Helicobacter Infection
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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. -
Genomics of Helicobacter Species 91
Genomics of Helicobacter Species 91 6 Genomics of Helicobacter Species Zhongming Ge and David B. Schauer Summary Helicobacter pylori was the first bacterial species to have the genome of two independent strains completely sequenced. Infection with this pathogen, which may be the most frequent bacterial infec- tion of humanity, causes peptic ulcer disease and gastric cancer. Other Helicobacter species are emerging as causes of infection, inflammation, and cancer in the intestine, liver, and biliary tract, although the true prevalence of these enterohepatic Helicobacter species in humans is not yet known. The murine pathogen Helicobacter hepaticus was the first enterohepatic Helicobacter species to have its genome completely sequenced. Here, we consider functional genomics of the genus Helico- bacter, the comparative genomics of the genus Helicobacter, and the related genera Campylobacter and Wolinella. Key Words: Cytotoxin-associated gene; H-Proteobacteria; gastric cancer; genomic evolution; genomic island; hepatobiliary; peptic ulcer disease; type IV secretion system. 1. Introduction The genus Helicobacter belongs to the family Helicobacteriaceae, order Campylo- bacterales, and class H-Proteobacteria, which is also known as the H subdivision of the phylum Proteobacteria. The H-Proteobacteria comprise of a relatively small and recently recognized line of descent within this extremely large and phenotypically diverse phy- lum. Other genera that colonize and/or infect humans and animals include Campylobac- ter, Arcobacter, and Wolinella. These organisms are all microaerophilic, chemoorgano- trophic, nonsaccharolytic, spiral shaped or curved, and motile with a corkscrew-like motion by means of polar flagella. Increasingly, free living H-Proteobacteria are being recognized in a wide range of environmental niches, including seawater, marine sedi- ments, deep-sea hydrothermal vents, and even as symbionts of shrimp and tubeworms in these environments. -
Diagnostic Assay for Helicobacter Hepaticus Based on Nucleotide Sequence of Its 16S Rrna Gene JANE K
JOURNAL OF CLINICAL MICROBIOLOGY, May 1995, p. 1344–1347 Vol. 33, No. 5 0095-1137/95/$04.0010 Copyright q 1995, American Society for Microbiology Diagnostic Assay for Helicobacter hepaticus Based on Nucleotide Sequence of Its 16S rRNA Gene JANE K. BATTLES,1 JAMES C. WILLIAMSON,1 KRISTEN M. PIKE,1 PETER L. GORELICK,2 3 1 JERROLD M. WARD, AND MATTHEW A. GONDA * Laboratory of Cell and Molecular Structure1 and Laboratory Animal Sciences Program,2 Program Resources, Inc./DynCorp, and Veterinary and Tumor Pathology Section, Office of Laboratory Animal Science,3 National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, Maryland 21702-1201 Received 17 November 1994/Returned for modification 3 January 1995/Accepted 7 February 1995 Conserved primers were used to PCR amplify 95% of the Helicobacter hepaticus 16S rRNA gene. Its sequence was determined and aligned to those of related bacteria, enabling the selection of primers to highly diverged regions of the 16S rRNA gene and an oligonucleotide probe for the development of a PCR-liquid hybridization assay. This assay was shown to be both sensitive and specific for H. hepaticus 16S rRNA gene sequences. Helicobacter hepaticus is a recently identified species of Helicobacter canis (34). Many PCR-based techniques have gram-negative, microaerophilic, urease-positive, spiral bacte- been developed to amplify 16S rRNA sequences of H. pylori rium that was originally isolated from the livers of mice with and related organisms (3, 6, 15, 16, 20, 24, 39, 44). chronic active hepatitis at the National Cancer Institute-Fred- In the present report, the objective was to develop a species- erick Cancer Research and Development Center. -
The Year in Helicobacter 2020
EDITOR: David Y. Graham, M.D. The Year in Helicobacter 2020 Guest Editors: Francis Mégraud & Peter Malfertheiner Online only from 2011 The Year in Helicobacter XXXIIIrd Internaঞ onal Workshop on Helicobacter & Microbiota in Infl ammaঞ on & Cancer Virtual Conference September 12, 2020 Guest editors: Francis Mégraud & Peter Malfertheiner This publicaঞ on has been supported by European Helicobacter and Microbiota Study Group Helicobacter VOLUME 25 SUPPLEMENT 1 SEPTEMBER 2020 CONTENTS REVIEW ARTICLES e12734 Review: Epidemiology of Helicobacter pylori Linda Mezmale, Luiz Gonzaga Coelho, Dmitry Bordin and Marcis Leja e12735 Review: Diagnosis of Helicobacter pylori infecঞ on Gauri Godbole, Francis Mégraud and Emilie Bessède e12736 Review: Pathogenesis of Helicobacter pylori infecঞ on Milica Denic, Elie e Touaࢼ and Hilde De Reuse e12737 Review - Helicobacter, infl ammaঞ on, immunology and vaccines Karen Robinson and Philippe Lehours e12738 Review - Helicobacter pylori and non-malignant upper gastro-intesঞ nal diseases Chrisࢼ an Schulz and Juozas Kupcˇinskas e12739 Review: Gastric cancer: Basic aspects Carlos Resende, Carla Pereira Gomes and Jose Carlos Machado e12740 Review: Prevenঞ on and management of gastric cancer Marino Venerito, Alexander C. Ford, Theodoros Rokkas and Peter Malfertheiner e12741 Review: Extragastric diseases and Helicobacter pylori Rinaldo Pellicano, Gianluca Ianiro, Sharmila Fagoonee, Carlo R. Se anni and Antonio Gasbarrini e12742 Review: Helicobacter pylori infecঞ on in children Ji-Hyun Seo, Kristen Bortolin and Nicola L. -
Guide D'antibiothérapie Raisonnée Des Infections Bactériennes Du Chien
ECOLE NATIONALE VETERINAIRE DE LYON Année 2009 - Thèse n° Guide d’Antibiothérapie Raisonnée des Infections Bactériennes du Chien THESE Présentée à l’UNIVERSITE CLAUDE-BERNARD - LYON I (Médecine - Pharmacie) et soutenue publiquement le 11 janvier 2010 pour obtenir le grade de Docteur Vétérinaire par RAMSEYER Jérémie Né le 18 mai 1984 À Roanne (42) ECOLE NATIONALE VETERINAIRE DE LYON Année 2009 - Thèse n° Guide d’Antibiothérapie Raisonnée des Infections Bactériennes du Chien THESE Présentée à l’UNIVERSITE CLAUDE-BERNARD - LYON I (Médecine - Pharmacie) et soutenue publiquement le 11 janvier 2010 pour obtenir le grade de Docteur Vétérinaire par RAMSEYER Jérémie Né le 18 mai 1984 À Roanne (42) 2 3 REMERCIEMENTS Aux membres de notre jury de thèse, pour l’honneur qu’ils nous ont fait de participer à ce jury. A Monsieur le Professeur PEYRAMOND, De la Faculté de Médecine de Lyon, Qui nous a fait l’honneur d’accepter la présidence de notre jury de thèse Hommages respectueux. A Madame le Docteur GUERIN-FAUBLEE, De l’Ecole Nationale Vétérinaire de Lyon, Qui nous a fait l’honneur d’accepter de nous encadrer, de nous corriger et de nous apporter une aide précieuse au cours de l’élaboration de ce travail. Pour toute sa gentillesse et sa disponibilité, Qu’elle trouve ici l’expression de notre reconnaissance et de notre respect les plus sincères. A Monsieur le Professeur BERNY, De l’Ecole Nationale Vétérinaire de Lyon, Qui a accepté de participer à notre jury de thèse. A Madame le Docteur PROUILLAC, De l’Ecole Nationale Vétérinaire de Lyon, Dont l’aide a été précieuse. -
R Graphics Output
883 | Desulfovibrio vulgaris | DvMF_2825 298701 | Desulfovibrio | DA2_3337 1121434 | Halodesulfovibrio aestuarii | AULY01000007_gene1045 207559 | Desulfovibrio alaskensis | Dde_0991 935942 | Desulfonatronum lacustre | KI912608_gene2193 159290 | Desulfonatronum | JPIK01000018_gene1259 1121448 | Desulfovibrio gigas | DGI_0655 1121445 | Desulfovibrio desulfuricans | ATUZ01000018_gene2316 525146 | Desulfovibrio desulfuricans | Ddes_0159 665942 | Desulfovibrio | HMPREF1022_02168 457398 | Desulfovibrio | HMPREF0326_00453 363253 | Lawsonia intracellularis | LI0397 882 | Desulfovibrio vulgaris | DVU_0784 1121413 | Desulfonatronovibrio hydrogenovorans | JMKT01000008_gene1463 555779 | Desulfonatronospira thiodismutans | Dthio_PD0935 690850 | Desulfovibrio africanus | Desaf_1578 643562 | Pseudodesulfovibrio aespoeensis | Daes_3115 1322246 | Pseudodesulfovibrio piezophilus | BN4_12523 641491 | Desulfovibrio desulfuricans | DND132_2573 1121440 | Desulfovibrio aminophilus | AUMA01000002_gene2198 1121456 | Desulfovibrio longus | ATVA01000018_gene290 526222 | Desulfovibrio salexigens | Desal_3460 1121451 | Desulfovibrio hydrothermalis | DESAM_21057 1121447 | Desulfovibrio frigidus | JONL01000008_gene3531 1121441 | Desulfovibrio bastinii | AUCX01000006_gene918 1121439 | Desulfovibrio alkalitolerans | dsat_0220 941449 | Desulfovibrio | dsx2_0067 1307759 | Desulfovibrio | JOMJ01000003_gene2163 1121406 | Desulfocurvus vexinensis | JAEX01000012_gene687 1304872 | Desulfovibrio magneticus | JAGC01000003_gene2904 573370 | Desulfovibrio magneticus | DMR_04750 -
Appendix a Bacteria
Appendix A Complete list of 594 pathogens identified in canines categorized by the following taxonomical groups: bacteria, ectoparasites, fungi, helminths, protozoa, rickettsia and viruses. Pathogens categorized as zoonotic/sapronotic/anthroponotic have been bolded; sapronoses are specifically denoted by a ❖. If the dog is involved in transmission, maintenance or detection of the pathogen it has been further underlined. Of these, if the pathogen is reported in dogs in Canada (Tier 1) it has been denoted by an *. If the pathogen is reported in Canada but canine-specific reports are lacking (Tier 2) it is marked with a C (see also Appendix C). Finally, if the pathogen has the potential to occur in Canada (Tier 3) it is marked by a D (see also Appendix D). Bacteria Brachyspira canis Enterococcus casseliflavus Acholeplasma laidlawii Brachyspira intermedia Enterococcus faecalis C Acinetobacter baumannii Brachyspira pilosicoli C Enterococcus faecium* Actinobacillus Brachyspira pulli Enterococcus gallinarum C C Brevibacterium spp. Enterococcus hirae actinomycetemcomitans D Actinobacillus lignieresii Brucella abortus Enterococcus malodoratus Actinomyces bovis Brucella canis* Enterococcus spp.* Actinomyces bowdenii Brucella suis Erysipelothrix rhusiopathiae C Actinomyces canis Burkholderia mallei Erysipelothrix tonsillarum Actinomyces catuli Burkholderia pseudomallei❖ serovar 7 Actinomyces coleocanis Campylobacter coli* Escherichia coli (EHEC, EPEC, Actinomyces hordeovulneris Campylobacter gracilis AIEC, UPEC, NTEC, Actinomyces hyovaginalis Campylobacter -
Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales
Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales TECHNICAL BIOSAFETY COMMITTEE (TBC) NATIONAL CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (BIOTEC) NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY (NSTDA) MINISTRY OF SCIENCE AND TECHNOLOGY (MOST) 2015 Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales TECHNICAL BIOSAFETY COMMITTEE (TBC) NATIONAL CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY (BIOTEC) NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY (NSTDA) MINISTRY OF SCIENCE AND TECHNOLOGY (MOST) 2015 Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales Technical Biosafety Committee National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency (NSTDA) © National Center for Genetic Engineering and Biotechnology 2015 ISBN : 978-616-12-0386-3 Tel : +66(0)2-564-6700 Fax : +66(0)2-564-6703 E-mail : [email protected] URL : http://www.biotec.or.th Printing House : P.A. Living Printing Co.,Ltd 4 Soi Sirintron 7 Road Sirintron District Bangplad Province Bangkok 10700 Tel : +66(0)2-881 9890 Fax : +66(0)2-881 9894 Preface Genetically Modified Microorganisms (GMMs) were first used in B.E. 2525 to produce insulin in industrial medicine. Currently, GMMs are used in various industries, such as the food, pharmaceutical and bioplastic industries, to manufacture a number of important consumer products. To ensure operator and environmental safety, the Technical Biosafety Committee (TBC) of the National Center for Genetic Engineering and Biotechnology (BIOTEC), the National Science and Technology Development Agency (NSTDA), has prepared guidelines for GMM work, publishing “Biosafety Guidelines for Contained Use of Genetically Modified Microorganisms at Pilot and Industrial Scales” in B.E. -
APUTS) Reporting Terminology and Codes Microbiology (V1.0
AUSTRALIAN PATHOLOGY UNITS AND TERMINOLOGY (APUTS) Reporting Terminology and Codes Microbiology (v1.0) 1 12/02/2013 APUTS Report Information Model - Urine Microbiology Page 1 of 1 Specimen Type Specimen Macro Time Glucose Bilirubin Ketones Specific Gravity pH Chemistry Protein Urobilinogen Nitrites Haemoglobin Leucocyte Esterases White blood cell count Red blood cells Cells Epithelial cells Bacteria Microscopy Parasites Microorganisms Yeasts Casts Crystals Other elements Antibacterial Activity No growth Mixed growth Urine MCS No significant growth Klebsiella sp. Bacteria ESBL Klebsiella pneumoniae Identification Virus Fungi Growth of >10^8 org/L 10^7 to 10^8 organism/L of mixed Range or number Colony Count growth of 3 organisms 19090-0 Culture Organism 1 630-4 LOINC >10^8 organisms/L LOINC Significant growth e.g. Ampicillin 18864-9 LOINC Antibiotics Susceptibility Method Released/suppressed None Organism 2 Organism 3 Organism 4 None Consistent with UTI Probable contamination Growth unlikely to be significant Comment Please submit a repeat specimen for testing if clinically indicated Catheter comments Sterile pyuria Notification to infection control and public health departments PUTS Urine Microbiology Information Model v1.mmap - 12/02/2013 - Mindjet 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Urine Page 1 of 3 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1 LOINC LOINC LOINC LOINC LOINC LOINC LOINC Urine Microbiology Report -