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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). -
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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
Clinical Microbiology 12Th Edition
Volume 1 Manual of Clinical Microbiology 12th Edition Downloaded from www.asmscience.org by IP: 94.66.220.5 MCM12_FM.indd 1 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Volume 1 Manual of Clinical Microbiology 12th Edition EDITORS-IN-CHIEF Karen C. Carroll Michael A. Pfaller Division of Medical Microbiology, Departments of Pathology and Epidemiology Department of Pathology, The Johns Hopkins (Emeritus), University of Iowa, University School of Medicine, Iowa City, and JMI Laboratories, Baltimore, Maryland North Liberty, Iowa VOLUME EDITORS Marie Louise Landry Robin Patel Laboratory Medicine and Internal Medicine, Infectious Diseases Research Laboratory, Yale University, New Haven, Connecticut Mayo Clinic, Rochester, Minnesota Alexander J. McAdam Sandra S. Richter Department of Laboratory Medicine, Boston Department of Laboratory Medicine, Children’s Hospital, Boston, Massachusetts Cleveland Clinic, Cleveland, Ohio David W. Warnock Atlanta, Georgia Washington, DC Downloaded from www.asmscience.org by IP: 94.66.220.5 MCM12_FM.indd 2 On: Thu, 18 Apr 2019 08:17:55 2/12/19 6:48 PM Volume 1 Manual of Clinical Microbiology 12th Edition EDITORS-IN-CHIEF Karen C. Carroll Michael A. Pfaller Division of Medical Microbiology, Departments of Pathology and Epidemiology Department of Pathology, The Johns Hopkins (Emeritus), University of Iowa, University School of Medicine, Iowa City, and JMI Laboratories, Baltimore, Maryland North Liberty, Iowa VOLUME EDITORS Marie Louise Landry Robin Patel Laboratory Medicine and Internal Medicine, Infectious Diseases Research Laboratory, Yale University, New Haven, Connecticut Mayo Clinic, Rochester, Minnesota Alexander J. McAdam Sandra S. Richter Department of Laboratory Medicine, Boston Department of Laboratory Medicine, Children’s Hospital, Boston, Massachusetts Cleveland Clinic, Cleveland, Ohio David W. -
Application for Consent to Release a GMO – Organisms Other Than Higher Plants
Department for Environment, Food and Rural Affairs Application for consent to release a GMO – organisms other than higher plants Part A1: Information required under schedule 2 of the Genetically Modified (Deliberate Release) Regulations 2002 Part I General information 1. The name and address of the applicant and the name, qualifications and experience of the scientist and of every other person who will be responsible for planning and carrying out the release of the organisms and for the supervision, monitoring and safety of the release. Clinical & Experimental Sciences, LC72 (MP814) South Academic Block, Southampton General Hospital, Tremona Road, Southampton, UK. Public Health England, Porton Down, Salisbury SP4 0JG, UK 2. The title of the project. “Experimental challenge of the human nasopharynx with recombinant Neisseria lactamica expressing the meningococcal type V autotransporter protein, Neisseria Adhesin A (NadA)”. 1 Part II Information relating to the organisms Characteristics of the donor, parental and recipient organisms 3. Scientific name and taxonomy. Donor: Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria; Neisseria meningitidis Taxonomy ID: 122586 Recipient: Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae; Neisseria; Neisseria lactamica Taxonomy ID: 869214 The purpose of the genetic modification is to construct a strain of the exclusively human, nasopharyngeal commensal bacterium, Neisseria lactamica (Nlac) that expresses on its surface the outer membrane protein, Neisseria Adhesin A (NadA). NadA is an adhesin protein found in the close relative of Nlac, Neisseria meningitidis (Nmen), which is the causative agent of meningococcal disease. The genetically modified organism (GMO) will be used to investigate the role of NadA in the colonisation of the nasopharynx and associated immune responses in a controlled human bacterial challenge. -
Genome Sequence Analyses Show That Neisseria Oralis Is the Same Species As ‘Neisseria Mucosa Var
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 3920–3926 DOI 10.1099/ijs.0.052431-0 Genome sequence analyses show that Neisseria oralis is the same species as ‘Neisseria mucosa var. heidelbergensis’ Julia S. Bennett, Keith A. Jolley and Martin C. J. Maiden Correspondence Department of Zoology, University of Oxford, Oxford OX1 3PS, UK Julia S. Bennett [email protected] Phylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing ‘Neisseria mucosa var. heidelbergensis’ and that this group was of equivalent taxonomic status to other well- described species of the genus Neisseria. Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava. Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. -
STUDIES of NEISSERIA MUSCULI TYPE IV PILUS and CAPSULE USING the NATURAL MOUSE MODEL of COLONIZATION and PERSISTENCE by Man Cheo
Studies of Neisseria musculi Type IV Pilus and Capsule Using the Natural Mouse Model of Colonization and Persistence Item Type text; Electronic Dissertation Authors Ma, Man Cheong Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 27/09/2021 11:29:10 Link to Item http://hdl.handle.net/10150/634345 STUDIES OF NEISSERIA MUSCULI TYPE IV PILUS AND CAPSULE USING THE NATURAL MOUSE MODEL OF COLONIZATION AND PERSISTENCE by Man Cheong Ma Copyright © Man Cheong Ma 2019 A Dissertation Submitted to the Faculty of the DEPARTMENT OF IMMUNOBIOLOGY In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2019 2 3 Table of Contents List of Figures ................................................................................................................................6 List of Tables ..................................................................................................................................7 Abstract ...........................................................................................................................................8 Chapter 1- Introduction ..................................................................................................................... -
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico 2 “Dead Zone” 3 4 J
bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. 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 4.0 International license. 1 Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico 2 “Dead Zone” 3 4 J. Cameron Thrash1*, Kiley W. Seitz2, Brett J. Baker2*, Ben Temperton3, Lauren E. Gillies4, 5 Nancy N. Rabalais5,6, Bernard Henrissat7,8,9, and Olivia U. Mason4 6 7 8 1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 9 2. Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port 10 Aransas, TX, USA 11 3. School of Biosciences, University of Exeter, Exeter, UK 12 4. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, 13 FL, USA 14 5. Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, 15 LA, USA 16 6. Louisiana Universities Marine Consortium, Chauvin, LA USA 17 7. Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 18 13288 Marseille, France 19 8. INRA, USC 1408 AFMB, F-13288 Marseille, France 20 9. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia 21 22 *Correspondence: 23 JCT [email protected] 24 BJB [email protected] 25 26 27 28 Running title: Decoding microbes of the Dead Zone 29 30 31 Abstract word count: 250 32 Text word count: XXXX 33 34 Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. -
Genome-Based Taxonomic Classification of the Phylum
ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences -
Diversity of Thermophilic Bacteria in Hot Springs and Desert Soil of Pakistan and Identification of Some Novel Species of Bacteria
Diversity of Thermophilic Bacteria in Hot Springs and Desert Soil of Pakistan and Identification of Some Novel Species of Bacteria By By ARSHIA AMIN BUTT Department of Microbiology Quaid-i-Azam University Islamabad, Pakistan 2017 Diversity of Thermophilic Bacteria in Hot Springs and Desert Soil of Pakistan and Identification of Some Novel Species of Bacteria By ARSHIA AMIN BUTT Thesis Submitted to Department of Microbiology Quaid-i-Azam University, Islamabad In the partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology Department of Microbiology Quaid-i-Azam University Islamabad, Pakistan 2017 ii IN THE NAME OF ALLAH, THE MOST COMPASSIONATE, THE MOST MERCIFUL, “And in the earth are tracts and (Diverse though) neighboring, gardens of vines and fields sown with corn and palm trees growing out of single roots or otherwise: Watered with the same water. Yet some of them We make more excellent than others to eat. No doubt, in that are signs for wise people.” (Sura Al Ra’d, Ayat 4) iii Author’s Declaration I Arshia Amin Butt hereby state that my PhD thesis titled A “Diversity of Thermophilic Bacteria in Hot Springs and Deserts Soil of Pakistan and Identification of Some Novel Species of Bacteria” is my own work and has not been submitted previously by me for taking any degree from this University (Name of University) Quaid-e-Azam University Islamabad. Or anywhere else in the country/world. At any time if my statement is found to be incorrect even after my Graduate the university has the right to withdraw my PhD degree. -
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Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients. Hoda M. Eid, Natural Health Products and Metabolic Diseases Laboratory Michelle L. Wright, Emory University N.V Anil Kumar, Manipal University Abdel Qawasmeh, Hebron University Sherif T. S. Hassan, University of Veterinary and Pharmaceutical Sciences Brno Andrei Mocan, Iuliu Hatieganu University of Medicine and Pharmacy Seyed M. Nabavi, Baqiyatallah University of Medical Sciences Luca Rastrelli, University of Salerno Atanas G. Atanasov, Institute of Genetics and Animal Breeding Pierre S. Haddad, Natural Health Products and Metabolic Diseases Laboratory Journal Title: Frontiers in Pharmacology Volume: Volume 8 Publisher: Frontiers Media | 2017, Pages 387-387 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.3389/fphar.2017.00387 Permanent URL: https://pid.emory.edu/ark:/25593/s4366 Final published version: http://dx.doi.org/10.3389/fphar.2017.00387 Copyright information: © 2017 Eid, Wright, Anil Kumar, Qawasmeh, Hassan, Mocan, Nabavi, Rastrelli, Atanasov and Haddad. This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). Accessed September 24, 2021 4:14 PM EDT REVIEW published: 30 June 2017 doi: 10.3389/fphar.2017.00387 Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients Hoda M. Eid 1, 2, 3, Michelle L. Wright 4, N. V. Anil Kumar 5, Abdel Qawasmeh 6, Sherif T. S. Hassan 7, Andrei Mocan 8, 9, Seyed M. Nabavi 10, Luca Rastrelli 11, Atanas G. Atanasov 12, 13, 14* and Pierre S. -
The Neisseria Gonorrhoeae Cell Division Interactome and the Roles
The Neisseria gonorrhoeae cell division interactome and the roles of FtsA and N-terminus of FtsI in cell division and antimicrobial resistance A thesis Presented to The College of Graduate and Postdoctoral Studies In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Microbiology & Immunology University of Saskatchewan Saskatoon By YINAN ZOU © Copyright Yinan Zou, August, 2018. All rights reserved Permission to Use In presenting this exhibition statement in partial fulfillment of the requirements for a Graduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this exhibition statement in any manner, in whole or in part, for scholarly purposes may be granted by the professor or the professors who supervised my exhibition statement work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis/exhibition work was completed. It is understood that any copying or publication or use of this exhibition statement or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my exhibition statement. Requests for permission to copy or to make use of materials in this thesis/exhibition statement in whole or part should be addressed to: Department Head Biochemistry, Microbiology and Immunology College of Medicine University of Saskatchewan 107 Wiggins Road Saskatoon, Saskatchewan S7N 5E5 Canada or i Dean College of Graduate and Postdoctoral Studies University of Saskatchewan 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada ii Abstract Bacterial cell division is an essential biological process which is driven by the formation of a ring-like structure at the division site. -
Arthrobacter Sp
Journal of Genomics 2019, Vol. 7 18 Ivyspring International Publisher Journal of Genomics 2019; 7: 18-25. doi: 10.7150/jgen.32194 Research Paper Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert Konosuke Mark Ii1,2, Nobuaki Kono1,3, Ivan Glaucio Paulino-Lima4, Masaru Tomita1,2,3, Lynn Justine Rothschild5, Kazuharu Arakawa1,2,3 1. Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan 2. Faculty of Environment and Information Studies, Keio University, Yamagata, 997-0052, Japan 3. Graduate School of Media and Governance, Keio University, Yamagata, 997-0052, Japan 4. Blue Marble Space Institute of Science at NASA Ames Research Center, Mountain View, CA, USA, 94035-0001 5. NASA Ames Research Center, Moffett Field, CA, USA, 94035-0001 Corresponding author: Kazuharu Arakawa, Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan. E-mail: [email protected] © Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2018.12.18; Accepted: 2019.01.08; Published: 2019.02.08 Abstract Arthrobacter sp. strain MN05-02 is a UV-resistant bacterium isolated from a manganese deposit in the -2 Sonoran Desert, Arizona, USA. The LD10 of this strain is 123 Jm , which is twice that of Escherichia coli, and therefore can be a useful resource for comparative study of UV resistance and the role of manganese on this phenotype.