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54. Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group

Author

Christo-Foroux, Eugene, primary, Vallaeys, Tatiana, additional, Loux, Valentin, additional, Dassa, Elie, additional, Deutscher, Josef, additional, Wandersman, Cécile, additional, Livernois, Aurélien, additional, Hot, Chloe, additional, Criscuolo, Alexis, additional, Dauga, Catherine, additional, Clermont, Dominique, additional, and Chesneau, Olivier, additional

Published
2017
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56. Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

Author

Perrin, Amandine, primary, Larsonneur, Elise, additional, Nicholson, Ainsley C., additional, Edwards, David J., additional, Gundlach, Kristin M., additional, Whitney, Anne M., additional, Gulvik, Christopher A., additional, Bell, Melissa E., additional, Rendueles, Olaya, additional, Cury, Jean, additional, Hugon, Perrine, additional, Clermont, Dominique, additional, Enouf, Vincent, additional, Loparev, Vladimir, additional, Juieng, Phalasy, additional, Monson, Timothy, additional, Warshauer, David, additional, Elbadawi, Lina I., additional, Walters, Maroya Spalding, additional, Crist, Matthew B., additional, Noble-Wang, Judith, additional, Borlaug, Gwen, additional, Rocha, Eduardo P. C., additional, Criscuolo, Alexis, additional, Touchon, Marie, additional, Davis, Jeffrey P., additional, Holt, Kathryn E., additional, McQuiston, John R., additional, and Brisse, Sylvain, additional

Published
2017
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58. The Nagoya Protocol and its implications for Users of Microbial Resources

Author

Hurtado-Ortiz, Raquel, Clermont, Dominique, Bizet, Chantal, Smith, David, Stackebrandt, Erko, and Verkleij, Gerard

Subjects
microorganism, MIRRI, Nagoya Protocol, Access and Benefit Sharing
Abstract

The Nagoya Protocol (NP), which entered into force on October 12th 2014, is an international agreement which aims at sharing the benefits arising from the utilization of genetic resources in a fair and equitable way, including by appropriate access to genetic resources and by appropriate transfer of relevant technologies, taking into account all rights over those resources and to technologies, and by appropriate funding, thereby contributing to the conservation of biological diversity and the sustainable use of its components. The European Union has designed the legal instruments needed for its implementation in their areas of jurisdiction. Alongside, some European microbial domain Biological Resource Centres (mBRCs) have initiated communications with their national competent authorities and National Focal Points to discuss the situation and draw attention to concerns and problems that the mBRCs could experience now that the NP has entered into force in the Union. The topic of Access and Benefit Sharing (ABS) and its implementation are very complex, especially for users of microbial resources. Users obtaining resources from a registered collection are considered to have exercised due diligence as regards the seeking of information providing proof that the resources were legally accessed. Whether seeking inclusion into the Register or not, mBRCS need to develop strategies and tools to ensure that mBRCs comply with the Nagoya Protocol. These strategies will support users, as well as providers and other holders of microbial resources, to utilise the material in a legally compliant way.

Published
2015
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59. Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Author

Njamkepo, Elisabeth, Fawal, Nizar, Tran-Dien, Alicia, Hawkey, Jane, Strockbine, Nancy, Jenkins, Claire, Talukder, Kaisar A, Bercion, Raymond, Kuleshov, Konstantin, Kolínská, Renáta, Russell, Julie E, Kaftyreva, Lidia, Accou-Demartin, Marie, Karas, Andreas, Vandenberg, Olivier, Mather, Alison AE, Mason, Carl J, Page, Andrew J, Ramamurthy, Thandavarayan, Bizet, Chantal, Gamian, Andrzej, Carles, Isabelle, Sow, Amy Gassama, Bouchier, Christiane, Wester, Astrid Louise, Lejay-Collin, Monique, Fonkoua, Marie-Christine, Hello, Simon Le, Blaser, Martin J, Jernberg, Cecilia, Ruckly, Corinne, Mérens, Audrey, Page, Anne-Laure, Aslett, Martin, Roggentin, Peter, Fruth, Angelika, Denamur, Erick, Venkatesan, Malabi, Bercovier, Hervé, Bodhidatta, Ladaporn, Chiou, Chien-Shun, Clermont, Dominique, Colonna, Bianca, Egorova, Svetlana, Pazhani, Gururaja GP, Ezernitchi, Analia V, Guigon, Ghislaine, Harris, Simon R, Izumiya, Hidemasa, Korzeniowska-Kowal, Agnieszka, Lutyńska, Anna, Gouali, Malika, Grimont, Francine, Langendorf, Céline, Marejková, Monika, Peterson, Lorea A M LA, Perez-Perez, Guillermo, Ngandjio, Antoinette, Podkolzin, Alexander, Souche, Erika, Makarova, Mariia, Shipulin, German A, Ye, Changyun, Zemlickova, Helena, Herpay, Mária, Grimont, Patrick A D PA, Parkhill, Julian, Sansonetti, Philippe, Holt, Kathryn KE, Brisse, Sylvain, Thomson, Nicholas R, Weill, François-Xavier, Njamkepo, Elisabeth, Fawal, Nizar, Tran-Dien, Alicia, Hawkey, Jane, Strockbine, Nancy, Jenkins, Claire, Talukder, Kaisar A, Bercion, Raymond, Kuleshov, Konstantin, Kolínská, Renáta, Russell, Julie E, Kaftyreva, Lidia, Accou-Demartin, Marie, Karas, Andreas, Vandenberg, Olivier, Mather, Alison AE, Mason, Carl J, Page, Andrew J, Ramamurthy, Thandavarayan, Bizet, Chantal, Gamian, Andrzej, Carles, Isabelle, Sow, Amy Gassama, Bouchier, Christiane, Wester, Astrid Louise, Lejay-Collin, Monique, Fonkoua, Marie-Christine, Hello, Simon Le, Blaser, Martin J, Jernberg, Cecilia, Ruckly, Corinne, Mérens, Audrey, Page, Anne-Laure, Aslett, Martin, Roggentin, Peter, Fruth, Angelika, Denamur, Erick, Venkatesan, Malabi, Bercovier, Hervé, Bodhidatta, Ladaporn, Chiou, Chien-Shun, Clermont, Dominique, Colonna, Bianca, Egorova, Svetlana, Pazhani, Gururaja GP, Ezernitchi, Analia V, Guigon, Ghislaine, Harris, Simon R, Izumiya, Hidemasa, Korzeniowska-Kowal, Agnieszka, Lutyńska, Anna, Gouali, Malika, Grimont, Francine, Langendorf, Céline, Marejková, Monika, Peterson, Lorea A M LA, Perez-Perez, Guillermo, Ngandjio, Antoinette, Podkolzin, Alexander, Souche, Erika, Makarova, Mariia, Shipulin, German A, Ye, Changyun, Zemlickova, Helena, Herpay, Mária, Grimont, Patrick A D PA, Parkhill, Julian, Sansonetti, Philippe, Holt, Kathryn KE, Brisse, Sylvain, Thomson, Nicholas R, and Weill, François-Xavier

Abstract

info:eu-repo/semantics/published

Published
2016

60. Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

Author

Da Cunha, Violette, Davies, Mark R., Douarre, Pierre-Emmanuel, Rosinski-Chupin, Isabelle, Margarit, Immaculada, Spinali, Sebastien, Perkins, Tim, Lechat, Pierre, Dmytruk, Nicolas, Sauvage, Elisabeth, Laurence, Ma, Romi, Benedetta, Tichit, Magali, Lopez-Sanchez, Maria-José, Descorps-Declere, Stéphane, Souche, Erika, Buchrieser, Carmen, Trieu-Cuot, Patrick, Moszer, Ivan, Clermont, Dominique, Maione, Domenico, Bouchier, Christiane, Mcmillan, David J., Parkhill, Julian, Telford, John L., Dougan, Gordan, Walker, Mark J., Holden, Matthew T. G., Poyart, Claire, Glaser, Philippe, Melin, Pierette, Decheva, Antoaneta, Petrunov, Bogdan, Kriz, Paula, Berner, Reinhard, Buchele, Anna, Hufnagel, Markus, Kunze, Mirjam, Creti, Roberta, Baldassarri, Lucilla, Orefici, Graziella, Berardi, Alberto, Granger, Javier Rodriguez, Fraile, Manuel De La Rosa, Afshar, Baharak, Efstratiou, Androulla, Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, University of Queensland [Brisbane], The Wellcome Trust Sanger Institute [Cambridge], Novartis Vaccines and Diagnostics [Siena], Centre national de Référence des Streptocoques (CNR), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre d'Informatique pour la Biologie, Institut Pasteur [Paris], Génomique (Plate-Forme) - Genomics Platform, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Collection de l'Institut Pasteur (CIP), QIMR Berghofer Medical Research Institute, Inflammation and Healing Research Cluster, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French National Research Agency (Grant ANR-08-GENM-027-001 and 2010-PATH-004-02) and by the Labex IBEID. The Institut Pasteur Genopole is a member of France Génomique (ANR10-IBNS-09-08). M.R.D. is supported by the National Health and Medical Research Council of Australia (565526 and 635250). M.T.G.H. and J.P. were supported by Wellcome Trust grant 098051. This study was in part supported by the European Commission Seventh Framework (grant agreement number 200481) as part of the DEVANI program. We would like to acknowledge Dr Sri Sriprakash and Ms Karen Taylor for their involvement with the Australian GBS strain collection and Alexandre Almeida for critical reading of the manuscript., ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 200481,EC:FP7:HEALTH,FP7-HEALTH-2007-A,DEVANI(2008), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Lassailly-Bondaz, Anne, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, and Design of a vaccine to immunize neonates against GBS infections through a durable maternal immune response - DEVANI - - EC:FP7:HEALTH2008-01-01 - 2011-06-30 - 200481 - VALID

Subjects
Serotype, Genetics and Molecular Biology (all), General Physics and Astronomy, medicine.disease_cause, Genome, Biochemistry, Phylogeny, 0303 health sciences, education.field_of_study, Multidisciplinary, Streptococcus, Chemistry (all), Tetracycline Resistance, Bacterial, High-Throughput Nucleotide Sequencing, Single Nucleotide, Corrigenda, 3. Good health, Anti-Bacterial Agents, Europe, medicine.drug, Tetracycline, Population, Molecular Sequence Data, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, Microbiology, Streptococcus agalactiae, 03 medical and health sciences, Physics and Astronomy (all), Antibiotic resistance, Genetic, Streptococcal Infections, medicine, Humans, Selection, Genetic, Polymorphism, education, Selection, 030304 developmental biology, Molecular epidemiology, Base Sequence, 030306 microbiology, General Chemistry, Clone Cells, DNA Transposable Elements, North America, Genes, Bacterial, Genome, Bacterial, Biochemistry, Genetics and Molecular Biology (all), [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genes, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by comparative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates.

Published
2014

61. Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Author

Njamkepo, Elisabeth, primary, Fawal, Nizar, additional, Tran-Dien, Alicia, additional, Hawkey, Jane, additional, Strockbine, Nancy, additional, Jenkins, Claire, additional, Talukder, Kaisar A., additional, Bercion, Raymond, additional, Kuleshov, Konstantin, additional, Kolínská, Renáta, additional, Russell, Julie E., additional, Kaftyreva, Lidia, additional, Accou-Demartin, Marie, additional, Karas, Andreas, additional, Vandenberg, Olivier, additional, Mather, Alison E., additional, Mason, Carl J., additional, Page, Andrew J., additional, Ramamurthy, Thandavarayan, additional, Bizet, Chantal, additional, Gamian, Andrzej, additional, Carle, Isabelle, additional, Sow, Amy Gassama, additional, Bouchier, Christiane, additional, Wester, Astrid Louise, additional, Lejay-Collin, Monique, additional, Fonkoua, Marie-Christine, additional, Le Hello, Simon, additional, Blaser, Martin J., additional, Jernberg, Cecilia, additional, Ruckly, Corinne, additional, Mérens, Audrey, additional, Page, Anne-Laure, additional, Aslett, Martin, additional, Roggentin, Peter, additional, Fruth, Angelika, additional, Denamur, Erick, additional, Venkatesan, Malabi, additional, Bercovier, Hervé, additional, Bodhidatta, Ladaporn, additional, Chiou, Chien-Shun, additional, Clermont, Dominique, additional, Colonna, Bianca, additional, Egorova, Svetlana, additional, Pazhani, Gururaja P., additional, Ezernitchi, Analia V., additional, Guigon, Ghislaine, additional, Harris, Simon R., additional, Izumiya, Hidemasa, additional, Korzeniowska-Kowal, Agnieszka, additional, Lutyńska, Anna, additional, Gouali, Malika, additional, Grimont, Francine, additional, Langendorf, Céline, additional, Marejková, Monika, additional, Peterson, Lorea A.M., additional, Perez-Perez, Guillermo, additional, Ngandjio, Antoinette, additional, Podkolzin, Alexander, additional, Souche, Erika, additional, Makarova, Mariia, additional, Shipulin, German A., additional, Ye, Changyun, additional, Žemličková, Helena, additional, Herpay, Mária, additional, Grimont, Patrick A. D., additional, Parkhill, Julian, additional, Sansonetti, Philippe, additional, Holt, Kathryn E., additional, Brisse, Sylvain, additional, Thomson, Nicholas R., additional, and Weill, François-Xavier, additional

Published
2016
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62. Whole-Genome Sequence of Corynebacterium auriscanis Strain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom

Author

Tiwari, Sandeep, primary, Jamal, Syed Babar, additional, Oliveira, Leticia Castro, additional, Clermont, Dominique, additional, Bizet, Chantal, additional, Mariano, Diego, additional, de Carvalho, Paulo Vinicius Sanches Daltro, additional, Souza, Flavia, additional, Pereira, Felipe Luiz, additional, de Castro Soares, Siomar, additional, Guimarães, Luis C., additional, Dorella, Fernanda, additional, Carvalho, Alex, additional, Leal, Carlos, additional, Barh, Debmalya, additional, Figueiredo, Henrique, additional, Hassan, Syed Shah, additional, Azevedo, Vasco, additional, and Silva, Artur, additional

Published
2016
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63. Paenibacillus faecis sp. nov., isolated from human faeces

Author

Clermont, Dominique, primary, Gomard, Maïté, additional, Hamon, Sylviane, additional, Bonne, Isabelle, additional, Fernandez, José-Carlos, additional, Wheeler, Richard, additional, Malosse, Christian, additional, Chamot-Rooke, Julia, additional, Gribaldo, Simonetta, additional, Boneca, Ivo Gomperts, additional, and Bizet, Chantal, additional

Published
2015
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64. Draft Genome Sequence of [i][/i] Lactobacillus pasteurii[i][/i] CRBIP 24.76T

Author

Cousin, Sylvie, Clermont, Dominique, Creno, Sophie, Ma, Laurence, Loux, Valentin, Bizet, Chantal, Bouchier, Christiane, Centre de Ressources biologiques de l'Institut Pasteur - Biological Resource Center of the Institut Pasteur (CRBIP), Institut Pasteur [Paris], Génomique (Plate-Forme) - Genomics Platform, Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), This communication is an initiative of the European Consortium of Microbial Resources Centres (EMbaRC), supported by the European Commission’s Seventh Framework Programme (FP7, 2007–2013), Research Infrastructures action, under the grant agreement no. FP7-228310., European Project: 228310,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,EMBARC(2009), Centre de Ressources biologiques de l'Institut Pasteur (CRBIP), Génomique (Plate-Forme), Institut Pasteur [Paris] (IP), and Unité Mathématique Informatique et Génome (MIG)

Subjects
[SDV]Life Sciences [q-bio], food and beverages
Abstract

We report the draft genome sequence of the type strain Lactobacillus pasteurii CRBIP 24.76, which is closely related to L. gigeriorum CRBIP 24.85(T), isolated from a chicken crop. The total length of the 29 contigs is about 1.9 Mb, with a G+C content of 40% and 1,946 coding sequences.

Published
2013

65. Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov.

Author

Nicholson, Ainsley C., Gulvik, Christopher A., Whitney, Anne M., Humrighouse, Ben W., Graziano, James, Emery, Brian, Bell, Melissa, Loparev, Vladimir, Juieng, Phalasy, Gartin, Jarrett, Bizet, Chantal, Clermont, Dominique, Criscuolo, Alexis, Brisse, Sylvain, and McQuiston, John R.

Abstract

The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146 = DSM 2975 = CCUG 69503 = CIP 111191) and Elizabethkingia ursingii sp. nov. (type strain, G4122 = DSM 2974 = CCUG 69496 = CIP 111192), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070 = DSM 2976 = CCUG 69505 = CIP 111193), is proposed. [ABSTRACT FROM AUTHOR]

Published
2018
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67. Correction: Corrigendum: Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

Author

Da Cunha, Violette, primary, Davies, Mark R., additional, Douarre, Pierre-Emmanuel, additional, Rosinski-Chupin, Isabelle, additional, Margarit, Immaculada, additional, Spinali, Sebastien, additional, Perkins, Tim, additional, Lechat, Pierre, additional, Dmytruk, Nicolas, additional, Sauvage, Elisabeth, additional, Ma, Laurence, additional, Romi, Benedetta, additional, Tichit, Magali, additional, Lopez-Sanchez, Maria-José, additional, Descorps-Declere, Stéphane, additional, Souche, Erika, additional, Buchrieser, Carmen, additional, Trieu-Cuot, Patrick, additional, Moszer, Ivan, additional, Clermont, Dominique, additional, Maione, Domenico, additional, Bouchier, Christiane, additional, McMillan, David J., additional, Parkhill, Julian, additional, Telford, John L., additional, Dougan, Gordan, additional, Walker, Mark J., additional, Holden, Matthew T G., additional, Poyart, Claire, additional, and Glaser, Philippe, additional

Published
2015
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68. The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences

Author

Touchon, Marie, primary, Cury, Jean, additional, Yoon, Eun-Jeong, additional, Krizova, Lenka, additional, Cerqueira, Gustavo C., additional, Murphy, Cheryl, additional, Feldgarden, Michael, additional, Wortman, Jennifer, additional, Clermont, Dominique, additional, Lambert, Thierry, additional, Grillot-Courvalin, Catherine, additional, Nemec, Alexandr, additional, Courvalin, Patrice, additional, and Rocha, Eduardo P.C., additional

Published
2014
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70. Identification of 50 Class D β-Lactamases and 65 Acinetobacter-Derived Cephalosporinases in Acinetobacter spp

Author

Périchon, Bruno, primary, Goussard, Sylvie, additional, Walewski, Violaine, additional, Krizova, Lenka, additional, Cerqueira, Gustavo, additional, Murphy, Cheryl, additional, Feldgarden, Michael, additional, Wortman, Jennifer, additional, Clermont, Dominique, additional, Nemec, Alexandr, additional, and Courvalin, Patrice, additional

Published
2014
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72. Draft Genome Sequences of Five Strains of Lactobacillus acidophilus, Strain CIP 76.13 T , Isolated from Humans, Strains CIRM-BIA 442 and CIRM-BIA 445, Isolated from Dairy Products, and Strains DSM 20242 and DSM 9126 of Unknown Origin

Author

Falentin, Hélène, primary, Cousin, Sylvie, additional, Clermont, Dominique, additional, Creno, Sophie, additional, Ma, Laurence, additional, Chuat, Victoria, additional, Loux, Valentin, additional, Rüdiger, Pukall, additional, Bizet, Chantal, additional, and Bouchier, Christiane, additional

Published
2013
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75. Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names

Author

Yarza, Pablo, primary, Spröer, Cathrin, additional, Swiderski, Jolantha, additional, Mrotzek, Nicole, additional, Spring, Stefan, additional, Tindall, Brian J., additional, Gronow, Sabine, additional, Pukall, Rüdiger, additional, Klenk, Hans-Peter, additional, Lang, Elke, additional, Verbarg, Susanne, additional, Crouch, Audra, additional, Lilburn, Timothy, additional, Beck, Brian, additional, Unosson, Christel, additional, Cardew, Sofia, additional, Moore, Edward R.B., additional, Gomila, Margarita, additional, Nakagawa, Yasuyoshi, additional, Janssens, Danielle, additional, De Vos, Paul, additional, Peiren, Jindrich, additional, Suttels, Timo, additional, Clermont, Dominique, additional, Bizet, Chantal, additional, Sakamoto, Mitsuo, additional, Iida, Toshiya, additional, Kudo, Takuji, additional, Kosako, Yoshimasa, additional, Oshida, Yumi, additional, Ohkuma, Moriya, additional, R. Arahal, David, additional, Spieck, Eva, additional, Pommerening Roeser, Andreas, additional, Figge, Marian, additional, Park, Duckchul, additional, Buchanan, Peter, additional, Cifuentes, Ana, additional, Munoz, Raul, additional, Euzéby, Jean P., additional, Schleifer, Karl-Heinz, additional, Ludwig, Wolfgang, additional, Amann, Rudolf, additional, Glöckner, Frank Oliver, additional, and Rosselló-Móra, Ramon, additional

Published
2013
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76. Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov.

Author

Cousin, Sylvie, primary, Motreff, Laurence, additional, Gulat-Okalla, Marie-Laure, additional, Gouyette, Catherine, additional, Spröer, Cathrin, additional, Schumann, Peter, additional, Begaud, Evelyne, additional, Bouchier, Christiane, additional, Clermont, Dominique, additional, and Bizet, Chantal, additional

Published
2013
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80. Listeria rocourtiae sp. nov.

Author

Leclercq, Alexandre, primary, Clermont, Dominique, additional, Bizet, Chantal, additional, Grimont, Patrick A. D., additional, Le Flèche-Matéos, Anne, additional, Roche, Sylvie M., additional, Buchrieser, Carmen, additional, Cadet-Daniel, Véronique, additional, Le Monnier, Alban, additional, Lecuit, Marc, additional, and Allerberger, Franz, additional

Published
2010
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86. Characterization of the chromosomal class A β-lactamase CKO from Citrobacter koseri.

Author

Petrella, Stephanie, Renard, Murielle, Ziental-Gelus, Nathalie, Clermont, Dominique, Jarlier, Vincent, and Sougakoff, Wladimir

Subjects
BETA lactamases, POLYMERASE chain reaction, GENETIC mutation, MICROBIOLOGY, MICROORGANISMS, BACTERIOLOGY
Abstract

The gene blaCKO encoding the chromosomal class A β-lactamase of Citrobacter koseri was cloned and sequenced. CKO was found to display only 41% identity with SED-1 from Citrobacter sedlakii and 36% with CdiA from Citrobacter amalonaticus (formerly Citrobacter diversus). No transcriptional regulator was found upstream from blaCKO. Silent and missense mutations were detected in four blaCKO genes amplified from different C. koseri clinical isolates, but the CKO variants displayed identical biochemical behaviours. A blaCKO-specific polymerase chain reaction confirmed that blaCKO is present only in C. koseri and therefore represents an interesting tool with which to differentiate C. koseri from the other Citrobacter spp. [ABSTRACT FROM AUTHOR]

Published
2006
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87. Identification of 50 Class D β-Lactamases and 65 Acinetobacter-Derived Cephalosporinases in Acinetobacterspp

Author

Périchon, Bruno, Goussard, Sylvie, Walewski, Violaine, Krizova, Lenka, Cerqueira, Gustavo, Murphy, Cheryl, Feldgarden, Michael, Wortman, Jennifer, Clermont, Dominique, Nemec, Alexandr, and Courvalin, Patrice

Abstract

ABSTRACTWhole-genome sequencing of a collection of 103 Acinetobacterstrains belonging to 22 validly named species and another 16 putative species allowed detection of genes for 50 new class D β-lactamases and 65 new Acinetobacter-derived cephalosporinases (ADC). All oxacillinases (OXA) contained the three typical motifs of class D β-lactamases, STFK, (F/Y)GN, and K(S/T)G. The phylogenetic tree drawn from the OXA sequences led to an increase in the number of OXA groups from 7 to 18. The topologies of the OXA and RpoB phylogenetic trees were similar, supporting the ancient acquisition of blaOXAgenes by Acinetobacterspecies. The class D β-lactamase genes appeared to be intrinsic to several species, such as Acinetobacter baumannii, Acinetobacter pittii, Acinetobacter calcoaceticus, and Acinetobacter lwoffii. Neither blaOXA-40/143- nor blaOXA-58-like genes were detected, and their origin remains therefore unknown. The phylogenetic tree analysis based on the alignment of the sequences deduced from blaADCrevealed five main clusters, one containing ADC belonging to species closely related to A. baumanniiand the others composed of cephalosporinases from the remaining species. No indication of blaOXAor blaADCtransfer was observed between distantly related species, except for blaOXA-279, possibly transferred from Acinetobactergenomic species 6 to Acinetobacter parvus. Analysis of β-lactam susceptibility of seven strains harboring new oxacillinases and cloning of the corresponding genes in Escherichia coliand in a susceptible A. baumanniistrain indicated very weak hydrolysis of carbapenems. Overall, this study reveals a large pool of β-lactamases in different Acinetobacterspp., potentially transferable to pathogenic strains of the genus.

Published
2013
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88. Identification of Strains ofAlcaligenesand Agrobacteriumby a Polyphasic Approach

Author

Clermont, Dominique, Harmant, Christine, and Bizet, Chantal

Abstract

ABSTRACTThe number of stable discriminant biochemical characters is limited in the genera AlcaligenesandAgrobacterium, whose species are consequently difficult to distinguish from one another by conventional tests. Moreover, genomic studies have recently drastically modified the nomenclature of these genera; for example, Alcaligenes xylosoxidanswas transferred to the genus Achromobacterin 1998. Twenty-five strains of Achromobacter xylosoxidans, three strains of an Agrobacteriumsp., five strains of anAlcaligenessp., and four unnamed strains belonging to the Centers for Disease Control and Prevention group IVc-2 were examined. These strains were characterized by conventional tests, including biochemical tests. The assimilation of 99 carbohydrates, organic acids, and amino acids was studied by using Biotype-100 strips, and rRNA gene restriction patterns were obtained with the automated Riboprinter microbial characterization system after cleavage of total DNA with EcoRI or PstI restriction endonuclease. This polyphasic approach allowed the two subspecies ofA. xylosoxidansto be clearly separated. Relationships between five strains and the Ralstonia pauculatype strain were demonstrated. Likewise, three strains were found to be related to the Ochrobactrum anthropitype strain. We showed that substrate assimilation tests and automated ribotyping provide a simple, rapid, and reliable means of identifying A. xylosoxidanssubspecies and that these two methods can be used as alternative methods to characterize unidentified strains rapidly when discriminant biochemical characters are missing.

Published
2001
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89. Novel Class A β-Lactamase Sed-1 fromCitrobacter sedlakii: Genetic Diversity of β-Lactamases within the CitrobacterGenus

Author

Petrella, Stephanie, Clermont, Dominique, Casin, Isabelle, Jarlier, Vincent, and Sougakoff, Wladimir

Abstract

ABSTRACTCitrobacter sedlakii2596, a clinical strain resistant to aminopenicillins, carboxypenicillins, and early cephalosporins such as cephalothin, but remaining susceptible to acylureidopenicillins, carbapenems, and later cephalosporins such as cefotaxime, was isolated from the bile of a patient treated with β-lactam and quinolone antibiotics. The isolate produced an inducible class A β-lactamase of pI 8.6, named Sed-1, which was purified. Characterized by a molecular mass of 30 kDa, Sed-1 preferentially hydrolyzed benzylpenicillin, cephalothin, and cloxacillin. The corresponding gene,blaSed-1, was cloned and sequenced. Its deduced amino acid sequence shared more than 60% identity with the chromosome-encoded β-lactamases from Citrobacter koseri(formerly C. diversus) (84%), Klebsiella oxytoca(74%), Serratia fonticola(67%), andProteus vulgaris(63%) and 71% identity with the plasmid-mediated enzyme MEN-1. A gene coding for a LysR transcriptional regulator was found upstream from blaSed-1. This regulator, named SedR, displayed 90% identity with the AmpR sequence of the chromosomal β-lactamase from C. koseriand 63 and 50% identity with the AmpR sequences of P. vulgarisand Enterobacter cloacae, respectively. By using DNA-DNA hybridization, a blaSed-1-like gene was identified in two reference strains, C. sedlakii(CIP-105037) and Citrobacter rodentium(CIP-104675), but not in the 18 strains of C. koseristudied. Two DNA fragments were amplified and sequenced from the reference strains ofC. sedlakiiCIP-105037 and C. rodentiumCIP-104675 using two primers specific forblaSed-1. They shared 98 and 80% identity withblaSed-1, respectively, confirming the diversity of the chromosomally encoded class A β-lactamases found inCitrobacter.

Published
2001
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90. Corrigendum: Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline.

Author

Da Cunha, Violette, Davies, Mark R., Douarre, Pierre-Emmanuel, Rosinski-Chupin, Isabelle, Margarit, Immaculada, Spinali, Sebastien, Perkins, Tim, Lechat, Pierre, Dmytruk, Nicolas, Sauvage, Elisabeth, Ma, Laurence, Romi, Benedetta, Tichit, Magali, Lopez-Sanchez, Maria-José, Descorps-Declere, Stéphane, Souche, Erika, Buchrieser, Carmen, Trieu-Cuot, Patrick, Moszer, Ivan, and Clermont, Dominique

Published
2015
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91. Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T, Isolated from a Chicken Crop.

Author

Cousin, Sylvie, Ma, Laurence, Creno, Sophie, Clermont, Dominique, Loux, Valentin, Bizet, Chantal, and Bouchier, Christiane

Subjects
*LACTOBACILLUS, *GENOMES, *CHICKENS, *PROTEINS, *GENETICS
Abstract

We report the draft genome of the strain Lactobacillus gigeriorum CRBIP 24.85T, isolated from a chicken crop. The total length of the 60 scaffolds is about 1.9 Mb, with a GC content of 38% and 2,062 protein-coding sequences (CDS). [ABSTRACT FROM AUTHOR]

Published
2012
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92. Neisseria leonii sp. nov., isolated from the nose, lung, and liver of rabbits.

Author

Boutroux M, Favre-Rochex S, Gorgette O, Touak G, Mühle E, Bouchier C, Chesneau O, Veyrier FJ, Clermont D, and Rahi P

Subjects
Animals, Rabbits, Fatty Acids analysis, Base Composition, RNA, Ribosomal, 16S genetics, Phylogeny, Neisseria isolation & purification, Neisseria classification, Neisseria genetics, DNA, Bacterial genetics, Bacterial Typing Techniques, Sequence Analysis, DNA, Liver microbiology, Lung microbiology
Abstract

A taxogenomic study of three strains (3986 T , 51.81, and JF 2415) isolated from rabbits between 1972 and 2000 led to the description of a new Neisseria species. The highest sequence similarity of the 16S rRNA gene was found to Neisseria animalis NCTC 10212 T (96.7 %). The 16S rRNA gene similarity above 99 % and average nucleotide identity (ANI) values above 96 % among the strains, indicated that they belong to the same species. At the same time, the strains shared ANI values below 81 % and dDDH values below 24 % with all described Neisseria species. In the bac120 gene phylogenetic tree, the three strains clustered near Neisseria elongata and Neisseria bacilliformis in the Neisseria clade. However, the Neisseria clade is not monophyletic, and includes the type strains of Morococcus cerebrosus , Bergeriella denitrificans , Kingella potus , Uruburuella suis , and Uruburuella testudinis. Neisseria shayeganii clustered outside the clade with members of the genus Eikenella . Amino acid identity (AAI) values were calculated, and a threshold of 71 % was used to circumscribe the genus Neisseria . According to this proposed AAI threshold, strains 3986 T , 51.81, and JF 2415 were placed within the genus Neisseria . The cells of the three strains were Gram-stain-negative diplococcobacilli and non-motile. Optimal growth on trypticase soy agar occurred at 37 °C and pH 8.5 in aerobic conditions. Notably, all strains exhibited indole production in the API-NH test, which is atypical for Neisseria and the family Neisseriaceae . The strains exhibited a common set of 68 peaks in their MALDI-TOF MS profiles, facilitating the swift and accurate identification of this species. Based on genotypic and phenotypic data, it is proposed that strains 3986 T , 51.81, and JF 2415 represent a novel species within the genus Neisseria , for which the name Neisseria leonii sp. nov. is proposed (type strain 3986 T =R726 T =CIP 109994 T =LMG 32907 T ).

Published
2024
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93. A Ranking Tool for "Category Killer" Microbial Biobanks.

Author

Boutroux M, Chiarelli A, Ferrari ML, Chesneau O, Clermont D, and Betsou F

Abstract

Microbial biobanks preserve and provide microbial bioresources for research, training, and quality control purposes. They ensure the conservation of biodiversity, contribute to taxonomical research, and support scientific advancements. Microbial biobanks can cover a wide range of phylogenetic and metabolic diversity ("category killers") or focus on specific taxonomic, thematic, or disease areas. The strategic decisions about strain selection for certain applications or for the biobank culling necessitate a method to support prioritization and selection. Here, we propose an unbiased scoring approach based on objective parameters to assess, categorize, and assign priorities among samples in stock in a microbial biobank. We describe the concept of this ranking tool and its application to identify high-priority strains for whole genome sequencing with two main goals: (i) genomic characterization of quality control, reference, and type strains; (ii) genome mining for the discovery of natural products, bioactive and antimicrobial molecules, with focus on human diseases. The general concept of the tool can be useful to any biobank and for any ranking or culling needs.

Published
2024
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94. Genome sequence-based identification of Enterobacter strains and description of Enterobacter pasteurii sp. nov.

Author

Rahi P, Mühle E, Scandola C, Touak G, and Clermont D

Subjects
Phylogeny, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Enterobacter genetics
Abstract

Importance: Accurate taxonomy is essential for microbial biological resource centers, since the microbial resources are often used to support new discoveries and subsequent research. Here, we used genome sequence data, alongside matrix-assisted laser desorption/ionization time-of-flight mass spectrometer biotyper-based protein profiling, to accurately identify six Enterobacter cloacae complex strains. This approach effectively identified distinct species within the E. cloacae complex, including Enterobacter asburiae , " Enterobacter xiangfangensis ," and Enterobacter quasihormaechei . Moreover, the study revealed the existence of a novel species within the Enterobacter genus, for which we proposed the name Enterobacter pasteurii sp. nov. In summary, this study demonstrates the significance of adopting a genome sequence-driven taxonomy approach for the precise identification of bacterial strains in a biological resource center and expands our understanding of the E. cloacae complex., Competing Interests: The authors declare no conflict of interest.

Published
2024
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95. Chryseobacterium oryctis sp. nov., isolated from the gut of the beetle Oryctes rhinoceros , and Chryseobacterium kimseyorum sp. nov., isolated from a stick insect rearing cage.

Author

Shelomi M, Han CJ, Chen WM, Chen HK, Liaw SJ, Mühle E, and Clermont D

Subjects
Animals, Fatty Acids chemistry, Bacterial Typing Techniques, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, DNA, Bacterial genetics, Base Composition, Phylogeny, Insecta, Nucleic Acid Hybridization, Perissodactyla genetics, Chryseobacterium, Coleoptera
Abstract

Two strains of Chryseobacterium identified from different experiments are proposed to represent new species. Strain WLa1L2M3 T was isolated from the digestive tract of an Oryctes rhinoceros beetle larva. Strain 09-1422 T was isolated from a cage housing the stick insect Eurycantha calcarata . Sequence analysis of the 16S rRNA and rpoB genes found both strains to be similar but not identical to other Chryseobacterium species. Whole-genome sequencing suggested the isolates represent new species, with average nucleotide identity values ranging from 74.6 to 80.5 %. Genome-to-genome distance calculations produced values below 25.3 %, and digital DNA-DNA hybridization values were 13.7-29.9 %, all suggesting they are distinct species. The genomic DNA G+C content of WLa1L2M3 T is approximately 32.53 %, and of 09-1422 T is approximately 35.89 %. The predominant cellular fatty acids of strain WLa1L2M3 T are C 15 : 0 iso, summed feature 9 (C 16 : 0 10OH or C 17 : 1 iso ω6 c ), C 17 : 0 iso 3OH, summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6c), C 15 : 0 iso 3OH, C 15 : 0 anteiso and C 13 : 0 iso, and those of strain 09-1422 T are C 15 : 0 iso, summed feature 3 (C 16 : 1 ω7c and/or C 16 : 1 ω6 c ), C 17 : 0 iso 3OH, C 15 : 0 anteiso, C 15 : 0 iso 3OH, C 16 : 1 ω7 c , C 17 : 0 2OH and C 18 : 0 . In addition, physiological and biochemical tests revealed phenotypic differences from related Chryseobacterium type strains. These cumulative data indicate that the two strains represent novel species of the genus Chryseobacterium for which the names Chryseobacterium oryctis sp. nov. and Chryseobacterium kimseyorum sp. nov. are proposed with WLa1L2M3 T (=BCRC 81350 T =JCM 35215 T =CIP 112035 T ) and 09-1422 T (=UCDFST 09-1422 T =BCRC 81359 T =CIP 112165 T ), as type strains, respectively.

Published
2023
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96. Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline.

Author

Da Cunha V, Davies MR, Douarre PE, Rosinski-Chupin I, Margarit I, Spinali S, Perkins T, Lechat P, Dmytruk N, Sauvage E, Ma L, Romi B, Tichit M, Lopez-Sanchez MJ, Descorps-Declere S, Souche E, Buchrieser C, Trieu-Cuot P, Moszer I, Clermont D, Maione D, Bouchier C, McMillan DJ, Parkhill J, Telford JL, Dougan G, Walker MJ, Holden MTG, Poyart C, and Glaser P

Subjects
Base Sequence, Clone Cells, DNA Transposable Elements, Europe epidemiology, High-Throughput Nucleotide Sequencing, Humans, Molecular Sequence Data, North America epidemiology, Phylogeny, Polymorphism, Single Nucleotide, Selection, Genetic, Streptococcal Infections drug therapy, Streptococcal Infections microbiology, Streptococcus agalactiae classification, Streptococcus agalactiae drug effects, Streptococcus agalactiae isolation & purification, Tetracycline Resistance genetics, Anti-Bacterial Agents pharmacology, Genes, Bacterial, Genome, Bacterial, Streptococcal Infections epidemiology, Streptococcus agalactiae genetics, Tetracycline pharmacology, Tetracycline Resistance drug effects
Abstract

Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by comparative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates.

Published
2014
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98. Draft Genome Sequences of Lactobacillus equicursoris CIP 110162T and Lactobacillus sp. Strain CRBIP 24.137, Isolated from Thoroughbred Racehorse Feces and Human Urine, Respectively.

Author

Cousin S, Loux V, Ma L, Creno S, Clermont D, Bizet C, and Bouchier C

Abstract

We report the draft genome sequences of strain Lactobacillus equicursoris CIP 110162(T), isolated from racehorse breed feces, and Lactobacillus sp. strain CRBIP 24.137, isolated from human urine; the two strains are closely related. The total lengths of the 116 and 62 scaffolds are about 2.157 and 2.358 Mb, with G+C contents of 46 and 45% and 2,279 and 2,342 coding sequences (CDSs), respectively.

Published
2013
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99. Draft Genome Sequences of Five Strains of Lactobacillus acidophilus, Strain CIP 76.13T, Isolated from Humans, Strains CIRM-BIA 442 and CIRM-BIA 445, Isolated from Dairy Products, and Strains DSM 20242 and DSM 9126 of Unknown Origin.

Author

Falentin H, Cousin S, Clermont D, Creno S, Ma L, Chuat V, Loux V, Rüdiger P, Bizet C, and Bouchier C

Abstract

Lactobacillus acidophilus is a natural inhabitant of mammalian gastrointestinal systems and is used in dairy and pharmaceutical products. Five draft genome sequences, covering 1,995,790 nucleotides (nt) on average, are divided into 19 to 34 scaffolds covering 1,995 to 2,053 genes. The draft genome sequences were compared to the sequence of the L. acidophilus NCFM dairy strain.

Published
2013
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100. Draft genome sequence of Lactobacillus gigeriorum CRBIP 24.85T, isolated from a chicken crop.

Author

Cousin S, Ma L, Creno S, Clermont D, Loux V, Bizet C, and Bouchier C

Subjects
Animals, Bacterial Proteins genetics, Base Composition, Chickens microbiology, Feces microbiology, Lactobacillus isolation & purification, Molecular Sequence Data, DNA, Bacterial chemistry, DNA, Bacterial genetics, Genome, Bacterial, Lactobacillus genetics, Sequence Analysis, DNA
Abstract

We report the draft genome of the strain Lactobacillus gigeriorum CRBIP 24.85(T), isolated from a chicken crop. The total length of the 60 scaffolds is about 1.9 Mb, with a GC content of 38% and 2,062 protein-coding sequences (CDS).

Published
2012
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