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Comparative Phylogeny of the Genus Bordetella Using Sequence Analysis of 16S Rrna and Ompa Genes
J Med Bacteriol. Vol. 6, No. 3, 4 (2017): pp.1-13 jmb.tums.ac.ir Comparative Phylogeny of the Genus Bordetella Using Sequence Analysis of 16S rRNA and ompA Genes Ali Badamchi 1, Moslem Papizadeh 2* 1 Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran. 2 Department of Microbiology, Pasteur Institute of Iran (IPI), Tehran, Iran. ARTICLE INFO ABSTRACT Article type: Background: The genus Bordetella harbors 16 species; three of them are well-known for their high Original Article medical importance. The phylogenetic diversity of the genus is currently not very well investigated. Methods: In this study, 16S rRNA gene sequence of 16 type strains of the Bordetella species were Article history: analyzed. Also, phylogenies conducted on the same gene of 247 isolates of Bordetella species, Received: 19 Jan 2017 comprising a wide physiological as well as ecological diversity and encompassing ex-type Revised: Jun Mar 2017 representatives of the 16 Bordetella species, were analyzed. Accepted: 11 Sep 2017 Results: It was found that the phylogenetic diversity of the genus may be very different from that is Published: 15 Oct 2017 currently assumed. Interestingly, the 16S rRNA gene signals could not resolve some species with Keywords: promising bootstrap and posterior probability values as our phylogenies, using maximum likelihood Alcaligenaceae, and Bayesian inference methods, showed. Biogeography, Bordetella Conclusion: Our results indicate a probable need for additional phylogenetic signals which can be species, Ecological provided by coding genes. Therefore, sequence data of ompA gene of Bordetella species, a critically distribution, Phylogenetic significant genomic region in pathogenesis, was here analyzed, phylogenetically. -
Rapid NH System Rapid Spot Indole Reagent (R8309002, Supplied Separately) • When Using the 1-Hour Procedure, Only Selective Notes: (15 Ml/Bottle) Agars Can Be Used
n,n-Dimethyl-1-naphthylamine ..................................... 6.0 g Selective Media: Thayer-Martin Agar; Martin-Lewis 6. Return the panel to a level position. If necessary, gently Glacial Acetic Acid ................................................... 280.0 ml Agar; New York City Agar. tap the panel on the bench top to remove any air Demineralized Water ............................................... 720.0 ml Notes: trapped in the cavities. RapID NH System RapID Spot Indole Reagent (R8309002, supplied separately) • When using the 1-hour procedure, only selective Notes: (15 ml/Bottle) agars can be used. • Examine the test cavities which should appear R8311001 .................................................20 Tests/Kit ρ-Dimethylaminocinnamaldehyde .............................. 10.0 g • Cultures used for inoculum preparation should bubble-free and uniformly filled. Slight irregularities 1. INTENDED USE Hydrochloric Acid .................................................... 100.0 ml preferably be 18-24 hours old. Slow-growing isolates in test cavity fills are acceptable and will not affect Remel RapID™ NH System is a qualitative micromethod Demineralized Water ............................................... 900.0 ml may be tested using 48-hour cultures. test performance. If the panel is grossly misfilled, employing conventional and chromogenic substrates for the *Adjusted as required to meet performance standards. a new panel should be inoculated and the misfilled • The use of media other than those recommended panel discarded. identification of medically important species of Neisseria, 5. PRECAUTIONS may compromise test performance. Haemophilus, and other bacteria isolated from human • Complete the inoculation of each panel receiving in vitro clinical specimens. A complete listing of the organisms This product is for diagnostic use and should be used 3. Using a cotton swab or inoculating loop, suspend inoculation fluid before inoculating additional addressed by RapID NH System is provided in the RapID NH by properly trained individuals. -
ﺑﺴﻢ اﷲ اﻟﺮﺣﻤﻦ اﻟﺮﺣﻴﻢ Molecular Characterization Of
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by KhartoumSpace ﺑﺴﻢ اﷲ اﻟﺮﺣﻤﻦ اﻟﺮﺣﻴﻢ Molecular Characterization of Pasteurella multocida Vaccine Strains By: Hajir Badawi Mohammed Ahmed B.V.M Khartoum University (2006) Supervisor: Dr. Awad A. Ibrahim A dissertation submitted to the University of Khartoum in partial fulfillment of the requirements for the degree of M. Sc. in Microbiology Department of Microbiology, Faculty of Veterinary Medicine, University of Khartoum June, 2010 Dedication To my mother Father Brother, sister and friends With great love Acknowledgments First and foremost, I would like to thank my Merciful Allah, the most beneficent for giving me strength and health to accomplish this work. Then I would like to deeply thank my supervisor Dr. Awad A. Ibrahim for his advice, continuous encouragement and patience throughout the period of this work. My gratitude is also extended to prof. Mawia M. Mukhtar and for Dr. Manal Gamal El-dein, Institute of Endemic Disease. My thanks extend to members of Department of Microbiology Faculty of Veterinary Medicine for unlimited assistant and for staff of Central Laboratory Soba. I am grateful to my family for their continuous support and standing beside me all times. My thanks also extended to all whom I didn’t mention by name and to the forbearance of my friends, and colleagues who helped me. Finally I am indebted to all those who helped me so much to make this work a success. Abstract The present study was carried out to study the national haemorrhagic septicaemia vaccine strains at their molecular level. -
Bordetella Petrii Clinical Isolate Isolates of This Species Have Been Previously Reported from 4
routine laboratory protocols. Initial susceptibility testing Bordetella petrii using disk diffusion indicated apparent susceptibility of the isolate to erythromycin, gentamicin, ceftriaxone, and Clinical Isolate piperacillin/tazobactam. The isolate was resistant to amox- icillin, co-amoxiclav, tetracycline, clindamycin, ciproflo- Norman K. Fry,* John Duncan,* Henry Malnick,* xacin, and metronidazole. After initial sensitivity results, a Marina Warner,* Andrew J. Smith,† 6-week course of oral clarithromycin (500 mg, 8 hourly) Margaret S. Jackson,† and Ashraf Ayoub† was begun. We describe the first clinical isolate of Bordetella petrii At follow-up appointments 3 months and 6 months from a patient with mandibular osteomyelitis. The only pre- after antimicrobial drug therapy ceased, clinical and radi- viously documented isolation of B. petrii occurred after the ographic findings were not unusual, and the infected area initial culture of a single strain from an environmental healed successfully. Despite the successful clinical out- source. come, the isolate was subsequently shown to be resistant to clarithromycin in vitro (Table). Improvement of the 67-year-old man visited an emergency dental clinic, osteomyelitis may also have been facilitated by the biopsy Awhere he complained of toothache in the lower right procedure, during which a sequestrum of bone was mandibular quadrant. Examination showed a root-filled removed. lower right canine tooth that was mobile and tender to per- The gram-negative bacillus (designated strain cussion. The tooth was extracted uneventfully under local GDH030510) was submitted to the Health Protection anesthesia. The patient returned after several days with Agency, Centre for Infections, London, for identification. pain at the extraction site. A localized alveolar osteitis was Preliminary tests results were consistent with those diagnosed, and local debridement measures were institut- described for members of the genus Bordetella. -
Identification of Pasteurella Species and Morphologically Similar Organisms
UK Standards for Microbiology Investigations Identification of Pasteurella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Pasteurella species and Morphologically Similar Organisms 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 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Pasteurella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS ......................................................................................................... -
Chapitre IV: Bacilles Gram Négatifs Aéro- Anaérobie Facultatifs ______Les Entérobactéries, Cours De Microbiologie Systématique Dr
Chapitre IV: Bacilles Gram négatifs aéro- anaérobie facultatifs __________________________________________Les entérobactéries, Cours de Microbiologie Systématique Dr. BOUSSENA 1. Enterobacteriaceae 1.1. Définition Les entérobactéries sont une famille très hétérogène pour ce qui est de leur pathogénie et de leur écologie. Les espèces qui composent cette famille sont en effet soit parasites (Shigella, Yersinia pestis), soit commensales (Escherichia coli, Proteus mirabilis, Klebsiella sp), soit encore saprophytes (Serratia sp, Enterobacter sp). 1.2. Habitat et pouvoir pathogène Le domaine des entérobactéries commensales ne se limite pas à l’intestin : on les trouve aussi dans la cavité buccale, au niveau des voies aériennes supérieures et sur les organes génitaux. Les entérobactéries sont présentes dans le monde entier et elles ont un habitat très large : eau douce, eau de mer (Alterococcus agarolyticus), sol, végétaux, animaux et elles peuvent contaminer des denrées alimentaires. Certaines espèces sont responsables de diarrhée et/ou d'infections opportunistes (infections urinaires, infections respiratoires, surinfections des plaies, septicémies, méningites...). 1.3. Répartition en genres Au sein des entérobactéries, on distingue de nombreux genres (Shigella, Escherichia, Enterobacter, Serratia, etc…) (tableau 3-1 et 3-2). La distinction entre les genres se fait par l'étude des caractères biochimiques dont les plus importants sont : fermentation du lactose, production d'indole, production d'uréase, production d'acetoïne (réaction dite VP+), utilisation du citrate, désamination du tryptophane. 1.4. Caractérisation des espèces Au sein de chaque genre, on individualise des espèces, par l'étude des caractères biochimiques ou antigéniques. Les entérobactéries possèdent toutes des antigènes de paroi (« somatiques ») ou antigènes O. Les entérobactéries mobiles possèdent en plus des antigènes de flagelle (« flagellaires ») ou antigènes H. -
Antibiotic Use Guidelines for Companion Animal Practice (2Nd Edition) Iii
ii Antibiotic Use Guidelines for Companion Animal Practice (2nd edition) iii Antibiotic Use Guidelines for Companion Animal Practice, 2nd edition Publisher: Companion Animal Group, Danish Veterinary Association, Peter Bangs Vej 30, 2000 Frederiksberg Authors of the guidelines: Lisbeth Rem Jessen (University of Copenhagen) Peter Damborg (University of Copenhagen) Anette Spohr (Evidensia Faxe Animal Hospital) Sandra Goericke-Pesch (University of Veterinary Medicine, Hannover) Rebecca Langhorn (University of Copenhagen) Geoffrey Houser (University of Copenhagen) Jakob Willesen (University of Copenhagen) Mette Schjærff (University of Copenhagen) Thomas Eriksen (University of Copenhagen) Tina Møller Sørensen (University of Copenhagen) Vibeke Frøkjær Jensen (DTU-VET) Flemming Obling (Greve) Luca Guardabassi (University of Copenhagen) Reproduction of extracts from these guidelines is only permitted in accordance with the agreement between the Ministry of Education and Copy-Dan. Danish copyright law restricts all other use without written permission of the publisher. Exception is granted for short excerpts for review purposes. iv Foreword The first edition of the Antibiotic Use Guidelines for Companion Animal Practice was published in autumn of 2012. The aim of the guidelines was to prevent increased antibiotic resistance. A questionnaire circulated to Danish veterinarians in 2015 (Jessen et al., DVT 10, 2016) indicated that the guidelines were well received, and particularly that active users had followed the recommendations. Despite a positive reception and the results of this survey, the actual quantity of antibiotics used is probably a better indicator of the effect of the first guidelines. Chapter two of these updated guidelines therefore details the pattern of developments in antibiotic use, as reported in DANMAP 2016 (www.danmap.org). -
Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella Multocida Isolates from Pneumonic Cases of Cattle in Ethiopia
Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella multocida Isolates from Pneumonic Cases of Cattle in Ethiopia Mirtneh Akalu Yilma ( [email protected] ) Koneru Lakshmaiah Education Foundation https://orcid.org/0000-0001-5936-6873 Murthy Bhadra Vemulapati Koneru Lakshmaiah Education Foundation Takele Abayneh Tefera Veterinaerinstituttet Martha Yami VeterinaryInstitute Teferi Degefa Negi VeterinaryInstitue Alebachew Belay VeterinaryInstitute Getaw Derese VeterinaryInstitute Esayas Gelaye Leykun Veterinaerinstituttet Research article Keywords: Biovar, Capsular type, Cattle, Ethiopia, Pasteurella multocida Posted Date: January 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-61749/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract Background: Pasteurella multocida is a heterogeneous species and opportunistic pathogen associated with pneumonia in cattle. Losses due to pneumonia and associated expenses are estimated to be higher in Ethiopia with limited information about the distribution of capsular serotypes. Hence, this study was designed to determine the phenotypic and capsular serotypes of P. multocida from pneumonic cases of cattle. Methods: A cross sectional study with purposive sampling method was employed in 400 cattle from April 2018 to January 2019. Nasopharyngeal swabs and lung tissue samples were collected from clinically suspected pneumonic cases of calves (n = 170) and adult cattle (n = 230). Samples were analyzed using bacteriological and molecular assay. Results: Bacteriological analysis revealed isolation of 61 (15.25%) P. multocida subspecies multocida. Incidence was higher in calves 35 (57.38%) compared to adult cattle 26 (42.62%) at P < 0.5. PCR assay targeting KMT1 gene (~460 bp) conrmed P. -
Identification by 16S Ribosomal RNA Gene Sequencing of Arcobacter
182 ORIGINAL ARTICLE Identification by 16S ribosomal RNA gene sequencing of Mol Path: first published as 10.1136/mp.55.3.182 on 1 June 2002. Downloaded from Arcobacter butzleri bacteraemia in a patient with acute gangrenous appendicitis SKPLau,PCYWoo,JLLTeng, K W Leung, K Y Yuen ............................................................................................................................. J Clin Pathol: Mol Pathol 2002;55:182–185 Aims: To identify a strain of Gram negative facultative anaerobic curved bacillus, concomitantly iso- lated with Escherichia coli and Streptococcus milleri, from the blood culture of a 69 year old woman with acute gangrenous appendicitis. The literature on arcobacter bacteraemia and arcobacter infections associated with appendicitis was reviewed. Methods: The isolate was phenotypically investigated by standard biochemical methods using conventional biochemical tests. Genotypically, the 16S ribosomal RNA (rRNA) gene of the bacterium was amplified by the polymerase chain reaction (PCR) and sequenced. The sequence of the PCR prod- uct was compared with known 16S rRNA gene sequences in the GenBank by multiple sequence align- ment. Literature review was performed by MEDLINE search (1966–2000). Results: The bacterium grew on blood agar, chocolate agar, and MacConkey agar to sizes of 1 mm in diameter after 24 hours of incubation at 37°C in 5% CO2. It grew at 15°C, 25°C, and 37°C; it also grew in a microaerophilic environment, and was cytochrome oxidase positive and motile, typically a member of the genus arcobacter. Furthermore, phenotypic testing showed that the biochemical profile See end of article for of the isolate did not fit into the pattern of any of the known arcobacter species. -
Pocket Guide to Clinical Microbiology
4TH EDITION Pocket Guide to Clinical Microbiology Christopher D. Doern 4TH EDITION POCKET GUIDE TO Clinical Microbiology 4TH EDITION POCKET GUIDE TO Clinical Microbiology Christopher D. Doern, PhD, D(ABMM) Assistant Professor, Pathology Director of Clinical Microbiology Virginia Commonwealth University Health System Medical College of Virginia Campus Washington, DC Copyright © 2018 Amer i can Society for Microbiology. All rights re served. No part of this publi ca tion may be re pro duced or trans mit ted in whole or in part or re used in any form or by any means, elec tronic or me chan i cal, in clud ing pho to copy ing and re cord ing, or by any in for ma tion stor age and re trieval sys tem, with out per mis sion in writ ing from the pub lish er. Disclaimer: To the best of the pub lish er’s knowl edge, this pub li ca tion pro vi des in for ma tion con cern ing the sub ject mat ter cov ered that is ac cu rate as of the date of pub li ca tion. The pub lisher is not pro vid ing le gal, med i cal, or other pro fes sional ser vices. Any ref er ence herein to any spe cific com mer cial prod ucts, pro ce dures, or ser vices by trade name, trade mark, man u fac turer, or oth er wise does not con sti tute or im ply en dorse ment, rec om men da tion, or fa vored sta tus by the Ameri can Society for Microbiology (ASM). -
Bacterial Diversity Within the Human Subgingival Crevice
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Veterans Affairs Staff Publications U.S. Department of Veterans Affairs 12-7-1999 Bacterial diversity within the human subgingival crevice Ian Kroes Stanford University School of Medicine Paul W. Lepp Stanford University School of Medicine, [email protected] David A. Relman Stanford University School of Medicine, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/veterans Kroes, Ian; Lepp, Paul W.; and Relman, David A., "Bacterial diversity within the human subgingival crevice" (1999). U.S. Department of Veterans Affairs Staff Publications. 18. https://digitalcommons.unl.edu/veterans/18 This Article is brought to you for free and open access by the U.S. Department of Veterans Affairs at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in U.S. Department of Veterans Affairs Staff Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Bacterialdiversity within the human subgingivalcrevice Ian Kroes, Paul W. Lepp, and David A. Relman* Departmentsof Microbiologyand Immunology,and Medicine,Stanford University School of Medicine,Stanford, CA 94305, and VeteransAffairs Palo Alto HealthCare System, Palo Alto,CA 94304 Editedby Stanley Falkow, Stanford University, Stanford, CA, and approvedOctober 15, 1999(received for review August 2, 1999) Molecular, sequence-based environmental surveys of microorgan- associated with disease (9-11). However, a directcomparison isms have revealed a large degree of previously uncharacterized between cultivation-dependentand -independentmethods has diversity. However, nearly all studies of the human endogenous not been described. In this study,we characterizedbacterial bacterial flora have relied on cultivation and biochemical charac- diversitywithin a specimenfrom the humansubgingival crevice terization of the resident organisms. -
Swedres-Svarm 2019
2019 SWEDRES|SVARM Sales of antibiotics and occurrence of antibiotic resistance in Sweden 2 SWEDRES |SVARM 2019 A report on Swedish Antibiotic Sales and Resistance in Human Medicine (Swedres) and Swedish Veterinary Antibiotic Resistance Monitoring (Svarm) Published by: Public Health Agency of Sweden and National Veterinary Institute Editors: Olov Aspevall and Vendela Wiener, Public Health Agency of Sweden Oskar Nilsson and Märit Pringle, National Veterinary Institute Addresses: The Public Health Agency of Sweden Solna. SE-171 82 Solna, Sweden Östersund. Box 505, SE-831 26 Östersund, Sweden Phone: +46 (0) 10 205 20 00 Fax: +46 (0) 8 32 83 30 E-mail: [email protected] www.folkhalsomyndigheten.se National Veterinary Institute SE-751 89 Uppsala, Sweden Phone: +46 (0) 18 67 40 00 Fax: +46 (0) 18 30 91 62 E-mail: [email protected] www.sva.se Text, tables and figures may be cited and reprinted only with reference to this report. Images, photographs and illustrations are protected by copyright. Suggested citation: Swedres-Svarm 2019. Sales of antibiotics and occurrence of resistance in Sweden. Solna/Uppsala ISSN1650-6332 ISSN 1650-6332 Article no. 19088 This title and previous Swedres and Svarm reports are available for downloading at www.folkhalsomyndigheten.se/ Scan the QR code to open Swedres-Svarm 2019 as a pdf in publicerat-material/ or at www.sva.se/swedres-svarm/ your mobile device, for reading and sharing. Use the camera in you’re mobile device or download a free Layout: Dsign Grafisk Form, Helen Eriksson AB QR code reader such as i-nigma in the App Store for Apple Print: Taberg Media Group, Taberg 2020 devices or in Google Play.