APUTS) Reporting Terminology and Codes Microbiology (V1.0
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Susceptibility and Resistance Data
toku-e logo For a complete list of references, please visit antibiotics.toku-e.com Imipenem Microorganism Genus, Species, and Strain (if shown) Concentration Range (μg/ml)Susceptibility and Achromobacter xylosoxidans subsp. denitrificans 0.25 - 4 Minimum Inhibitory Acinetobacter anitratus ≤0.008 128 Acinetobacter baumannii Concentration0.008 - 512 (MIC) Data Acinetobacter calcoaceticus 0.016 - >8 Issue date 01/06/2020 Acinetobacter haemolyticus ≤0.008 >16 Acinetobacter junii ≤0.12 >8 Acinetobacter lwoffii ≤0.008 >16 Acinetobacter spp. 0.008 - >64 Actinomyces gerencseriae ≤0.015 8 Actinomyces graevenitzii ≤0.015 0.25 Actinomyces israelii ≤0.015 8 Actinomyces meyeri ≤0.015 8 Actinomyces naeslundii 0.015 - 8 Actinomyces neuii ≤0.015 0.25 Actinomyces odontolyticus ≤0.015 8 Actinomyces radingae ≤0.015 0.25 Actinomyces schalii ≤0.015 0.25 Actinomyces spp. ≤0.008 8 Actinomyces turicensis ≤0.015 0.25 Actinomyces viscosus ≤0.015 0.5 Aerococcus spp. ≤0.008 4 Aerococcus urinae ≤0.008 4 Aeromonas caviae 0.25 - 4 Aeromonas hydrophila 0.25 - 16 Aeromonas spp. 0.12 - 4 Agrobacterium radiobacter 0.06 - 1 Alcaligenes faecalis 0.06 - >16 Alcaligenes odorans 0.25 - 1 Anaerococcus prevotii ≤0.016 0.25 Anaerococcus tetradius ≤0.016 0.03 Arcanobacterium pyogenes ≤0.03 0.25 Atopobium parvulum 0.25 Bacillus proteus 4 Bacillus spp. ≤0.008 4 Bacillus subtilis <0.025 Bacteroides caccae ≤0.06 8 Bacteroides capillosus 0.06 - 0.25 Bacteroides distasonis 0.03 - 8 Bacteroides eggerthii ≤0.125 0.5 Bacteroides fragilis ≤0.008 >128 Bacteroides fragilis gr. 0.03 - 4 Bacteroides levii 0.06 - 0.25 Bacteroides merdae ≤0.06 4 Bacteroides ovatus 0.03 - 16 Bacteroides splanchnicus 0.06 - 0.25 Bacteroides spp. -
Expanding the Knowledge on the Skillful Yeast Cyberlindnera Jadinii
Journal of Fungi Review Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii Maria Sousa-Silva 1,2 , Daniel Vieira 1,2, Pedro Soares 1,2, Margarida Casal 1,2 and Isabel Soares-Silva 1,2,* 1 Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; [email protected] (M.S.-S.); [email protected] (D.V.); [email protected] (P.S.); [email protected] (M.C.) 2 Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal * Correspondence: [email protected]; Tel.: +351-253601519 Abstract: Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. -
Table of Contents
MARCH 2013 • VOLUME 51 • NO. 3 TABLE OF CONTENTS PHOTO QUIZ Bacteremia in a Patient with Hepatic Encephalopathy Benjamin H. Hinrichs, Robert C. Jerris, 739 Eileen M. Burd Answer to Photo Quiz Benjamin H. Hinrichs, Robert C. Jerris, 1062–1063 Eileen M. Burd POINT-COUNTERPOINT Quantitative Cultures of Bronchoscopically Obtained Vickie Baselski, J. Stacey Klutts 740–744 Specimens Should Be Performed for Optimal Management of Ventilator-Associated Pneumonia BACTERIOLOGY Pan-PCR, a Computational Method for Designing Bacterium- Joy Y. Yang, Shelise Brooks, Jennifer A. 752–758 Typing Assays Based on Whole-Genome Sequence Data Meyer, Robert R. Blakesley, Adrian M. Zelazny, Julia A. Segre, Evan S. Snitkin Identification of Anaerobic Bacteria by Bruker Biotyper Matrix- Bryan H. Schmitt, Scott A. 782–786 Assisted Laser Desorption Ionization–Time of Flight Mass Cunningham, Aaron L. Dailey, Spectrometry with On-Plate Formic Acid Preparation Daniel R. Gustafson, Robin Patel Use of Universal 16S rRNA Gene PCR as a Diagnostic Tool for M. Guembe, M. Marín, P. Martín- 799–804 Venous Access Port-Related Bloodstream Infections Rabadán, A. Echenagusia, F. Camúñez, G. Rodríguez-Rosales, G. Simó, M. Echenagusia, E. Bouza, on behalf of the GEIDI Study Group Rapid Identification of Bacteria and Yeasts from Positive-Blood- Amy Fothergill, Vyjayanti Kasinathan, 805–809 Culture Bottles by Using a Lysis-Filtration Method and Matrix- Jay Hyman, John Walsh, Tim Drake, Assisted Laser Desorption Ionization–Time of Flight Mass Yun F. (Wayne) Wang Spectrum Analysis with the SARAMIS Database Pseudo-Outbreak of Vancomycin-Resistant-Enterococcus Rita M. Gander, Dominick Cavuoti, 810–813 (VRE) Colonization in a Neonatal Intensive Care Unit Using Adnan Alatoom, Paul Southern, Jr., Spectra VRE Surveillance Medium Debra Grant, Kathleen Salinas, Donna Gaffney, Jennifer MacKenzie, Linda Byrd Changes in Molecular Epidemiology of Streptococcus Bruno Pichon, Shamez N. -
NCTC) Bacterial Strain Equivalents to American Type Culture Collection (ATCC) Bacterial Strains
This list shows National Collection of Type Cultures (NCTC) bacterial strain equivalents to American Type Culture Collection (ATCC) bacterial strains. NCTC Number CurrentName ATCC Number NCTC 7212 Acetobacter pasteurianus ATCC 23761 NCTC 10138 Acholeplasma axanthum ATCC 25176 NCTC 10171 Acholeplasma equifetale ATCC 29724 NCTC 10128 Acholeplasma granularum ATCC 19168 NCTC 10172 Acholeplasma hippikon ATCC 29725 NCTC 10116 Acholeplasma laidlawii ATCC 23206 NCTC 10134 Acholeplasma modicum ATCC 29102 NCTC 10188 Acholeplasma morum ATCC 33211 NCTC 10150 Acholeplasma oculi ATCC 27350 NCTC 10198 Acholeplasma parvum ATCC 29892 NCTC 8582 Achromobacter denitrificans ATCC 15173 NCTC 10309 Achromobacter metalcaligenes ATCC 17910 NCTC 10807 Achromobacter xylosoxidans subsp. xylosoxidans ATCC 27061 NCTC 10808 Achromobacter xylosoxidans subsp. xylosoxidans ATCC 17062 NCTC 10809 Achromobacter xylosoxidans subsp. xylosoxidans ATCC 27063 NCTC 12156 Acinetobacter baumannii ATCC 19606 NCTC 10303 Acinetobacter baumannii ATCC 17904 NCTC 7844 Acinetobacter calcoaceticus ATCC 15308 NCTC 12983 Acinetobacter calcoaceticus ATCC 23055 NCTC 8102 acinetobacter dna group 13 ATCC 17903 NCTC 10304 Acinetobacter genospecies 13 ATCC 17905 NCTC 10306 Acinetobacter haemolyticus ATCC 17907 NCTC 10305 Acinetobacter haemolyticus subsp haemolyticus ATCC 17906 NCTC 10308 Acinetobacter johnsonii ATCC 17909 NCTC 10307 Acinetobacter junii ATCC 17908 NCTC 5866 Acinetobacter lwoffii ATCC 15309 NCTC 12870 Actinobacillus delphinicola ATCC 700179 NCTC 8529 Actinobacillus equuli ATCC 19392 -
M.Sc. Dissertation
2 ACKNOWLEDGEMENTS I wish to thank the following: God , for giving me the strength and guidance to start each day with new hope. Prof. J. L. F. Kock , for his guidance, understanding and passion for research. Prof. P. W. J. van Wyk and Miss B. Janecke for their patience and assistance with the SEM, TEM and CLSM. Dr. C. H. Pohl , for her encouragement and assistance. Mrs. A. van Wyk , for providing the yeast cultures used during this study and also for her encouragement and support. Mr. S. F. Collett , for assisting with the graphical design of this dissertation. My colleagues in Lab 28 , for always being supportive and helpful. My mother, Mrs. M. M. Swart and grandmother, Mrs. M. M. Coetzer , for their patience, love and encouragement. My family for their encouragement and for believing in me. Mr. P. S. Delport , for his love, understanding and patience. 3 CONTENTS Page Title Page 1 Acknowledgements 3 Contents 4 CHAPTER 1 Literature Review 1.1 Motivation 9 1.2 Automictic yeasts 10 1.2.1 Definition of a yeast 10 1.2.2 Automixis 11 1.3 Oxylipins 19 1.3.1 Background 19 1.3.2 3-OH oxylipins 19 1.3.2.1 Chemical structure and production 19 1.3.2.2 Distribution 20 1.3.2.3 Function 23 1.3.2.4 ASA inhibition 23 1.4 Purpose of research 24 1.5 References 26 4 CHAPTER 2 Oxylipin accumulation and acetylsalicylic acid sensitivity in fermentative and non-fermentative yeasts 2.1 Abstract 38 2.2 Introduction 40 2.3 Materials and Methods 41 2.3.1 Strains used and cultivation 41 2.3.2 Ultrastructure 42 2.3.2.1 Scanning electron microscopy (SEM) -
Legionella Shows a Diverse Secondary Metabolism Dependent on a Broad Spectrum Sfp-Type Phosphopantetheinyl Transferase
Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase Nicholas J. Tobias1, Tilman Ahrendt1, Ursula Schell2, Melissa Miltenberger1, Hubert Hilbi2,3 and Helge B. Bode1,4 1 Fachbereich Biowissenschaften, Merck Stiftungsprofessur fu¨r Molekulare Biotechnologie, Goethe Universita¨t, Frankfurt am Main, Germany 2 Max von Pettenkofer Institute, Ludwig-Maximilians-Universita¨tMu¨nchen, Munich, Germany 3 Institute of Medical Microbiology, University of Zu¨rich, Zu¨rich, Switzerland 4 Buchmann Institute for Molecular Life Sciences, Goethe Universita¨t, Frankfurt am Main, Germany ABSTRACT Several members of the genus Legionella cause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella. Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict Submitted 29 June 2016 some novel compounds that are probably involved in cell-cell communication, Accepted 25 October 2016 Published 24 November 2016 differing to known communication systems. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Oxylipin Distribution in Eremothecium
1 Oxylipin distribution in Eremothecium by Ntsoaki Joyce Leeuw Submitted in accordance with the requirements for the degree Magister Scientiae in the Department of Microbial, Biochemical and Food Biotechnology Faculty of Natural and Agricultural Sciences University of the Free State Bloemfontein South Africa Supervisor: Prof J.L.F. Kock Co- supervisors: Dr C.H. Pohl Prof P.W.J. Van Wyk November 2006 2 This dissertation is dedicated to the following people: My mother (Nkotseng Leeuw) My brother (Kabelo Leeuw) My cousins (Bafokeng, Lebohang, Mami, Thabang and Rorisang) Mr. Eugean Malebo 3 ACKNOWLEDGEMENTS I wish to thank and acknowledge the following: ) God, to You be the glory for the things You have done in my life. ) My family (especially my mom) – for always being there for me when I’m in need. ) Prof. J.L.F Kock for his patience, constructive criticisms and guidance during the course of this study. ) Dr. C.H. Pohl for her encouragement and assistance in the writing up of this dissertation. ) Mr. P.J. Botes for assistance with the GC-MS. ) Prof. P.W.J. Van Wyk and Miss B. Janecke for assistance with the CLSM and SEM. ) My fellow colleagues (especially Chantel and Desmond) for their assistance, support and encouragement. ) Mr. Eugean Malebo for always being there when I needed you. 4 CONTENTS Page Title page I Acknowledgements II Contents III CHAPTER 1 Introduction 1.1 Motivation 2 1.2 Definition and classification of yeasts 3 1.3 Classification of Eremothecium and related genera 5 1.4 Pathogenicity 12 1.5 Oxylipins 13 1.5.1 Definition -
The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
Evaluation of the Relatedness of Brucella Spp. and Ochrobactrum Anthropi and Description of Ochrobactrum Intermedium Sp
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Dadun, University of Navarra International Journal of Systematic Bacteriology (1 998), 48, 759-768 Printed in Great Britain Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella SPP. Julian Velasco,’ Conchi Romero,’ lgnacio Lopez-Got%,’ Jose Leiva,2 Ramon Diaz1f2and lgnacio Moriydn’ Author for correspondence : Ignacio Moriyon. Tel : + 34 48 425600. Fax : + 34 48 425649. e-mail : [email protected] Departamento de The relatedness of Brucella spp. and Ochrobactrum anthropi was studied by M icrob io I og ia, Un ive rs id ad protein profiling, Western blot, immunoelectrophoresis and 16s rRNA analysis. de Navarra, Aptdo 1771 and Servicio de Microbiologia, Whole-cell and soluble proteins of brucellae and 0. anthropi showed Clinica Universitaria de serological cross-reactivities quantitatively and qualitatively more intense Navarraz, Pamplona, Spain than those existing with similar extracts of Agrobacterium spp. Numerical analysis of Western blot profiles of whole-cell extracts showed that 0. anthropi LMG 3301 was closer to Brucella spp. than to 0. anthropi LMG 3331T, a result not obtained by protein profiling. These differences were not observed by Western blot with soluble fractions, and immunoelectrophoretic analyses suggested that this was due to destruction of conformational epitopes in Western blot procedures with the subsequent simplification of antigenic profile. Analysis of the 165 rRNA sequences of strains previously used in the species definition confirmed that strain LMG 3301, and also LMG 3306, were closer to the brucellae, and that LMG 3331Twas in a separate cluster. -
Tumor Mimicking Actinomycosis of the Upper Lip: Report of Two Cases
Oral Med Pathol 15 (2011) 95 Tumor mimicking actinomycosis of the upper lip: report of two cases Kayo Kuyama1, 2, Yan Sun1, Kenji Fukui2, Satoshi Maruyama3, Eriko Ochiai2, Masahiko Fukumoto4, Nobuyuki Ikeda5, Toshiro Kondoh6, Kimiharu Iwadate2, Ritsuo Takagi5, Takashi Saku3, 7, Hirotsugu Yamamoto1 1Department of Oral Pathology, Nihon University School of Dentistry at Matsudo, Matsudo, Japan 2Department of Forensic Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, Japan 3Oral Pathology Section, Department of Surgical Pathology, Niigata University Hospital, Niigata, Japan 4Department of Laboratory Medicine for Dentistry, Nihon University School of Dentistry at Matsudo, Matsudo, Japan 5Division of Oral and Maxillofacial Surgery, Department of Oral Health Science, Niigata University Graduate School of Medical and Dental Sciences 6Department of Maxillofacial Surgery, Nihon University School of Dentistry at Matsudo, Matsudo, Japan 7Division of Oral Pathology, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan Abstract: Peculiar findings of orofacial actinomycosis mimicking the clinical appearance of a tumor of the upper lip were reported. A 68-year-old woman (case 1) and a 62-year-old woman (case 2) visited our hospitals towards the end of 2004 and 2007; the clinical diagnosis for each patient was upper labial tumor, and the lesions were surgically removed. Histologically, the excised specimens showed granulomas including bacterial colonies consisting of club-shaped filaments that formed a radiating rosette pattern in the submucosal layer. DNA samples were extracted from paraffin sections and examined by PCR for Actinomyces species. The PCR products examined by direct DNA sequencing demonstrated the presence of Actinomyces israelii and Actinomyces gerencseriae in both case 1 and case 2. -
Actinomyces Georgiae Sp. Nov. , Actinomyces Gerencseriae Sp. Nov
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1990, p. 273-286 Vol. 40, No. 3 0020-7713/90/070273-14$02.oo/o Copyright 0 1990, International Union of Microbiological Societies Actinomyces georgiae sp. nov. , Actinomyces gerencseriae sp. nov. , Designation of Two Genospecies of Actinomyces naeslundii, and Inclusion of A. naeslundii serotypes I1 and I11 and Actinomyces viscosus serotype I1 in A. naeslundii Genospecies 2 J. L. JOHNSON,l LILLIAN V. H. MOORE,l BEVERLY KANEK0,2 AND W. E. C. MOORE1* Department of Anaerobic Microbiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, and Microbial Diseases Laboratory, Department of Health Services, State of California, Berkeley, California 947M2 DNAs of type strains aod representative members of Actinomyces groups from the human periodontal flora and from other habitats were compared by using the S1 nuclease procedure to determine their genetic relatedness. One rather common group from the human periodontal flora, previously called “Actinomyces DOS,” is phenotypically distinct from, and genetically unrelated to, previously described species. We propose the name Actinomyces georgiae for this organism; the type strain is strain ATCC 49285. Another common group from the human periodontal flora is Actinomyces israelii serotype 11, which was found to be genetically distinct from the type strain of A. israelii (serotype I) and from other previously described species of Actinomyces. We propose the name Actinomyces gerencseriae for this organism; the type strain is strain ATCC 23860. A. naeslundii serotype I strains were distinct from the other strains studied. A separate genospecies which included strains of A. naeslundii serotypes I1 and I11 and A. viscosus serotype I1 was delineated.