized dystonia, generalized epilepsy, and mild intellectual disability.Methods: We performed exome sequencing in the parents and two affected siblings and characterized the expression of the identified gene by immunohistochemistry in control human and zebrafish brains.Results: We identified a novel missense variant (c.142G>A (NM_032192); p.Glu48Lys) in the protein phosphatase 1 regulatory inhibitor subunit 1B gene (PPP1R1B) that was homozygous in all three siblings and heterozygous in the parents. This gene is also known as dopamine and cAMP-regulated neuronal phosphoprotein 32 (DARPP-32) and has been involved in the pathophysiology of abnormal movements. The uncovered variant is absent in public databases and modifies the conserved glutamate 48 localized close to the serine 45 phosphorylation site. The PPP1R1B protein was shown to be expressed in cells and regions involved in movement control, including projection neurons of the caudate-putamen, substantia nigra neuropil, and cerebellar Purkinje cells. The latter cells were also confirmed to be positive for PPP1R1B expression in the zebrafish brain.Conclusions: We report the association of a PPP1R1B/DARPP-32 variant with generalized dystonia in man. It might be relevant to include the sequencing of this new gene in the diagnosis of patients with otherwise unexplained movement disorders. © 2021 International Parkinson and Movement Disorder Society.

Published
2022
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2. Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort

Author

Qian Zhang, Paul Bastard, Haiguo Wu, Adrian Gervais, Seiamak Bahram, Sylvain Mayeur, Sharvari Gujja, Anne Thomas, Alexandre Lederle, Julie Helms, Christiane Moog, Xavier Mariette, Alain Viari, Tristan Stemmelen, Christine Carapito, Olivier Hermine, Richard Li, Daniel A. Lidar, Cécile Macquin, Jean Sibilia, Géraldine Laumond, Shweta Kailasan, Leslie Muller, Sabrina Bibi-Triki, Sylvie Schmidt, Aurélie Hirschler, Raony Guimaraes, Michael Simons, Anne Molitor, Francis Schneider, Damien Sanlaville, Thiên-Nga Chamaraux-Tran, Samira Fafi-Kremer, Pierre-Louis Tharaux, Thomas Chittenden, Angélique Pichot, A. Hanauer, Raphael Carapito, Mirjana Radosavljevic, Véronique Rolli, Bernard Goichot, Yvon Ruch, Olivier Collange, Ouria Tahar, Julien Pottecher, Khaldoun Kuteifan, Razieh Mohseninia, Perrine Spinnhirny, Alice Bernard, Bernard Drenou, Jean-Laurent Casanova, Elisa Pin, Jeffrey R. Gulcher, Paul-Michel Mertes, M. Javad Aman, Peter Nilsson, Jose Malagon-Lopez, François Danion, Yves Hansmann, Ferhat Meziani, Maleka Schenck, Nicodème Paul, Annabel Larnicol, Julia Frappier, Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), GENOMAX [plateforme], Fédération Hospitalo-Universitaire OMICARE, Université de Strasbourg (UNISTRA), Nouvel Hôpital Civil de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Genuity Science [Boston], Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Rockefeller University [New York], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Les Hôpitaux Universitaires de Strasbourg (HUS), Hôpital de Hautepierre [Strasbourg], Yale School of Medicine [New Haven, Connecticut] (YSM), Hôpital Bicêtre, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Groupe hospitalier de la région de Mulhouse et Sud-Alsace, Integrated biotherapeutics [Rockville], Royal Institute of Technology [Stockholm] (KTH ), Auragen [Lyon], Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Synergie Lyon Cancer-Platform of Bioinformatics-Gilles Thomas, Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [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)-Centre Léon Bérard [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), Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Harvard Medical School [Boston] (HMS), ANR-10-IDEX-0002,UNISTRA,Par-delà les frontières, l'Université de Strasbourg(2010), ANR-20-SFRI-0012,STRAT'US,Façonner les talents en formation et en recherche à l'Université de Strasbourg(2020), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), CARAPITO, Christine, 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), LabEx Transplantex [Strasbourg], Fédération Hospitalo-Universitaire (OMICARE), Centre de Recherche d’Immunologie et d’Hématologie [Strasbourg], Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), 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)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Département Ecologie, Physiologie et Ethologie (DEPE-IPHC), Génétique Humaine des Maladies Infectieuses (Inserm U980), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Yale University School of Medicine, Immunologie des Maladies Virales et Autoimmunes (IMVA - U1184), Université Paris-Sud - Paris 11 (UP11)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Aucun, MEDLINE, Bioinformatics, 03 medical and health sciences, 0302 clinical medicine, Artificial Intelligence, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicine, Humans, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, business.industry, SARS-CoV-2, Confounding, COVID-19, Membrane Proteins, General Medicine, Respiration, Artificial, 3. Good health, ADAM Proteins, Intensive Care Units, 030220 oncology & carcinogenesis, Cohort, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Identification (biology), business
Abstract

International audience; The etiopathogenesis of critical COVID-19 remains unknown. Indeed given major confounding factors (age and comorbidities), true drivers of this condition have remained elusive. Here, we employ an unprecedented multi-omics analysis, combined with artificial intelligence, in a young patient cohort where major comorbidities have been excluded at the onset. Here, we established a three-tier cohort of individuals younger than 50 years without major comorbidities. These included 47 “critical” (in the ICU under mechanical ventilation) and 25 “non-critical” (in a non-critical care ward) COVID-19 patients as well as 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cells proteomics, cytokine profiling and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing and structural causal modeling led to key findings. Critical patients were characterized by exacerbated inflammation, perturbed lymphoid/myeloid compartments, coagulation and viral cell biology. Within a unique gene signature that differentiated critical from non-critical patients, several driver genes promoted critical COVID-19 among which the upregulated metalloprotease ADAM9 was key. This gene signature was supported in a second independent cohort of 81 critical and 73 recovered COVID-19 patients, as were ADAM9 transcripts, soluble form and proteolytic activity. Ex vivo ADAM9 inhibition affected SARS-CoV-2 uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, COVID-19 cohort, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. The key driver, ADAM9, interfered with SARS-CoV-2 biology. A repositioning strategy for anti-ADAM9 therapeutic is feasible.

Published
2021
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3. High salt exacerbates acute kidney injury by disturbing the activation of CD5L/apoptosis inhibitor of macrophage (AIM) protein

Author

Tetsushi Tezuka, Toru Miyazaki, Kimi Araki, Naoki Takeda, Ching-Ting Wang, Satoko Arai, univOAK, Archive ouverte, The University of Tokyo (UTokyo), Kumamoto University, Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), GENOMAX [plateforme], and Fédération Hospitalo-Universitaire OMICARE

Subjects
Apoptosis Inhibitor, Exacerbation, Physiology, Test Statistics, Pharmacology, Sodium Chloride, urologic and male genital diseases, Kidney Tubules, Proximal, Mathematical and Statistical Techniques, Blood Flow, Medicine and Health Sciences, Macrophage, Receptors, Scavenger, Mice, Inbred ICR, Multidisciplinary, Statistics, Acute kidney injury, Animal Models, Acute Kidney Injury, female genital diseases and pregnancy complications, Body Fluids, Chemistry, Blood, Experimental Organism Systems, Physical Sciences, Medicine, Female, Anatomy, Research Article, Histology, Science, Ischemia, Mouse Models, Research and Analysis Methods, Model Organisms, Chlorides, medicine, Kidney injury, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Salt intake, Sodium Chloride, Dietary, Statistical Methods, Analysis of Variance, business.industry, urogenital system, Chemical Compounds, Biology and Life Sciences, Kidneys, Renal System, medicine.disease, Animal Studies, Salts, business, Apoptosis Regulatory Proteins, Mathematics, Kidney disease
Abstract

International audience; The influence of excess salt intake on acute kidney injury (AKI) has not been examined precisely except for some clinical data, unlike in chronic kidney disease. Here, we addressed the influence of high salt (HS) on AKI and its underlying mechanisms in terms of the activity of circulating apoptosis inhibitor of macrophage (AIM, also called CD5L) protein, a facilitator of AKI repair. HS loading in mice subjected to ischemia/reperfusion (IR) resulted in high mortality with advanced renal tubular obstruction and marked exacerbation in biomarkers of proximal renal tubular damage. This AKI exacerbation appeared to be caused mainly by the reduced AIM dissociation from IgM pentamer in serum, as IgM-free AIM is indispensable for the removal of intratubular debris to facilitate AKI repair. Injection of recombinant AIM (rAIM) ameliorated the AKI induced by IR/HS, dramatically improving the tubular damage and mouse survival. The repair of lethal AKI by AIM was dependent on AIM/ kidney injury molecule-1 (KIM-1) axis, as rAIM injection was not effective in KIM-1 deficient mice. Our results demonstrate that the inhibition of AIM dissociation from IgM is an important reason for the exacerbation of AKI by HS, that AIM is a strong therapeutic tool for severe AKI.

Published
2021
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4. Genes-Basel

Author

Amjad Khan, Mohammad A Alshabeeb, Amir Ullah, Gudrun A. Rappold, Raphael Carapito, Muhammad Umair, Muhammad Ansar, Farooq Ahmad, Zhichao Miao, Muhammad Bilal, GENOMAX [plateforme], Fédération Hospitalo-Universitaire OMICARE, Immuno-Rhumatologie Moléculaire, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA)

Subjects
0301 basic medicine, METTL23, lcsh:QH426-470, In silico, autosomal recessive intellectual disability ndst1 mettl23 exome sequencing genetics mutations, NDST1, Case Report, Sciences du Vivant [q-bio]/Médecine humaine et pathologie, 030105 genetics & heredity, Biology, Genetic Condition, autosomal recessive intellectual disability, 03 medical and health sciences, symbols.namesake, Intellectual disability, Genetics, medicine, Homology modeling, Gene, Genetics (clinical), Exome sequencing, Brain function, Sanger sequencing, medicine.disease, lcsh:Genetics, 030104 developmental biology, symbols, exome sequencing, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Intellectual disability (ID) is a highly heterogeneous genetic condition with more than a thousand genes described so far. By exome sequencing of two consanguineous families presenting hallmark features of ID, we identified two homozygous variants in two genes previously associated with autosomal recessive ID: NDST1 (c.1966G>A; p.Asp656Asn) and METTL23 (c.310T>C; p.Phe104Leu). The segregation of the variants was validated by Sanger sequencing in all family members. In silico homology modeling of wild-type and mutated proteins revealed substantial changes in the secondary structure of both proteins, indicating a possible effect on function. The identification and validation of new pathogenic NDST1 and METTL23 variants in two cases of autosomal recessive ID further highlight the importance of these genes in proper brain function and development.

Published
2020
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5. Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements

Author

Xavier Argemi, Mickael Martin, Nicodème Paul, Gilles Prévost, Véronique Martin, Valentin Loux, Aurélie Velay, Yves Hansmann, Sandrine Dahyot, Philippe Riegel, Jérémie Lebeurre, Daniel Keller, A. Guffroy, Virulence Bactérienne Précoce : fonctions cellulaires et contrôle de l'infection aigüe et subaigüe, Université de Strasbourg (UNISTRA), CHU Strasbourg, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Immunopathologie et Chimie Thérapeutique/Equipe, Tolérance Cellulaire B et Auto-immunité, Centre National de la Recherche Scientifique (CNRS), Centre de recherche du médicament Medalis - Drug Discovery Center [LabEx], Fédération de Médecine Translationnelle de Strasbourg (FMTS), Laboratoire de Virologie [Strasbourg], Immuno-Rhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA), GENOMAX [plateforme], Fédération Hospitalo-Universitaire OMICARE, Centre Hospitalier Régional Universitaire de Strasbourg (CHRU de Strasbourg), Institut de bactériologie, Fédération de Médecine Translationelle de Strasbourg (FMTS), Maladies Infectieuses et Tropicales, Hôpitaux Universitaires, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Service d'Immunologie Clinique et de Médecine Interne, Centre National de Référence des Maladies Auto-immunes Rares, Hôpitaux Universitaires de Strasbourg, Laboratoire d'excellence Medalis, Institut de Biologie Moléculaire et Cellulaire (IBMC), Service d'Immunologie Clinique et de Médecine Interne - Centre National de Référence des Maladies Auto-immunes Rares, Institute of Molecular and Cellular Biology, Virology Laboratory, General Hospital Papageorgiou, UMR S1109, Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'ImmunoRhumatologie Moléculaire, and plateforme GENOMAX

Subjects
0301 basic medicine, plasmids, [SDV]Life Sciences [q-bio], Virulence, Staphylococcus lugdunensis, Staphylococcal infections, Genome, Microbiology, 03 medical and health sciences, Plasmid, prophages, Genetics, medicine, Ecology, Evolution, Behavior and Systematics, Prophage, Whole genome sequencing, next generation sequencing, biology, biology.organism_classification, medicine.disease, 3. Good health, virulence, 030104 developmental biology, Mobile genetic elements
Abstract

Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements. S. lugdunensis also bears various putative virulence genes but only one complete genome with extensive analysis has been published with one prophage sequence (φSL2) and a unique plasmid was previously described. In this study, we performed de novo sequencing, whole genome assembly and annotation of seven strains of S. lugdunensis from VISLISI clinical trial. We searched for the presence of virulence genes and mobile genetics elements using bioinformatics tools. We identified four new prophages, named φSL2 to φSL4, belonging to the Siphoviridae class and five plasmids, named pVISLISI_1 to pVISLISI_5. Three plasmids are homologous to known plasmids that include, amongst others, one S. aureus plasmid. The two other plasmids were not described previously. This study provides a new context for the study of S. lugdunensis virulence suggesting the occurrence of several genetic recombination' with other staphylococci.

Published
2017
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