Lecture 1 ― INTRODUCTION INTO MICROBIOLOGY
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Inactivation of CRISPR-Cas Systems by Anti-CRISPR Proteins in Diverse Bacterial Species April Pawluk1, Raymond H.J
LETTERS PUBLISHED: 13 JUNE 2016 | ARTICLE NUMBER: 16085 | DOI: 10.1038/NMICROBIOL.2016.85 Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species April Pawluk1, Raymond H.J. Staals2, Corinda Taylor2, Bridget N.J. Watson2, Senjuti Saha3, Peter C. Fineran2, Karen L. Maxwell4* and Alan R. Davidson1,3* CRISPR-Cas systems provide sequence-specific adaptive immu- MGE-encoded mechanisms that inhibit CRISPR-Cas systems. In nity against foreign nucleic acids1,2. They are present in approxi- support of this hypothesis, phages infecting Pseudomonas aeruginosa mately half of all sequenced prokaryotes3 and are expected to were found to encode diverse families of proteins that inhibit constitute a major barrier to horizontal gene transfer. We pre- the CRISPR-Cas systems of their host through several distinct viously described nine distinct families of proteins encoded in mechanisms4,5,17,18. However, homologues of these anti-CRISPR Pseudomonas phage genomes that inhibit CRISPR-Cas function4,5. proteins were found only within the Pseudomonas genus. Here, We have developed a bioinformatic approach that enabled us to we describe a bioinformatic approach that allowed us to identify discover additional anti-CRISPR proteins encoded in phages five novel families of functional anti-CRISPR proteins encoded in and other mobile genetic elements of diverse bacterial phages and other putative MGEs in species spanning the diversity species. We show that five previously undiscovered families of Proteobacteria. of anti-CRISPRs inhibit the type I-F CRISPR-Cas systems of The nine previously characterized anti-CRISPR protein families both Pseudomonas aeruginosa and Pectobacterium atrosepticum, possess no common sequence motifs, so we used genomic context to and a dual specificity anti-CRISPR inactivates both type I-F search for novel anti-CRISPR genes. -
(Batch Learning Self-Organizing Maps), to the Microbiome Analysis of Ticks
Title A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks Nakao, Ryo; Abe, Takashi; Nijhof, Ard M; Yamamoto, Seigo; Jongejan, Frans; Ikemura, Toshimichi; Sugimoto, Author(s) Chihiro The ISME Journal, 7(5), 1003-1015 Citation https://doi.org/10.1038/ismej.2012.171 Issue Date 2013-03 Doc URL http://hdl.handle.net/2115/53167 Type article (author version) File Information ISME_Nakao.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks Ryo Nakao1,a, Takashi Abe2,3,a, Ard M. Nijhof4, Seigo Yamamoto5, Frans Jongejan6,7, Toshimichi Ikemura2, Chihiro Sugimoto1 1Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan 2Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan 3Graduate School of Science & Technology, Niigata University, 8050, Igarashi 2-no-cho, Nishi- ku, Niigata 950-2181, Japan 4Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Königsweg 67, 14163 Berlin, Germany 5Miyazaki Prefectural Institute for Public Health and Environment, 2-3-2 Gakuen Kibanadai Nishi, Miyazaki 889-2155, Japan 6Utrecht Centre for Tick-borne Diseases (UCTD), Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands 7Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, 0110 Onderstepoort, South Africa aThese authors contributed equally to this work. Keywords: BLSOMs/emerging diseases/metagenomics/microbiomes/symbionts/ticks Running title: Tick microbiomes revealed by BLSOMs Subject category: Microbe-microbe and microbe-host interactions Abstract Ticks transmit a variety of viral, bacterial and protozoal pathogens, which are often zoonotic. -
Known Infectious Causes of Vasculitis in Man
PATHOGENESIS Known infectious causes of vasculitis in man STANLEY J. NAIDES, MD n array of pathogens is known to cause vasculi- and our ability to intervene in disease processes, have ren- tis in man.1,2 For several of these agents, vas- dered some causes of vasculitis far less common. culitis is the major manifestation of disease. The Amajority, however, typically present as infec- ■ VIRAL CAUSES OF VASCULITIS tious processes in which vasculitis is an occasional mani- Our knowledge of viral pathogenesis has exploded in the festation of disease. For many, vasculitis may be a compo- last quarter of the twentieth century, accelerated in large nent of disease pathogenesis but is not a prominent feature part by epidemics of “emerging” viral diseases. Hepatitis C of the clinical presentation. The various agents—viruses, virus, discovered in 1989, has worldwide prevalence.3 The bacteria, and fungi—share a common target, blood vessels. 10- to 20-year latent period before hepatic or rheumatic The involvement of vessels may be direct, with vascular manifestations of disease explains the increasing number structures serving as targets. Many infectious pathogens of cases of hepatitis C virus–mediated vasculitis currently have tissue tropism that includes endothelium. Other being seen in the United States following the epidemic of agents may bind to the vessel wall because the vascular en- new infections in the 1980s.4 Prior to the discovery and dothelium expresses specific receptors for the pathogen or characterization of hepatitis C virus in the late 1980s, the another moiety with which the pathogen travels. Even triad of arthritis, palpable purpura, and type II cryoglobu- when the agent does not enter the endothelial cell, the im- linemia was given the sobriquet “essential mixed cryo- mune response to the agent may be focused at the vessel globulinemia” and considered an idiopathic vasculitis. -
Diagnostic Code Descriptions (ICD9)
INFECTIONS AND PARASITIC DISEASES INTESTINAL AND INFECTIOUS DISEASES (001 – 009.3) 001 CHOLERA 001.0 DUE TO VIBRIO CHOLERAE 001.1 DUE TO VIBRIO CHOLERAE EL TOR 001.9 UNSPECIFIED 002 TYPHOID AND PARATYPHOID FEVERS 002.0 TYPHOID FEVER 002.1 PARATYPHOID FEVER 'A' 002.2 PARATYPHOID FEVER 'B' 002.3 PARATYPHOID FEVER 'C' 002.9 PARATYPHOID FEVER, UNSPECIFIED 003 OTHER SALMONELLA INFECTIONS 003.0 SALMONELLA GASTROENTERITIS 003.1 SALMONELLA SEPTICAEMIA 003.2 LOCALIZED SALMONELLA INFECTIONS 003.8 OTHER 003.9 UNSPECIFIED 004 SHIGELLOSIS 004.0 SHIGELLA DYSENTERIAE 004.1 SHIGELLA FLEXNERI 004.2 SHIGELLA BOYDII 004.3 SHIGELLA SONNEI 004.8 OTHER 004.9 UNSPECIFIED 005 OTHER FOOD POISONING (BACTERIAL) 005.0 STAPHYLOCOCCAL FOOD POISONING 005.1 BOTULISM 005.2 FOOD POISONING DUE TO CLOSTRIDIUM PERFRINGENS (CL.WELCHII) 005.3 FOOD POISONING DUE TO OTHER CLOSTRIDIA 005.4 FOOD POISONING DUE TO VIBRIO PARAHAEMOLYTICUS 005.8 OTHER BACTERIAL FOOD POISONING 005.9 FOOD POISONING, UNSPECIFIED 006 AMOEBIASIS 006.0 ACUTE AMOEBIC DYSENTERY WITHOUT MENTION OF ABSCESS 006.1 CHRONIC INTESTINAL AMOEBIASIS WITHOUT MENTION OF ABSCESS 006.2 AMOEBIC NONDYSENTERIC COLITIS 006.3 AMOEBIC LIVER ABSCESS 006.4 AMOEBIC LUNG ABSCESS 006.5 AMOEBIC BRAIN ABSCESS 006.6 AMOEBIC SKIN ULCERATION 006.8 AMOEBIC INFECTION OF OTHER SITES 006.9 AMOEBIASIS, UNSPECIFIED 007 OTHER PROTOZOAL INTESTINAL DISEASES 007.0 BALANTIDIASIS 007.1 GIARDIASIS 007.2 COCCIDIOSIS 007.3 INTESTINAL TRICHOMONIASIS 007.8 OTHER PROTOZOAL INTESTINAL DISEASES 007.9 UNSPECIFIED 008 INTESTINAL INFECTIONS DUE TO OTHER ORGANISMS -
WO 2014/134709 Al 12 September 2014 (12.09.2014) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2014/134709 Al 12 September 2014 (12.09.2014) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 31/05 (2006.01) A61P 31/02 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/CA20 14/000 174 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 4 March 2014 (04.03.2014) KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (25) Filing Language: English OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (26) Publication Language: English SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (30) Priority Data: ZW. 13/790,91 1 8 March 2013 (08.03.2013) US (84) Designated States (unless otherwise indicated, for every (71) Applicant: LABORATOIRE M2 [CA/CA]; 4005-A, rue kind of regional protection available): ARIPO (BW, GH, de la Garlock, Sherbrooke, Quebec J1L 1W9 (CA). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (72) Inventors: LEMIRE, Gaetan; 6505, rue de la fougere, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, Sherbrooke, Quebec JIN 3W3 (CA). -
Potential of Bacterial Cellulose Chemisorbed with Anti-Metabolites, 3-Bromopyruvate Or Sertraline, to Fight Against Helicobacter Pylori Lawn Biofilm
International Journal of Molecular Sciences Article Potential of Bacterial Cellulose Chemisorbed with Anti-Metabolites, 3-Bromopyruvate or Sertraline, to Fight against Helicobacter pylori Lawn Biofilm Paweł Krzy˙zek 1,* , Gra˙zynaGo´sciniak 1 , Karol Fijałkowski 2 , Paweł Migdał 3 , Mariusz Dziadas 4 , Artur Owczarek 5 , Joanna Czajkowska 6, Olga Aniołek 7 and Adam Junka 8 1 Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland; [email protected] 2 Department of Immunology, Microbiology and Physiological Chemistry, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 70-311 Szczecin, Poland; karol.fi[email protected] 3 Department of Environment, Hygiene and Animal Welfare, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; [email protected] 4 Faculty of Chemistry, University of Wroclaw, 50-353 Wroclaw, Poland; [email protected] 5 Department of Drug Form Technology, Wroclaw Medical University, 50-556 Wroclaw, Poland; [email protected] 6 Laboratory of Microbiology, Polish Center for Technology Development PORT, 54-066 Wroclaw, Poland; [email protected] 7 Faculty of Medicine, Lazarski University, 02-662 Warsaw, Poland; [email protected] 8 Department of Pharmaceutical Microbiology and Parasitology, Wroclaw Medical University, 50-556 Wroclaw, Poland; [email protected] * Correspondence: [email protected] Received: 23 November 2020; Accepted: 11 December 2020; Published: 14 December 2020 Abstract: Helicobacter pylori is a bacterium known mainly of its ability to cause persistent inflammations of the human stomach, resulting in peptic ulcer diseases and gastric cancers. Continuous exposure of this bacterium to antibiotics has resulted in high detection of multidrug-resistant strains and difficulties in obtaining a therapeutic effect. -
Identification of Microorganisms Using Nucleic Acid Probes
Identification of Microorganisms Using Page 1 of 45 Nucleic Acid Probes Medical Policy An Independent Licensee of the Blue Cross and Blue Shield Association Title: Identification of Microorganisms Using Nucleic Acid Probes See Also: Influenza Virus Diagnostic Testing and Treatment in the Outpatient Setting Professional Institutional Original Effective Date: July 8, 2008 Original Effective Date: July 16, 2009 Revision Date(s): June 16, 2009; Revision Date(s): March 1, 2012; March 1, 2012; June 5, 2012; June 5, 2012; November 19, 2012; November 19, 2012; January 15, 2013; January 15, 2013; November 12, 2013 November 12, 2013 Current Effective Date: November 12, 2013 Current Effective Date: November 12, 2013 State and Federal mandates and health plan member contract language, including specific provisions/exclusions, take precedence over Medical Policy and must be considered first in determining eligibility for coverage. To verify a member's benefits, contact Blue Cross and Blue Shield of Kansas Customer Service. The BCBSKS Medical Policies contained herein are for informational purposes and apply only to members who have health insurance through BCBSKS or who are covered by a self-insured group plan administered by BCBSKS. Medical Policy for FEP members is subject to FEP medical policy which may differ from BCBSKS Medical Policy. The medical policies do not constitute medical advice or medical care. Treating health care providers are independent contractors and are neither employees nor agents of Blue Cross and Blue Shield of Kansas and are solely responsible for diagnosis, treatment and medical advice. If your patient is covered under a different Blue Cross and Blue Shield plan, please refer to the Medical Policies of that plan. -
Rhinoscleroma in an Immigrant from Egypt: a Case Report
387 BRIEF COMMUNICATION Rhinoscleroma in an Immigrant From Egypt: A Case Report Edgardo Bonacina, MD,∗ Leonardo Chianura, MD, DTM&H,† Maurizio Sberna, MD,‡ Giuseppe Ortisi, MD,§ Giovanna Gelosa, MD,|| Alberto Citterio, MD,‡ Giovanni Gesu, MD,§ and Massimo Puoti, MD† Downloaded from https://academic.oup.com/jtm/article/19/6/387/1795562 by guest on 23 September 2021 Departments of ∗Pathological Anatomy; †Infectious Diseases; ‡Neuroradiology; §Microbiology, and; ||Otorinolaringoiatry, Niguarda Ca` Granda Hospital, Milano, Italy DOI: 10.1111/j.1708-8305.2012.00659.x Rhinoscleroma is a chronic indolent granulomatous infection of the nose and the upper respiratory tract caused by Klebsiella rhinoscleromatis; this condition is endemic to many regions of the world including North Africa. We present a case of rhinoscleroma in a 51-year-old Egyptian immigrant with 1-month history of epistaxis. We would postulate that with increased travel from areas where rhinoscleroma is endemic to other non-endemic areas, diagnosis of this condition will become more common. hough rarely observed, rhinoscleroma has to be nasal fossae and ethmoid sinuses with complete bony T taken into consideration in travelers returning destruction of bilateral nasal turbinates (Figure 1). with ear, nose, and throat presentations, particularly Endoscopic biopsy was performed under local anesthe- after traveling to developing countries or regions where sia. Histopathologic examination revealed numerous this condition is endemic.1,2 foamy macrophages (Mikulicz cells) containing bacteria (Figure 2); no fungal hyphae were found.3 Staphylococcus Case Report aureus and Klebsiella rhinoscleromatis were isolated by culture of the tissue biopsy. A diagnosis of rhinoscle- A 51-year-old Egyptian male immigrant presented on roma was made. -
Syphilis As Seen by a Hospital Physician
284 Prof. Monro?Syphilis as seen by a Hospital Physician. SYPHILIS AS SEEN BY A HOSPITAL PHYSICIAN* By T. K. MONRO, M.A., M.D., Professor of Medicine, University of Glasgow. \ " / Mr. President and Gentlemen,?I thank you heartily for the honour you have done me in inviting me to be Honorary President of this Faculty for the session which is now opening. I was duly informed by Dr. Wardlaw that my principal duty as incumbent of this honourable office was to deliver an address to the Faculty, and as his invitation reached me while I was on holiday, with other objects in view, I had time to contemplate the responsibility I had undertaken, and to consider how I was to face it. In getting over the usual initial difficulty as to the choice of a subject, some assistance was afforded me by the President's instruction that the address ought to be one for the general practitioner. Quite a number of subjects would be appropriate from this point of view. I should have been glad to say some- thing on oral sepsis, a condition often spoken of, and no doubt often wrongly blamed, but also apt to be overlooked. Dentists do not always realise how completely one may be misled by the absence of subjective and objective evidence; so that even an experienced man may pass as innocuous a tooth which subse- quent extraction shows to have disease at its root. Medical men sometimes make a mistake in the opposite direction, by insisting, without sufficient justification, on the removal of teeth, e.g., in epileptiform neuralgia. -
Downloaded 13 April 2017); Using Diamond
bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Re-evaluating the salty divide: phylogenetic specificity of 6 transitions between marine and freshwater systems 7 8 9 10 Sara F. Pavera, Daniel J. Muratorea, Ryan J. Newtonb, Maureen L. Colemana# 11 a 12 Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA 13 b School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA 14 15 Running title: Marine-freshwater phylogenetic specificity 16 17 #Address correspondence to Maureen Coleman, [email protected] 18 bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Marine and freshwater microbial communities are phylogenetically distinct and transitions 21 between habitat types are thought to be infrequent. We compared the phylogenetic diversity of 22 marine and freshwater microorganisms and identified specific lineages exhibiting notably high or 23 low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA 24 gene tag-sequencing datasets. As expected, marine and freshwater microbial communities 25 differed in the relative abundance of major phyla and contained habitat-specific lineages; at the 26 same time, however, many shared taxa were observed in both environments. 27 Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between 28 marine and freshwater sample pairs. -
WHO GUIDELINES for the Treatment of Treponema Pallidum (Syphilis)
WHO GUIDELINES FOR THE Treatment of Treponema pallidum (syphilis) WHO GUIDELINES FOR THE Treatment of Treponema pallidum (syphilis) WHO Library Cataloguing-in-Publication Data WHO guidelines for the treatment of Treponema pallidum (syphilis). Contents: Web annex D: Evidence profiles and evidence-to-decision frameworks - Web annex E: Systematic reviews for syphilis guidelines - Web annex F: Summary of conflicts of interest 1.Syphilis – drug therapy. 2.Treponema pallidum. 3.Sexually Transmitted Diseases. 4.Guideline. I.World Health Organization. ISBN 978 92 4 154980 6 (NLM classification: WC 170) © World Health Organization 2016 All rights reserved. Publications of the World Health Organization are available on the WHO website (http://www.who.int) or can be purchased from WHO Press, World Health Organization, 20 Avenue Appia, 1211 Geneva 27, Switzerland (tel.: +41 22 791 3264; fax: +41 22 791 4857; email: [email protected]). Requests for permission to reproduce or translate WHO publications – whether for sale or for non-commercial distribution– should be addressed to WHO Press through the WHO website (http://www.who.int/about/licensing/ copyright_form/index.html). The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of the World Health Organization concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted and dashed lines on maps represent approximate border lines for which there may not yet be full agreement. The mention of specific companies or of certain manufacturers’ products does not imply that they are endorsed or recommended by the World Health Organization in preference to others of a similar nature that are not mentioned. -
Microbiology & Infectious Diseases
Case Report Research Article Microbiology & Infectious Diseases Neuro Sarcoidosis Masquerading as Neuroborreliosis Chandra S Pingili1,2,4*, Saleh Obaid3,4,5 Kyle Dettbarn3,4,5, Jacques Tham6 and Greg Heiler7 1Infectious Diseases Department, Eau Claire, Wisconsin, USA. 2Prevea Health, Eau Claire, Wisconsin, USA. 3Eau Claire Medical Group, Eau Claire, Wi, USA. *Correspondence: Chandra Shekar Pingili MD, Infectious Diseases, Sacred Heart 4 Sacred Heart Hospital, Eau Claire, Wisconsin, USA. Hospital, 900 W Claremont Ave Eau Claire, WI 54701, USA, Tel: 917-373-9571; E-mail: [email protected]. 5Pulmonary & Critical Care, Sacred Heart Hospital, Eau Claire, Wisconsin, USA. Received: 13 September 2017; Accepted: 02 October 2017 6Department of Radiology, Sacred Geart Hospital, Eau Claire, Wisconsin, USA. 7Pathologist, Sacred Geart Hospital, Eau Claire, Wisconsin, USA. Citation: Chandra S Pingili, Saleh Obaid, Kyle Dettbarn, et al. Neuro Sarcoidosis masquerading as Neuroborreliosis. Microbiol Infect Dis. 2017; 1(2): 1-8. ABSTRACT Background: Medical syndromes often overlap in clinical presentations. Often there is one or more than underlying etiology responsible for the patient’s Clinical presentation. We are reporting a patient who was initially admitted with fevers and joint pains.Lymes IGG was positive .He was discharged home on Doxycycline and Prednisone suspecting gout. Patient however was re admitted twice within 3 weeks with cognitive impairment. Lymph node biopsy was positive for non Caseating granulomas suggesting Sarcoidosis. Clinically he responded dramatically to steroids. Case Report: 74 year old white male was admitted with fever and multiple joint pains. Tmax was 100.5.WBC was 15 with normal CBC. LFTs were elevated .Rest of the labs were normal.Lymes IGG was positive.