WO 2014/176636 A9 6 November 2014 (06.11.2014) P O P C T
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BD-CS-057, REV 0 | AUGUST 2017 | Page 1
EXPLIFY RESPIRATORY PATHOGENS BY NEXT GENERATION SEQUENCING Limitations Negative results do not rule out viral, bacterial, or fungal infections. Targeted, PCR-based tests are generally more sensitive and are preferred when specific pathogens are suspected, especially for DNA viruses (Adenovirus, CMV, HHV6, HSV, and VZV), mycobacteria, and fungi. The analytical sensitivity of this test depends on the cellularity of the sample and the concentration of all microbes present. Analytical sensitivity is assessed using Internal Controls that are added to each sample. Sequencing data for Internal Controls is quantified. Samples with Internal Control values below the validated minimum may have reduced analytical sensitivity or contain inhibitors and are reported as ‘Reduced Analytical Sensitivity’. Additional respiratory pathogens to those reported cannot be excluded in samples with ‘Reduced Analytical Sensitivity’. Due to the complexity of next generation sequencing methodologies, there may be a risk of false-positive results. Contamination with organisms from the upper respiratory tract during specimen collection can also occur. The detection of viral, bacterial, and fungal nucleic acid does not imply organisms causing invasive infection. Results from this test need to be interpreted in conjunction with the clinical history, results of other laboratory tests, epidemiologic information, and other available data. Confirmation of positive results by an alternate method may be indicated in select cases. Validated Organisms BACTERIA Achromobacter -
Studies on Oral Colonization of Periodontopathogenic Bacterium
Studies on oral colonization of periodontopathogenic bacterium Eikenella corrodens 㸦ṑ࿘ཎᛶ⣽⳦ (LNHQHOODFRUURGHQV ࡢཱྀ⭍ෆᐃ╔㛵ࡍࡿ◊✲㸧 㻌 㻌 FARIHA JASIN MANSUR 2017 㻌 㻌 DEDICATED TO MY BELOVED PARENTS CONTENTS CONTENTS…………………………………………………………. 1 LIST OF ABBREVIATIONS ……………………………………. 2 CHAPTER 1: GENERAL INTRODUCTION …………………………………... 4 CHAPTER 2 .………………………………………………………. 11 2.1 ABSTRACT ……………………………………………………. 12 2.2 INTRODUCTION ……………………………………………... 13 2.3 MATERIALS AND METHODS ……………………………… 16 2.4 RESULTS AND DISCUSSION ……………………………….. 21 CHAPTER 3 ………………………………………………………... 31 3.1 ABSTRACT …………………………………………………….. 32 3.2 INTRODUCTION ……………………………………………… 33 3.3 MATERIALS AND METHODS ………………………………. 35 3.4 RESULTS AND DISCUSSION ………………………………... 38 CHAPTER 4: GENERAL CONCLUSION ………………………………………... 44 SUMMARY ………………………………………………………….. 50 JAPANESE SUMMARY ……………………………………………. 52 ACKNOWLEDGEMENTS …………………………………………. 54 REFERENCES ……………………………………………………….. 56 LIST OF PUBLICATIONS ………………………………………….. 65 㻝㻌 㻌 LIST OF ABBREVIATIONS CE Cell envelope GalNAc㻌㻌㻌㻌㻌㻌 N-acetyl-D-galactosamine g Gram g/L Gram/litre HA㻌㻌㻌㻌㻌㻌㻌㻌 Hemagglutination ∆hlyA hlyA-deficient strain H hour IL Interleukin IPTG Isopropyl β-D-1-thiogalactopyranoside LB㻌 㻌 㻌 㻌 Luria broth M Molar mM Milimolar min Minute mL Mililitre mg/mL Milligram/mililitre NaCl Sodium chloride ORF Open reading frame PBS Phosphate-buffered saline㻌 PCR Polymerase chain reaction pH㻌㻌 㻌 㻌㻌㻌㻌㻌㻌㻌Potential of hydrogen SDS–PAGE Sodium dodecyl sulfate polyacrylamide gel electrophoresis TSB Tryptic soy broth 㻞㻌 㻌 μL Microlitre μM Micromolar -
( Eikenella Corrodens のクオラムセンシングと バイオフィルム形成の関連性に関する研究)
Studies on the relationship between quorum sensing and biofilm formation of Eikenella corrodens ( Eikenella corrodens のクオラムセンシングと バイオフィルム形成の関連性に関する研究) by MOHAMMAD MINNATUL KARIM Thesis Submitted to the United Graduate School of Agricultural Sciences Tottori University, Japan In partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY (PhD) The United Graduate School of Agricultural Sciences Tottori University, Japan September, 2013 1 DEDICATED TO MY BELOVED PARENTS 2 CONTENTS CONTENTS...............................................................................................ⅰ LIST OF ABBREVIATIONS...................................................................ⅱ GENERAL INTRODUCTION................................................................. 1 OBJECTIVES........................................................................................... 10 CHAPTER 1 ............................................................................................. 11 The Periodontopathogenic Bacterium Eikenella corrodens Produces an Autoinducer-2-Inactivating Enzyme 1.1 ABSTRACT ………………………………………………………… 12 1.2 INTRODUCTION …………………………………………………....13 1.3 MATERIALS AND METHODS ……………………………………..15 1.4 RESULTS …………………………………………………………… 19 1.5 DISCUSSION ………………………………………………………. 22 1.6 FIGURES …………………………………………………………….25 CHAPTER 2 …………………………………………………………… 32 LuxS affects biofilm maturation and detachment of the periodontopathogenic bacterium Eikenella corrodens 2.1 ABSTRACT …………………………………………………………. 33 2.2 INTRODUCTION …………………………………………………....34 -
Digestive Tract Infections •Skin & Soft Tissue Infections(SSTI)
EU Conference: Workshop #6 Macrolide Indications: •Ocular Infections •Stomatologic Infections •Digestive tract Infections •Skin & Soft Tissue Infections(SSTI) Dr. S. Simonian (NL) © CBG-MEB 1 Introduction • Problem statement: – What is the (un-)labelled use of individual macrolides in ocular, stomatologic, GI and SSTI infections? – What is the ultimate list of practical indications in these areas? • Approach: – Review information documented in data sheets & clinical literature. – From current global situation to agreed ----> by reconciliation of clinical experience with regulatory process----> state of the art indications. Focus will be primarily on systemic macrolides. © CBG-MEB 2 General Indications Ocular infections 1 ? Conjunctivitis (neonatal) C. trachomatis 2 ? Blepharitis Staphylococcal Stomatologic infections Eikenella corrodens? ? Periodontal disease3 Streptococci spp. Digestive tract infections HP peptic ulcer H. pylori* CJ Acute enteritis4 C. jejuni Cholecystitis5 SSTI Acne P. acnes Impetigo, erysipelas Streptococci spp. Furuncles, abcesses S. aureus Lyme disease?? B. burgdorferi Bartonella infections in HIV-patients ? Unlabelled use Questionable * In combination with PPI and other ?? antibiotics (eg. amoxicillin) As unlabelled alternative to beta-lactams and tetracyclines in early Lyme disease. As second-line in case tetracyline is inappropriate. © CBG-MEB 3 Indication status: Labelled(!), unlabelled & in research Ery Rox Clar Azit Telit Jos Spir Ocular infections Conjunctivitis(of the newborn) ! Blepharitis ! Trachoma -
Virulence Determinants, Drug Resistance and Mobile Genetic
Lau et al. Cell & Bioscience 2011, 1:17 http://www.cellandbioscience.com/content/1/1/17 Cell & Bioscience RESEARCH Open Access Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis Susanna KP Lau1,2,3,4*†, Gilman KM Wong4†, Alan KL Tsang4†, Jade LL Teng4, Rachel YY Fan4, Herman Tse1,2,3,4, Kwok-Yung Yuen1,2,3,4 and Patrick CY Woo1,2,3,4* Abstract Background: Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler’s diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements. Results: For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to b-lactam (n = 10) and multidrug efflux (n = 54). -
Intrathoracic Infections Due to Eikenella Corrodens
Thorax: first published as 10.1136/thx.42.9.700 on 1 September 1987. Downloaded from Thorax 1987;42:700-701 Intrathoracic infections due to Eikenella corrodens SHAHROKH JAVAHERI, RICHARD M SMITH, DAVID WILTSE From the Pulmonary Division and Department ofMedicine, Veterans Administration Medical Center, University ofCincinnati College ofMedicine; and the Pulmonary Division, Department ofMedicine, Good Samaritan Hospital, Cincinnati, Ohio, USA Eikenella corrodens, a fastidious facultative anaerobic Gram choscopy showed swelling of the left upper lobe bronchi; all negative bacillus,' is part of the normal human oral flora. specimens were negative for malignant cells. On day 7 a Although it has been implicated as the sole causative agent Gram negative rod was cultured from one of the blood cul- for certain infections, I- its pathogenetic importance ture bottles, and this was identified as E corrodens by mor- remains uncertain. E corrodens has been isolated in respira- phological and biochemical criteria.1 2 The organism was tory tract infections, including pneumonia, abscess, and resistant to clindamycin but sensitive to penicillin. All other empyema, where detailed bacteriological investigations have blood cultures, both aerobic and anaerobic, were negative; been performed, but only in association with other sputum grew normal flora. On day 9 ampicillin was given microbes.2 356 It was recently isolated by transtracheal or and gentamicin and clindamycin were stopped. He then percutaneous aspiration from seven patients with pneu- became afebrile and felt better and his appetite improved. monia or lung abscess,5 but in each case several other Repeated attempts to wean him from intravenous fluid organisms were cultured. The present report shows that E resulted in hypotension. -
Original Article COMPARISON of MAST BURKHOLDERIA CEPACIA, ASHDOWN + GENTAMICIN, and BURKHOLDERIA PSEUDOMALLEI SELECTIVE AGAR
European Journal of Microbiology and Immunology 7 (2017) 1, pp. 15–36 Original article DOI: 10.1556/1886.2016.00037 COMPARISON OF MAST BURKHOLDERIA CEPACIA, ASHDOWN + GENTAMICIN, AND BURKHOLDERIA PSEUDOMALLEI SELECTIVE AGAR FOR THE SELECTIVE GROWTH OF BURKHOLDERIA SPP. Carola Edler1, Henri Derschum2, Mirko Köhler3, Heinrich Neubauer4, Hagen Frickmann5,6,*, Ralf Matthias Hagen7 1 Department of Dermatology, German Armed Forces Hospital of Hamburg, Hamburg, Germany 2 CBRN Defence, Safety and Environmental Protection School, Science Division 3 Bundeswehr Medical Academy, Munich, Germany 4 Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Jena, Germany 5 Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany 6 Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany 7 Department of Preventive Medicine, Bundeswehr Medical Academy, Munich, Germany Received: November 18, 2016; Accepted: December 5, 2016 Reliable identification of pathogenic Burkholderia spp. like Burkholderia mallei and Burkholderia pseudomallei in clinical samples is desirable. Three different selective media were assessed for reliability and selectivity with various Burkholderia spp. and non- target organisms. Mast Burkholderia cepacia agar, Ashdown + gentamicin agar, and B. pseudomallei selective agar were compared. A panel of 116 reference strains and well-characterized clinical isolates, comprising 30 B. pseudomallei, 20 B. mallei, 18 other Burkholderia spp., and 48 nontarget organisms, was used for this assessment. While all B. pseudomallei strains grew on all three tested selective agars, the other Burkholderia spp. showed a diverse growth pattern. Nontarget organisms, i.e., nonfermentative rod-shaped bacteria, other species, and yeasts, grew on all selective agars. -
A New Symbiotic Lineage Related to Neisseria and Snodgrassella Arises from the Dynamic and Diverse Microbiomes in Sucking Lice
bioRxiv preprint doi: https://doi.org/10.1101/867275; this version posted December 6, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. A new symbiotic lineage related to Neisseria and Snodgrassella arises from the dynamic and diverse microbiomes in sucking lice Jana Říhová1, Giampiero Batani1, Sonia M. Rodríguez-Ruano1, Jana Martinů1,2, Eva Nováková1,2 and Václav Hypša1,2 1 Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic 2 Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czech Republic Author for correspondence: Václav Hypša, Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic, +42 387 776 276, [email protected] Abstract Phylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have experienced a complex history of symbiont acquisition, loss, and replacement during their evolution. By combining metagenomics and amplicon screening across several populations of two louse genera (Polyplax and Hoplopleura) we describe a novel louse symbiont lineage related to Neisseria and Snodgrassella, and show its' independent origin within dynamic lice microbiomes. While the genomes of these symbionts are highly similar in both lice genera, their respective distributions and status within lice microbiomes indicate that they have different functions and history. In Hoplopleura acanthopus, the Neisseria-related bacterium is a dominant obligate symbiont universally present across several host’s populations, and seems to be replacing a presumably older and more degenerated obligate symbiont. -
Use of the Diagnostic Bacteriology Laboratory: a Practical Review for the Clinician
148 Postgrad Med J 2001;77:148–156 REVIEWS Postgrad Med J: first published as 10.1136/pmj.77.905.148 on 1 March 2001. Downloaded from Use of the diagnostic bacteriology laboratory: a practical review for the clinician W J Steinbach, A K Shetty Lucile Salter Packard Children’s Hospital at EVective utilisation and understanding of the Stanford, Stanford Box 1: Gram stain technique University School of clinical bacteriology laboratory can greatly aid Medicine, 725 Welch in the diagnosis of infectious diseases. Al- (1) Air dry specimen and fix with Road, Palo Alto, though described more than a century ago, the methanol or heat. California, USA 94304, Gram stain remains the most frequently used (2) Add crystal violet stain. USA rapid diagnostic test, and in conjunction with W J Steinbach various biochemical tests is the cornerstone of (3) Rinse with water to wash unbound A K Shetty the clinical laboratory. First described by Dan- dye, add mordant (for example, iodine: 12 potassium iodide). Correspondence to: ish pathologist Christian Gram in 1884 and Dr Steinbach later slightly modified, the Gram stain easily (4) After waiting 30–60 seconds, rinse with [email protected] divides bacteria into two groups, Gram positive water. Submitted 27 March 2000 and Gram negative, on the basis of their cell (5) Add decolorising solvent (ethanol or Accepted 5 June 2000 wall and cell membrane permeability to acetone) to remove unbound dye. Growth on artificial medium Obligate intracellular (6) Counterstain with safranin. Chlamydia Legionella Gram positive bacteria stain blue Coxiella Ehrlichia Rickettsia (retained crystal violet). -
List of the Pathogens Intended to Be Controlled Under Section 18 B.E
(Unofficial Translation) NOTIFICATION OF THE MINISTRY OF PUBLIC HEALTH RE: LIST OF THE PATHOGENS INTENDED TO BE CONTROLLED UNDER SECTION 18 B.E. 2561 (2018) By virtue of the provision pursuant to Section 5 paragraph one, Section 6 (1) and Section 18 of Pathogens and Animal Toxins Act, B.E. 2558 (2015), the Minister of Public Health, with the advice of the Pathogens and Animal Toxins Committee, has therefore issued this notification as follows: Clause 1 This notification is called “Notification of the Ministry of Public Health Re: list of the pathogens intended to be controlled under Section 18, B.E. 2561 (2018).” Clause 2 This Notification shall come into force as from the following date of its publication in the Government Gazette. Clause 3 The Notification of Ministry of Public Health Re: list of the pathogens intended to be controlled under Section 18, B.E. 2560 (2017) shall be cancelled. Clause 4 Define the pathogens codes and such codes shall have the following sequences: (1) English alphabets that used for indicating the type of pathogens are as follows: B stands for Bacteria F stands for fungus V stands for Virus P stands for Parasites T stands for Biological substances that are not Prion R stands for Prion (2) Pathogen risk group (3) Number indicating the sequence of each type of pathogens Clause 5 Pathogens intended to be controlled under Section 18, shall proceed as follows: (1) In the case of being the pathogens that are utilized and subjected to other law, such law shall be complied. (2) Apart from (1), the law on pathogens and animal toxin shall be complied. -
Genetic and Functional Studies of the Mip Protein of Legionella
t1.ì. Genetic and Functional Studies of the Mip Protein of Legionella Rodney Mark Ratcliff, BSc (Hons)' MASM Infectious Diseases Laboratories Institute of Medical and Veterinary Science and Department of Microbiology and Immunology UniversitY of Adelaide. Adelaide, South Australia A thesis submitted to the University of Adelaide for the degree of I)octor of Philosophy 15'h March 2000 amended 14th June 2000 Colonies of several Legionella strains on charcoal yeast extract agar (CYE) after 4 days incubation at 37"C in air. Various magnifications show typical ground-glass opalescent appearance. Some pure strains exhibit pleomorphic growth or colour. The top two photographs demonstrate typical red (LH) and blue-white (RH) fluorescence exhibited by some species when illuminated by a Woods (IJV) Lamp. * t Table of Contents .1 Chapter One: Introduction .1 Background .............'. .2 Morphology and TaxonomY J Legionellosis ............. 5 Mode of transmission "..'....'. 7 Environmental habitat 8 Interactions between Legionella and phagocytic hosts 9 Attachment 11 Engulfment and internalisation.'.. 13 Intracellular processing 13 Intracellular replication of legionellae .. " "' " "' 15 Host cell death and bacterial release 18 Virulence (the Genetic factors involved with intracellular multiplication and host cell killing .20 icm/dot system) Legiolysin .25 Msp (Znn* metaloprotease) ...'..... .25 .28 Lipopolysaccharide .29 The association of flagella with disease.. .30 Type IV fimbriae.... .31 Major outer membrane proteins....'.......'. JJ Heat shock proteins'.'. .34 Macrophage infectivity potentiator (Mip) protein Virulenceiraits of Legionella species other than L. pneumophila..........' .39 phylogeny .41 Chapter One (continued): Introduction to bacterial classification and .41 Identificati on of Legionella...'.,..'.. .46 Phylogeny .52 Methods of phylogenetic analysis' .53 Parsimony methods.'.. .55 Distance methods UPGMA cluster analYsis.'.'... -
Circulatory and Lymphatic System Infections 1105
Chapter 25 | Circulatory and Lymphatic System Infections 1105 Chapter 25 Circulatory and Lymphatic System Infections Figure 25.1 Yellow fever is a viral hemorrhagic disease that can cause liver damage, resulting in jaundice (left) as well as serious and sometimes fatal complications. The virus that causes yellow fever is transmitted through the bite of a biological vector, the Aedes aegypti mosquito (right). (credit left: modification of work by Centers for Disease Control and Prevention; credit right: modification of work by James Gathany, Centers for Disease Control and Prevention) Chapter Outline 25.1 Anatomy of the Circulatory and Lymphatic Systems 25.2 Bacterial Infections of the Circulatory and Lymphatic Systems 25.3 Viral Infections of the Circulatory and Lymphatic Systems 25.4 Parasitic Infections of the Circulatory and Lymphatic Systems Introduction Yellow fever was once common in the southeastern US, with annual outbreaks of more than 25,000 infections in New Orleans in the mid-1800s.[1] In the early 20th century, efforts to eradicate the virus that causes yellow fever were successful thanks to vaccination programs and effective control (mainly through the insecticide dichlorodiphenyltrichloroethane [DDT]) of Aedes aegypti, the mosquito that serves as a vector. Today, the virus has been largely eradicated in North America. Elsewhere, efforts to contain yellow fever have been less successful. Despite mass vaccination campaigns in some regions, the risk for yellow fever epidemics is rising in dense urban cities in Africa and South America.[2] In an increasingly globalized society, yellow fever could easily make a comeback in North America, where A. aegypti is still present.