DOCSLIB.ORG

Gram-Positive Anaerobic Cocci: Clinical Relevance, Changed Taxonomy, Identification and Antibiotic Resistance

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Gram-Positive Anaerobic Cocci: Clinical Relevance, Changed Taxonomy, Identification and Antibiotic Resistance Gram-positive anaerobic cocci: clinical relevance, changed taxonomy, identification and antibiotic resistance © by author ESCMID Online Lecture Library Linda Veloo Contents Introduction Gram-positive anaerobic cocci Peptostreptococcus sp. (formerly) New species and taxonomy Identification © by author Antibiotic resistance ESCMID Online Lecture Library Virulence F. magna Introduction Gram-positive anaerobic cocci (GPAC): Peptococcus P.niger Seldomly isolated from clinical material Ruminococcus Faecel microbiota Seldomly ©isolated by fromauthor clinical material Insufficient culture methods? ESCMIDCoprococcus Online Lecture Library Isolated from faecal samples Gram positive anaerobic cocci, D.A. Murdoch Clinical Microbiology reviews, 1998 Introduction Atopobium Faecal microbiota and clinical material Sarcina Soil, abdominal samples, faecal samples from vegetarians and patients with gastro-intestinal abnormalities Unique cell© morphology: by author Groups of 8 cells which might produce spores ESCMID Online Lecture Library GPAC in general Clinical relevance: ± 30% of all anaerobes recovered from human clinical specimens Most GPAC: - mixed infections - susceptible for antibiotics usually used to treat anaerobic infections © by author Metronidazole-resistance: ESCMID- strict anaerobic Online cocci are Lecturegenerally sensitive Library - micro-aerophilic cocci are generally resistent Peptostreptococcus The genus Peptostreptococcus contained 13 species. Clinically most relevant (literature): P. anaerobius P. asaccharolyticus P. magnus P. micros © by author ESCMID Online Lecture Library New species, changed taxonomy (in chronological order) In 1997 3 new species were added to the genus Peptostreptococcus P. harei P. ivorii P. octavius Clinical relevance unknown© by author ESCMID Online Lecture Library Description of Three New Species of the Genus Peptostreptococcus from Human Clinical Specimens: P. harei sp. nov., P. ivorii sp. nov., and P. octavius sp. nov., D. A. Murdoch et al., Int. J. Syst. Bact. 1997 New taxonomy Reclassification of Peptostreptococcus magnus (Prevot 1933) Holdeman and Moore 1972 as Finegoldia magna comb. nov. and Peptostreptococcus micros (Prevot 1933) Smith 1957 as Micromonas micros comb. nov. Murdoch et al., Anaerobe,5, 1999 Proposal of the genera© Anaerococcus by author gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus EzakiESCMID et al., Int J syst Online Evol Microbiol, Lecture 51, 2001 Library A. murdochii Anaerococcus spp. Anaerobic cocci: anaerobic cocci Finegoldia magna MicromonasParvimonas micramicros Gallicola barnesea Helcococcus kunzii Peptoniphilus spp. P. gorbachii P. olsenii © by author ESCMID Online LecturePeptostreptoccus Library stomatis sp. P. stomatis nov., isolated from the human oral cavity. J. Downes et al. Int. J. P. anaerobius Syst. Evol. Microbiol. 2006 New genus and species Peptostreptococcus stomatis Peptostreptococcus anaerobius Peptostreptococcus canis Peptostreptococcus russellii Finegoldia magna Gallicola barnesae Parvimonas micra Murdochiella asaccharolytica Anaerococcus murdochii Anaerococcus lactolyticus Anaerococcus tetradius Anaerococcus prevotii Anaerococcus vaginalis Anaerococcus obensiensis Anaerococcus hydrogenalis Anaerococcus senegalensis Anaerococcus octavius Anaerococcus pacaensis Peptoniphilus indolicus Peptoniphilus asaccharolyticus ©Peptoniphilus by methioninivorax author Peptoniphilus ivorii Peptoniphilus coxii Candidatus Peptoniphilus Peptoniphilus tyrelliae(Peptoniphilus senegalensis) Peptoniphilus allenii ESCMID OnlinePeptoniphilus Lecture grossensis Library Peptoniphilus harei Peptoniphilus gorbachii Peptoniphilus timonensis Peptoniphilus olsenii Peptoniphilus lacrimalis Peptoniphilus koenoeniae Peptoniphilus duerdenii Peptoniphilus obesi Phenotypic identification Enzymatic tests derived from the API 32A (BioMerieux) Table Wadsworth manual Reliable identification: - F. magna - P. micra P. harei – P. asaccharolyticus similar biochemical features The addition of new species made© available by schemes author for the identification of GPAC less useful ESCMID Online Lecture Library Identification GPAC using 16S rRNA sequencing presented in NCBI Species Nucleotide collection 16S rRNA sequences remark Bacteria and Archaea A. murdochii only strain nr no A. tetradius species name yes A. lactolyticus species name yes A. octavius species name yes A. prevotii species name yes A. vaginalis species name yes A. hydrogenalis species name no sequence similarity with A. senegalensis is >99% A. pacaensis only strain nr no link with accession number yields species name A. senegalensis only strain nr no sequence similarity with A. hydrogenalis is >99% © by author link with accession number yields species name A. obesiensis species name no P. coxii species name no P. tyrelliae species name no sequence similarity with P. senegalensis is >99% P. harei species name yes P. ivorii species name yes also in NCBI under the species name P. ivoricus P. olsenii ESCMID only strain nr Online no Lecture type strain onlyLibrary mentioned with WAL number in NCBI clinical isolate with species name present in NCBI P. gorbachii only strain nr no type strain only mentioned with WAL number in NCBI clinical isolate with species name present in NCBI P. duerdenii species name no P. koenoeniae species name yes P. timonensis species name no Identification GPAC using 16S rRNA sequencing presented in NCBI Species Nucleotide collection 16S rRNA sequences remark Bacteria and Archaea P. grossensis species name no P. lacrimalis species name yes P. asaccharolyticus species name yes ………….. P. indolicus species name yes Candidatus P. massiliensis species name no this species is not officially described Candidatus P. allenii only strain nr no this species is not officially described P. rhinitidis no sequence of 16S rRNA gene available P. senegalensis only strain nr no sequence similarity with P. tyrelliae is >99% link with accession number yields species name P. obesi species name no P. micra species name ©yes by author F. magna species name yes P. anaerobius species name yes P. stomatis species name yes M. asaccharolytica species name no ESCMID Online Lecture Library Matrix Assisted Laser Desorption/Ionization time-of-flight Mass Spectrometry (MALDI-TOF MS) Vacuum flight tube Target at 15-25 kV Detector Ion source © by author ESCMID- “Time of flight” Online of individual Lecture proteins is converted Library into mass information. - Spectrum is produced - Database is built Veloo et al. Anaerobe 2011; 17:211-212 Identification of GPAC by MALDI-TOF MS Bruker system • 75% of GPAC encountered in human clinical specimens is identified by MALDI- TOF MS (estimated) • On target extraction with 70% formic acid is recommended • A. vaginalis is misidentifed as A. hydrogenalis • P. harei is correctly identified © by author • New species are not represented in de MALDI-TOF MS database ESCMID Online Lecture Library Identification of Gram-positive anaerobic cocci by MALDI-TOF mass spectrometry Veloo et al. Syst Appl Microbiol 2011; 34:58-62 Shimatzu/BioMerieux MS system Construction database: sequenced clinical isolates (n=77) and reference strains (n=12) reference strain P. harei is different compared to the clinical isolates P. harei © by author ValidationESCMID of constructed Online database: Lecture Library 107 genotypically identified clinical isolates of GPAC Validation database MALDI-TOF ID (n) Strain (n) correct ID no ID F. magna (32) 29 3 1 strain sequence similarity <98 % A. vaginalis (3) 2 1 P. ivorii (3) 1 2 sequence similarity <98 % P. octavius (1) 1 Bacterium N14-24 (1) 1 Not present in database GPAC (3) 3 © by author All other GPAC were correctly identified: P. micra (29) P. gorbachii (3) A. tetradius (1) ESCMIDP. harei (15) Online A. Lectureparvulum (3) LibraryP. lacrimalis (1) A. murdochii (6) P. niger (1) P. anaerobius (4) A. lactolyticus (1) Correctly identified: 96 strains No identification: 11 strains - 2 strains, no reference spectra present in database - 6 strains, <98 % sequence similarity with closest relative - 3 strains, unknown © by author 90 % correctly identified ESCMID Online Lecture Library Clustering P. anaerobius P. niger © by author P. micra ESCMID Online Lecture Library P. ivorii 100 Atopobium parvulum, AF292372 Dendrogram MALDI-TOF Peptococcus niger, X55797 100 RuminococcusPhylogeneticAtopobium gnavus, treeparvulum,X94967 AF292372 100 PeptostreptococcusPeptococcus niger, anaerobius,X55797 L04168 PeptostreptococcusRuminococcus gnavus, stomatis,X94967DQ160208 100 gpac228Peptostreptococcus94.8 % anaerobius, L04168 100Peptostreptococcus stomatis,Atopobium parvulum, AF292372 gpac216 94.4Peptococcus % niger, DQ160208 gpac228 X55797 97 gpac103 94.694.8 Ruminococcus %% gnavus, X94967 gpac216 10094.4Peptostreptococcus % anaerobius, L04168 gpac003 95.0Peptostreptococcus % stomatis, DQ160208 gpac103 94.6 % 97 gpac007 94.7gpac228 % 94.8 % gpac003 95.0gpac216 % 94.4 % gpac0749794.1gpac103 % 94.6 % 95 gpac007gpac018A94.7gpac003 % 95.0 % 100 gpac074 94.3 % Peptoniphilus94.1gpac007 %ivorii,94.7Y07840 % 100 95 gpac018A 94.3gpac074 % 94.1 % 100 Peptoniphilus100 95 gpac018A harei,94.3 % Y07839 Peptoniphilus ivorii, Y07840 gpac090Peptoniphilus97.8 % ivorii, Y07840 100 Peptoniphilus100 Peptoniphilus harei, Y07839harei, Y07839 Peptoniphilusgpac090 gorbachii,97.8 % DQ911241 gpac090 97.8 % gpac055 97.4Peptoniphilus % gorbachii, DQ911241 Peptoniphilusgpac055 gorbachii,97.4 % DQ911241 gpac018B 97.8 % gpac055 97.4gpac018B % 97.8 % 100 gpac121100 gpac12196.3 %
Load more

Recommended publications
  • Genomics 98 (2011) 370–375
    Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc.
    [Show full text]
  • Peptoniphilus Stercorisuis Sp. Nov., Isolated from a Swine Manure Storage Tank and Description of Peptoniphilaceae Fam
    10848 International Journal of Systematic and Evolutionary Microbiology (2014), 64, 3538–3545 DOI 10.1099/ijs.0.058941-0 Peptoniphilus stercorisuis sp. nov., isolated from a swine manure storage tank and description of Peptoniphilaceae fam. nov. Crystal N. Johnson,1 Terence R. Whitehead,2 Michael A. Cotta,2 Robert E. Rhoades1 and Paul A. Lawson1,3 Correspondence 1Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Paul A. Lawson OK 73019 USA [email protected] 2Bioenergy Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, 1815 N. University Street, Peoria, IL 61604, USA 3Ecology and Evolutionary Biology Program, University of Oklahoma, Norman, OK 73019 USA A species of a previously unknown Gram-positive-staining, anaerobic, coccus-shaped bacterium recovered from a swine manure storage tank was characterized using phenotypic, chemotaxonomic, and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies and biochemical characteristics demonstrated that this organism is genotypically and phenotypically distinct, and represents a previously unknown sub-line within the order Clostridiales, within the phylum Firmicutes. Pairwise sequence analysis demonstrated that the novel organism clustered within the genus Peptoniphilus, most closely related to Peptoniphilus methioninivorax sharing a 16S rRNA gene sequence similarity of 95.5 %. The major long-chain fatty acids were found to be C14 : 0 (22.4 %), C16 : 0 (15.6 %), C16 : 1v7c (11.3 %) and C16 : 0 ALDE (10.1 %) and the DNA G +C content was 31.8 mol%. Based upon the phenotypic and phylogenetic findings presented, a novel species Peptoniphilus stercorisuis sp. nov. is proposed. The type strain is SF-S1T (5DSM 27563T5NBRC 109839T).
    [Show full text]
  • Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections
    fmicb-11-01688 July 20, 2020 Time: 12:22 # 1 ORIGINAL RESEARCH published: 22 July 2020 doi: 10.3389/fmicb.2020.01688 Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections Fatemah Sadeghpour Heravi1, Martha Zakrzewski2, Karen Vickery1, Matthew Malone3,4,5 and Honghua Hu1* 1 Surgical Infection Research Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia, 2 QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia, 3 Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, NSW, Australia, 4 Liverpool Hospital, South Western Sydney LHD, Sydney, NSW, Australia, 5 Liverpool Diabetes Collaborative Research Unit, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance Edited by: Qi Zhao, of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different Liaoning University, China infection severities (P < 0.05). Mild and severe stages of infections were dominated Reviewed by: by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of Patrick R. M. Harnarayan, The University of the West Indies 132 metabolic pathways were identified of which ribosome and thiamin being among the at St. Augustine, Trinidad and Tobago most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, Maria José Saavedra, primarily involved in the multidrug efflux pumps/exporters, were identified.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Intraspecies Comparative Genomics of Rickettsia
    AIX ͲMARSEILLE UNIVERSITÉ FACULTÉ DE MÉDECINE DE MARSEILLE ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ T H È S E Présentée et publiquement soutenue devant LA FACULTÉ DE MÉDECINE DE MARSEILLE Le 13 décembre 2013 Par M. Erwin SENTAUSA Né le 16 décembre 1979 àMalang, Indonésie INTRASPECIES COMPARATIVE GENOMICS OF RICKETTSIA Pour obtenir le grade de DOCTORAT d’AIX ͲMARSEILLE UNIVERSITÉ SPÉCIALITÉ :PATHOLOGIE HUMAINE Ͳ MALADIES INFECTIEUSES Membres du Jury de la Thèse : Dr. Patricia RENESTO Rapporteur Pr. Max MAURIN Rapporteur Dr. Florence FENOLLAR Membre du Jury Pr. Pierre ͲEdouard FOURNIER Directeur de thèse Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes UM63, CNRS 7278, IRD 198, Inserm 1095 Avant Propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master de Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené àrespecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe permettant un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre àl’étudiant de le commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail.
    [Show full text]
  • Bacteria Clostridia Bacilli Eukaryota CFB Group
    AM935842.1.1361 uncultured Burkholderiales bacterium Class Betaproteobacteria AY283260.1.1552 Alcaligenes sp. PCNB−2 Class Betaproteobacteria AM934953.1.1374 uncultured Burkholderiales bacterium Class Betaproteobacteria AJ581593.1.1460 uncultured betaAM936569.1.1351 proteobacterium uncultured Class Betaproteobacteria Derxia sp. Class Betaproteobacteria AJ581621.1.1418 uncultured beta proteobacterium Class Betaproteobacteria DQ248272.1.1498 uncultured soil bacterium soil uncultured DQ248272.1.1498 DQ248235.1.1498 uncultured soil bacterium RS49 DQ248270.1.1496 uncultured soil bacterium DQ256489.1.1211 Variovorax paradoxus Class Betaproteobacteria Class paradoxus Variovorax DQ256489.1.1211 AF523053.1.1486 uncultured Comamonadaceae bacterium Class Betaproteobacteria AY706442.1.1396 uncultured bacterium uncultured AY706442.1.1396 AJ536763.1.1422 uncultured bacterium CS000359.1.1530 Variovorax paradoxus Class Betaproteobacteria Class paradoxus Variovorax CS000359.1.1530 AY168733.1.1411 uncultured bacterium AJ009470.1.1526 uncultured bacterium SJA−62 Class Betaproteobacteria Class SJA−62 bacterium uncultured AJ009470.1.1526 AY212561.1.1433 uncultured bacterium D16212.1.1457 Rhodoferax fermentans Class Betaproteobacteria Class fermentans Rhodoferax D16212.1.1457 AY957894.1.1546 uncultured bacterium AJ581620.1.1452 uncultured beta proteobacterium Class Betaproteobacteria RS76 AY625146.1.1498 uncultured bacterium RS65 DQ316832.1.1269 uncultured beta proteobacterium Class Betaproteobacteria DQ404909.1.1513 uncultured bacterium uncultured DQ404909.1.1513 AB021341.1.1466 bacterium rM6 AJ487020.1.1500 uncultured bacterium uncultured AJ487020.1.1500 RS7 RS86RC AF364862.1.1425 bacterium BA128 Class Betaproteobacteria AY957931.1.1529 uncultured bacterium uncultured AY957931.1.1529 CP000884.723807.725332 Delftia acidovorans SPH−1 Class Betaproteobacteria AY957923.1.1520 uncultured bacterium uncultured AY957923.1.1520 RS18 AY957918.1.1527 uncultured bacterium uncultured AY957918.1.1527 AY945883.1.1500 uncultured bacterium AF526940.1.1489 uncultured Ralstonia sp.
    [Show full text]
  • Urinicoccus Massiliensis Gen. Nov., Sp. Nov., a New Bacterium Isolated from a Human Urine Sample from a 7-Year-Old Boy Hospitalized for Dental Care
    NEW SPECIES Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care E. K. Yimagou1, H. Anani2, A. Yacouba1, I. Hasni1, J.-P. Baudoin1, D. Raoult3 and J. Y. Bou Khalil1 1) Aix Marseille University, IRD, AP-HM, MEPHI, 2) Aix Marseille Univ, IRD, AP-HM, VITROME, IHU-Méditerranée Infection, Marseille, France and 3) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. © 2019 The Authors. Published by Elsevier Ltd. Keywords: Culturomics, new species, taxonogenomics, urine, Urinicoccus massiliensis Original Submission: 16 July 2019; Revised Submission: 10 October 2019; Accepted: 17 October 2019 Article published online: 30 October 2019 previously described [7]. The obtained spectra (Fig. 1) were Corresponding author. J. Y. Bou Khalil, MEPHI, Institut Hospitalo- imported into MALDI Biotyper 3.0 software (Bruker Daltonics) Universitaire Méditerranée Infection, 19–21 Boulevard Jean Moulin 13385 Marseille Cedex 05. France and analysed against the main spectra of the bacteria included in E-mail: [email protected] the database (Bruker database constantly updated http://www. mediterraneeinfection.com/article.php?larub=280&titre=urms- database). The initial growth was obtained 10 days after culture on a blood culture vial (Becton Dickinson, Le Pont-de-Claix, Introduction France) supplemented with 5 mL of 0.2-μm-filtered rumen fluid in anaerobic conditions at 37°C and pH 7.5. Culturomics is a concept involving the development of different Strain identification culture conditions in order to enlarge our knowledge of the The 16S rRNA gene was sequenced in order to classify this human microbiota through the discovery of previously uncul- bacterium.
    [Show full text]
  • A Genomic Journey Through a Genus of Large DNA Viruses
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Virology Papers Virology, Nebraska Center for 2013 Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses Adrien Jeanniard Aix-Marseille Université David D. Dunigan University of Nebraska-Lincoln, [email protected] James Gurnon University of Nebraska-Lincoln, [email protected] Irina V. Agarkova University of Nebraska-Lincoln, [email protected] Ming Kang University of Nebraska-Lincoln, [email protected] See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/virologypub Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons, Cell and Developmental Biology Commons, Genetics and Genomics Commons, Infectious Disease Commons, Medical Immunology Commons, Medical Pathology Commons, and the Virology Commons Jeanniard, Adrien; Dunigan, David D.; Gurnon, James; Agarkova, Irina V.; Kang, Ming; Vitek, Jason; Duncan, Garry; McClung, O William; Larsen, Megan; Claverie, Jean-Michel; Van Etten, James L.; and Blanc, Guillaume, "Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses" (2013). Virology Papers. 245. https://digitalcommons.unl.edu/virologypub/245 This Article is brought to you for free and open access by the Virology, Nebraska Center for at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Virology Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Adrien Jeanniard, David D. Dunigan, James Gurnon, Irina V. Agarkova, Ming Kang, Jason Vitek, Garry Duncan, O William McClung, Megan Larsen, Jean-Michel Claverie, James L. Van Etten, and Guillaume Blanc This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ virologypub/245 Jeanniard, Dunigan, Gurnon, Agarkova, Kang, Vitek, Duncan, McClung, Larsen, Claverie, Van Etten & Blanc in BMC Genomics (2013) 14.
    [Show full text]
  • The Influence of Sodium Chloride on the Performance of Gammarus Amphipods and the Community Composition of Microbes Associated with Leaf Detritus
    THE INFLUENCE OF SODIUM CHLORIDE ON THE PERFORMANCE OF GAMMARUS AMPHIPODS AND THE COMMUNITY COMPOSITION OF MICROBES ASSOCIATED WITH LEAF DETRITUS By Shelby McIlheran Leaf litter decomposition is a fundamental part of the carbon cycle and helps support aquatic food webs along with being an important assessment of the health of rivers and streams. Disruptions in this organic matter breakdown can signal problems in other parts of ecosystems. One disruption is rising chloride concentrations. Chloride concentrations are increasing in many rivers worldwide due to anthropogenic sources that can harm biota and affect ecosystem processes. Elevated chloride concentrations can lead to lethal or sublethal impacts. While many studies have shown that excessive chloride uptake impacts health (e.g. lowered respiration and growth rates) in a wide variety of aquatic organisms including microbes and benthic invertebrates). The impacts of high chloride concentrations on decomposers are less well understood. My research objective was to assess how increasing chloride concentrations affect the performance and diversity of decomposer organisms in freshwater systems. I experimentally manipulated chloride concentrations in microcosms containing leaves colonized by microbes or containing leaves, microbes and amphipods. Respiration rate, decomposition, and community composition of the microbes were measured along with the amphipod growth rate, egestion rate, and mortality. Elevated chloride concentration did not impact microbial respiration rates or leaf decomposition, but had large impacts on bacteria community composition. It did cause a decrease in instantaneous growth rate, and 100% mortality in the highest amphipod chloride treatment, but amphipod egestion rate was not significantly affected. The results of my research suggest that the widespread increases in chloride concentrations in rivers will have an impact on decomposer communities in these systems.
    [Show full text]
  • UK Standards for Microbiology Investigations
    UK Standards for Microbiology Investigations Identification of Anaerobic Cocci Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 14 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 29 © Crown copyright 2015 Identification of Anaerobic Cocci Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 14 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 29 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Anaerobic Cocci Contents ACKNOWLEDGMENTS .........................................................................................................
    [Show full text]
  • Outline Release 7 7C
    Garrity, et. al., March 6, 2007 Taxonomic Outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 7 – The Bacteria: Phylum “Firmicutes”: Class “Clostridia” George M. Garrity, Timothy G. Lilburn, James R. Cole, Scott H. Harrison, Jean Euzéby, and Brian J. Tindall F Phylum Firmicutes AL N4Lid DOI: 10.1601/nm.3874 Class "Clostridia" N4Lid DOI: 10.1601/nm.3875 71 Order Clostridiales AL Prévot 1953. N4Lid DOI: 10.1601/nm.3876 Family Clostridiaceae AL Pribram 1933. N4Lid DOI: 10.1601/nm.3877 Genus Clostridium AL Prazmowski 1880. GOLD ID: Gi00163. GCAT ID: 000971_GCAT. Entrez genome id: 80. Sequenced strain: BC1 is from a non-type strain. Genome sequencing is incomplete. Number of genomes of this species sequenced 6 (GOLD) 6 (NCBI). N4Lid DOI: 10.1601/nm.3878 Clostridium butyricum AL Prazmowski 1880. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 19398. High-quality 16S rRNA sequence S000436450 (RDP), M59085 (Genbank). N4Lid DOI: 10.1601/nm.3879 Clostridium aceticum VP (ex Wieringa 1940) Gottschalk and Braun 1981. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 35044. High-quality 16S rRNA sequence S000016027 (RDP), Y18183 (Genbank). N4Lid DOI: 10.1601/nm.3881 Clostridium acetireducens VP Örlygsson et al. 1996. Source of type material recommended for DOE sponsored genome sequencing by the JGI: DSM 10703. High-quality 16S rRNA sequence S000004716 (RDP), X79862 (Genbank). N4Lid DOI: 10.1601/nm.3882 Clostridium acetobutylicum AL McCoy et al. 1926. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 824.
    [Show full text]
  • Urinicoccus Massiliensis Gen. Nov., Sp. Nov., a New Bacterium Isolated from a Human Urine Sample from a 7-Year-Old Boy Hospitalized for Dental Care
    NEW SPECIES Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care E. K. Yimagou1, H. Anani2, A. Yacouba1, I. Hasni1, J.-P. Baudoin1, D. Raoult3 and J. Y. Bou Khalil1 1) Aix Marseille University, IRD, AP-HM, MEPHI, 2) Aix Marseille Univ, IRD, AP-HM, VITROME, IHU-Méditerranée Infection, Marseille, France and 3) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. © 2019 The Authors. Published by Elsevier Ltd. Keywords: Culturomics, new species, taxonogenomics, urine, Urinicoccus massiliensis Original Submission: 16 July 2019; Revised Submission: 10 October 2019; Accepted: 17 October 2019 Article published online: 30 October 2019 previously described [7]. The obtained spectra (Fig. 1) were Corresponding author. J. Y. Bou Khalil, MEPHI, Institut Hospitalo- imported into MALDI Biotyper 3.0 software (Bruker Daltonics) Universitaire Méditerranée Infection, 19–21 Boulevard Jean Moulin 13385 Marseille Cedex 05. France and analysed against the main spectra of the bacteria included in E-mail: [email protected] the database (Bruker database constantly updated http://www. mediterraneeinfection.com/article.php?larub=280&titre=urms- database). The initial growth was obtained 10 days after culture on a blood culture vial (Becton Dickinson, Le Pont-de-Claix, Introduction France) supplemented with 5 mL of 0.2-μm-filtered rumen fluid in anaerobic conditions at 37°C and pH 7.5. Culturomics is a concept involving the development of different Strain identification culture conditions in order to enlarge our knowledge of the The 16S rRNA gene was sequenced in order to classify this human microbiota through the discovery of previously uncul- bacterium.
    [Show full text]