Technological Advances in the Molecular Biology of Leptospira
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Whole Genome Analysis of Leptospira Licerasiae Provides Insight Into Leptospiral Evolution and Pathogenicity
Whole Genome Analysis of Leptospira licerasiae Provides Insight into Leptospiral Evolution and Pathogenicity Jessica N. Ricaldi1,2., Derrick E. Fouts3., Jeremy D. Selengut3, Derek M. Harkins3, Kailash P. Patra2, Angelo Moreno2, Jason S. Lehmann2, Janaki Purushe3, Ravi Sanka3, Michael Torres4, Nicholas J. Webster5, Joseph M. Vinetz1,2,4*, Michael A. Matthias2* 1 Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru, 2 Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America, 3 J. Craig Venter Institute, Rockville, Maryland, United States of America, 4 Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigacio´n y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru, 5 Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America Abstract The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010T and MMD0835 possess two prophage elements. -
Comparative Genomic Analysis of the Genus Leptospira
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. Derrick E Fouts, Michael A Matthias, Haritha Adhikarla, Ben Adler, Luciane Amorim-Santos, Douglas E Berg, Dieter Bulach, Alejandro Buschiazzo, Yung-Fu Chang, Renee L Galloway, et al. To cite this version: Derrick E Fouts, Michael A Matthias, Haritha Adhikarla, Ben Adler, Luciane Amorim-Santos, et al.. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Lep- tospira.. PLoS Neglected Tropical Diseases, Public Library of Science, 2016, 10 (2), pp.e0004403. 10.1371/journal.pntd.0004403. pasteur-01436457 HAL Id: pasteur-01436457 https://hal-pasteur.archives-ouvertes.fr/pasteur-01436457 Submitted on 16 Apr 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons CC0 - Public Domain Dedication| 4.0 International License RESEARCH ARTICLE What Makes a Bacterial Species Pathogenic?: Comparative Genomic Analysis of the Genus Leptospira Derrick E. Fouts1*, Michael A. Matthias2, Haritha Adhikarla3, Ben Adler4, Luciane Amorim- Santos3,5, Douglas E. Berg2, Dieter Bulach6, Alejandro Buschiazzo7,8, Yung-Fu Chang9, Renee L. Galloway10, David A. Haake11,12, Daniel H. Haft1¤, Rudy Hartskeerl13, Albert I. -
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira
UC San Diego UC San Diego Previously Published Works Title What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. Permalink https://escholarship.org/uc/item/0g08233z Journal PLoS neglected tropical diseases, 10(2) ISSN 1935-2727 Authors Fouts, Derrick E Matthias, Michael A Adhikarla, Haritha et al. Publication Date 2016-02-18 DOI 10.1371/journal.pntd.0004403 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RESEARCH ARTICLE What Makes a Bacterial Species Pathogenic?: Comparative Genomic Analysis of the Genus Leptospira Derrick E. Fouts1*, Michael A. Matthias2, Haritha Adhikarla3, Ben Adler4, Luciane Amorim- Santos3,5, Douglas E. Berg2, Dieter Bulach6, Alejandro Buschiazzo7,8, Yung-Fu Chang9, Renee L. Galloway10, David A. Haake11,12, Daniel H. Haft1¤, Rudy Hartskeerl13, Albert I. Ko3,5, Paul N. Levett14, James Matsunaga11,12, Ariel E. Mechaly7, Jonathan M. Monk15, Ana L. T. Nascimento16,17, Karen E. Nelson1, Bernhard Palsson15, Sharon J. Peacock18, Mathieu Picardeau19, Jessica N. Ricaldi20, Janjira Thaipandungpanit21, Elsio A. Wunder, Jr.3,5, X. Frank Yang22, Jun-Jie Zhang22, Joseph M. Vinetz2,20,23* 1 J. Craig Venter Institute, Rockville, Maryland, United States of America, 2 Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America, 3 Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States -
University of Malaya Kuala Lumpur
EPIDEMIOLOGY OF HUMAN LEPTOSPIROSIS AND MOLECULAR CHARACTERIZATION OF Leptospira spp. ISOLATED FROM THE ENVIRONMENT AND ANIMAL HOSTS IN PENINSULAR BENACER DOUADI FACULTY OF SCIENCE UniversityUNIVERSITY OF of MALAYA Malaya KUALA LUMPUR 2017 EPIDEMIOLOGY OF HUMAN LEPTOSPIROSIS AND MOLECULAR CHARACTERIZATION OF Leptospira spp. ISOLATED FROM THE ENVIRONMENT AND ANIMAL HOSTS IN PENINSULAR MALAYSIA BENACER DOUADI THESIS SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY INSTITUTE OF BIOLOGICAL SCIENCES UniversityFACULTY OF SCIENCEof Malaya UNIVERSITY OF MALAYA KUALA LUMPUR 2017 ABSTRACT Leptospirosis is a globally important zoonotic disease caused by spirochetes from the genus Leptospira. Transmission to humans occurs either directly from exposure to contaminated urine or infected tissues, or indirectly via contact with contaminated soil or water. In Malaysia, leptospirosis is an important emerging zoonotic disease with dramatic increase of reported cases over the last decade. However, there is a paucity of data on the epidemiology and genetic characteristics of Leptopsira in Malaysia. The first objective of this study was to provide an epidemiological description of human leptospirosis cases over a 9-year period (2004–2012) and disease relationship with meteorological, geographical, and demographical information. An upward trend of leptospirosis cases were reported between 2004 to 2012 with a total of 12,325 cases recorded. Three hundred thirty-eight deaths were reported with an overall case fatality rate of 2.74%, with higher incidence in males (9696; 78.7%) compared with female patients (2629; 21.3%). The average incidence was highest amongst Malays (10.97 per 100,000 population), followed by Indians (7.95 per 100,000 population). -
International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Leptospira Minutes of Meetings, 1 and 2 July 1994, Prague, Czech Republic
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1995, p. 872-874 Vol. 45. No. 4 0020-77 13/95/$04.00+ 0 International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Leptospira Minutes of Meetings, 1 and 2 July 1994, Prague, Czech Republic Minute 1. Call to order. The meeting was called to order by The subcommittee expressed general concern about the the Secretary, R. Marshall, at 0930 on 1 July 1994. The opening WHO’S lack of support. consisted of a welcoming introduction, following which R. Minute 9. Usefiklness of PCR-based strategies (MRSP and Marshall was unanimously asked to act as Chairman for the PCR} for genospecies delimitation and molecular typing. P. Pero- meeting in the absence, because of illness, of the chairman, K. lat presented a paper on the use of two PCR-based character- Yanagawa. W. Ellis accepted the job of meeting Secretary. ization methods for Leptospira reference strains and isolates. Following this meeting there were additional open meetings at Arbitrarily primed PCR generates simple and reproducible 1400 on 1 July 1994 and at 0900 on 2 July 1994. A closed fingerprints that can be used to identify leptospires at both the meeting was held at 1300 on 2 July 1994. genospecies and serovar levels and for molecular epidemiol- Minute 2. Record of attendance. The members present were ogy. Furthermore, a new PCR strategy, which is based on the R. Marshall (Secretary), B. Cacciapuoti, M. Cinco, H. Dikken, study of mapped restriction site polymorphisms (MRSP) in W. Ellis, S. Faine, E. Kmety, R. Johnson, N. Stallman, W. PCR-amplified rrs (16s rRNA) and M (23s rRNA) eubacterial Terpstra, and Y. -
EID Vol15no4 Cover Copy
Peer-Reviewed Journal Tracking and Analyzing Disease Trends pages 519–688 EDITOR-IN-CHIEF D. Peter Drotman Managing Senior Editor EDITORIAL BOARD Polyxeni Potter, Atlanta, Georgia, USA Dennis Alexander, Addlestone Surrey, United Kingdom Senior Associate Editor Barry J. Beaty, Ft. Collins, Colorado, USA Brian W.J. Mahy, Atlanta, Georgia, USA Martin J. Blaser, New York, New York, USA Christopher Braden, Atlanta, GA, USA Associate Editors Carolyn Bridges, Atlanta, GA, USA Paul Arguin, Atlanta, Georgia, USA Arturo Casadevall, New York, New York, USA Charles Ben Beard, Ft. Collins, Colorado, USA Kenneth C. Castro, Atlanta, Georgia, USA David Bell, Atlanta, Georgia, USA Thomas Cleary, Houston, Texas, USA Charles H. Calisher, Ft. Collins, Colorado, USA Anne DeGroot, Providence, Rhode Island, USA Michel Drancourt, Marseille, France Vincent Deubel, Shanghai, China Paul V. Effl er, Perth, Australia Ed Eitzen, Washington, DC, USA K. Mills McNeill, Kampala, Uganda David Freedman, Birmingham, AL, USA Nina Marano, Atlanta, Georgia, USA Kathleen Gensheimer, Augusta, ME, USA Martin I. Meltzer, Atlanta, Georgia, USA Peter Gerner-Smidt, Atlanta, GA, USA David Morens, Bethesda, Maryland, USA Duane J. Gubler, Singapore J. Glenn Morris, Gainesville, Florida, USA Richard L. Guerrant, Charlottesville, Virginia, USA Patrice Nordmann, Paris, France Scott Halstead, Arlington, Virginia, USA Tanja Popovic, Atlanta, Georgia, USA David L. Heymann, Geneva, Switzerland Jocelyn A. Rankin, Atlanta, Georgia, USA Daniel B. Jernigan, Atlanta, Georgia, USA Didier Raoult, Marseille, France Charles King, Cleveland, Ohio, USA Pierre Rollin, Atlanta, Georgia, USA Keith Klugman, Atlanta, Georgia, USA Dixie E. Snider, Atlanta, Georgia, USA Takeshi Kurata, Tokyo, Japan Frank Sorvillo, Los Angeles, California, USA S.K. Lam, Kuala Lumpur, Malaysia David Walker, Galveston, Texas, USA Bruce R. -
Analysis of Genes Encoding Outer Membrane Protein Of
Analysis of Genes Encoding Outer Membrane Protein of Leptospira interrogans and Its Modulation Due to Host Factors: An Approach for Understanding Host-Pathogen Crosstalk A thesis Submitted in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY by KARUKRITI KAUSHIK GHOSH Under the supervision of Dr. Manish Kumar Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati Guwahati-781039, Assam, India. February, 2019 TH-2331_136106014 TH-2331_136106014 Analysis of Genes Encoding Outer Membrane Protein of Leptospira interrogans and Its Modulation Due to Host Factors: An Approach for Understanding Host-Pathogen Crosstalk by Karukriti Kaushik Ghosh IIT Guwahati, 2019 Doctoral Committee Dr. Manish Kumar (Department of Biosciences and Bioengineering) Supervisor Dr. Anil Mukund Limaye (Department of Biosciences and Bioengineering) Chairperson Dr. Sachin Kumar (Department of Biosciences and Bioengineering) Member Dr. Debasis Manna (Department of Chemistry) Member TH-2331_136106014 TH-2331_136106014 DEDICATION I dedicate this work to my grandparents and parents for their selfless sacrifices and belief in my abilities. They are my inspiration and pillars of strength. TH-2331_136106014 TH-2331_136106014 DECLARATION I hereby declare that the matter embodied in this thesis entitled “Analysis of Genes Encoding Outer Membrane Protein of Leptospira interrogans and Its Modulation Due to Host Factors: An Approach for Understanding Host-Pathogen Crosstalk” is the result of investigations carried out by me in the Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India under the supervision of Dr. Manish Kumar. In keeping with the general practice of reporting scientific observations, due acknowledgments have been made wherever the work of other investigators are referred. -
Sequedex Documentation Release 1.0-Rc1
Sequedex Documentation Release 1.0-rc1 Joel Berendzen, Judith Cohn, Nicolas Hengartner, Mira Dimitrijevic, Benjamin McMahon January 06, 2016 Contents 1 Copyright notice 1 2 Introduction to Sequedex 3 2.1 What is Sequedex?............................................3 2.2 What does Sequedex do?.........................................3 2.3 How is Sequedex different from other sequence analysis packages?..................4 2.4 Who uses Sequedex?...........................................4 2.5 How is Sequedex used with other software?...............................5 2.6 How does Sequedex work?........................................5 2.7 Sequedex’s outputs............................................8 3 Installation instructions 15 3.1 System requirements........................................... 16 3.2 Downloading and unpacking for Mac.................................. 16 3.3 Downloading and unpacking for Linux................................. 17 3.4 Downloading and unpacking for Windows 7 or 8............................ 17 3.5 Using Sequedex with Cygwin installed under Windows......................... 19 3.6 Installation and updates without network access............................. 20 3.7 Testing your installation......................................... 20 3.8 Running Sequedex on an example data file............................... 20 3.9 Obtaining a node-locked license file................................... 21 3.10 Installing new data modules and upgrading Sequedex - User-installs.................. 21 3.11 Installing new data modules -
The Magnitude and Diversity of Infectious Diseases
Chapter 1 The Magnitude and Diversity of Infectious Diseases “All interest in disease and death is only another expression of interest in life.” Thomas Mann THE IMPORTANCE OF INFECTIOUS DISEASES IN TERMS OF HUMAN MORTALITY According to the U.S. Census Bureau, on July 20, 2011, the USA population was 311 806 379, and the world population was 6 950 195 831 [2]. The U.S. Central Intelligence agency estimates that the USA crude death rate is 8.36 per 1000 and the world crude death rate is 8.12 per 1000 [3]. This translates to 2.6 million people dying in 2011 in the USA, and 56.4 million people dying worldwide. These numbers, calculated from authoritative sources, correlate surprisingly well with the widely used rule of thumb that 1% of the human population dies each year. How many of the world’s 56.4 million deaths can be attributed to infectious diseases? According to World Health Organization, in 1996, when the global death toll was 52 million, “Infectious diseases remain the world’s leading cause of death, accounting for at least 17 million (about 33%) of the 52 million people who die each year” [4]. Of course, only a small fraction of infections result in death, and it is impossible to determine the total incidence of infec- tious diseases that occur each year, for all organisms combined. Still, it is useful to consider some of the damage inflicted by just a few of the organisms that infect humans. Malaria infects 500 million people. About 2 million people die each year from malaria [4]. -
Tatiana Rodrigues Fraga Identificação De Proteases
TATIANA RODRIGUES FRAGA IDENTIFICAÇÃO DE PROTEASES DE LEPTOSPIRA ENVOLVIDAS COM MECANISMOS DE ESCAPE DO SISTEMA COMPLEMENTO HUMANO Tese apresentada ao Programa de Pós‐Graduação em Imunologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, para obtenção do Título de Doutor em Ciências. Área de concentração: Imunologia Orientadora: Profa. Dra. Lourdes Isaac Co-orientadora: Profa. Dra. Angela Silva Barbosa Versão original São Paulo 2014 RESUMO Fraga TR. Identificação de proteases de leptospira envolvidas com mecanismos de escape do sistema complemento humano. [tese (Doutorado em Imunologia)]. São Paulo: Instituto de Ciências Biomédicas, Universidade de São Paulo; 2014. A leptospirose é uma zoonose mundialmente disseminada que representa um grave problema de saúde pública. Microrganismos patogênicos, notadamente os que atingem a circulação sanguínea como a leptospira, desenvolveram múltiplas estratégias de evasão ao sistema imune do hospedeiro, em especial ao sistema complemento. Neste contexto, o principal objetivo deste trabalho foi analisar a secreção de proteases capazes de clivar moléculas do sistema complemento por leptospiras patogênicas, o que constituiria um novo mecanismo de evasão imune para este patógeno. Nove estirpes de leptospira foram selecionadas para este trabalho: sete patogênicas e duas saprófitas. Para a obtenção dos sobrenadantes de cultura, bactérias cultivadas em meio EMJH modificado foram transferidas para PBS pH 7,4 e incubadas a 37 oC por diferentes tempos. Após incubação, os sobrenadantes foram coletados e analisados quanto à atividade inibitória e proteolítica sobre componentes do sistema complemento. O efeito sobre a ativação do complemento foi quantificado por ELISA, onde a atividade das três vias foi medida separadamente. Verificamos que o sobrenadante de leptospiras patogênicas foi capaz de inibir a ativação de todas as vias do complemento, enquanto o da espécie saprófita não inibiu nenhuma delas. -
Guidelines for Safe Recreational Water Environments
GUIDELINES FOR SAFE RECREA TIONAL WATER ENVIRONMENTS TIONAL WATER Guidelines for Safe Recreational Water Environments Volume 2: Swimming Pools and Similar Environments provides an authoritative referenced review and Guidelines for assessment of the health hazards associated with recreational waters of this type; their monitoring and assessment; and activities available for their control through safe recreational water education of users, good design and construction, and good operation and management. The Guidelines include both specific guideline values and good practices. They address a wide range of types of hazard, including hazards leading environments to drowning and injury, water quality, contamination of associated facilities and VOLUME 2 air quality. VOLUME 2. SWIMMING POOLS2. AND SIMILAR ENVIRONMENTS VOLUME SWIMMING POOLS AND The preparation of this volume has covered a period of over a decade and has involved the participation of numerous institutions and more than 60 experts from SIMILAR ENVIRONMENTS 20 countries worldwide. This is the first international point of reference to provide comprehensive guidance for managing swimming pools and similar facilities so that health benefits are maximized while negative public health impacts are minimized. This volume will be useful to a variety of different stakeholders with interests in ensuring the safety of pools and similar environments, including national and local authorities; facility owners, operators and designers (public, semi-public and domestic facilities); special interest groups; public health professionals; scientists and researchers; and facility users. ISBN 92 4 154680 8 WHO GGuidelinesuidelines fforor ssafeafe reecreationalcreational wwaterater eenvironmentsnvironments VVOLUMEOLUME 22:: SSWIMMINGWIMMING PPOOLSOOLS AANDND SSIMILARIMILAR EENVIRONMENTSNVIRONMENTS WORLD HEALTH ORGANIZATION 2006 llayoutayout SSafeafe WWater.inddater.indd 1 224.2.20064.2.2006 99:56:44:56:44 WHO Library Cataloguing-in-Publication Data World Health Organization. -
Tatiana Rodrigues Fraga Identificação De Proteases
TATIANA RODRIGUES FRAGA IDENTIFICAÇÃO DE PROTEASES DE LEPTOSPIRA ENVOLVIDAS COM MECANISMOS DE ESCAPE DO SISTEMA COMPLEMENTO HUMANO Tese apresentada ao Programa de Pós‐Graduação em Imunologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, para obtenção do Título de Doutor em Ciências. São Paulo 2014 TATIANA RODRIGUES FRAGA IDENTIFICAÇÃO DE PROTEASES DE LEPTOSPIRA ENVOLVIDAS COM MECANISMOS DE ESCAPE DO SISTEMA COMPLEMENTO HUMANO Tese apresentada ao Programa de Pós‐Graduação em Imunologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, para obtenção do Título de Doutor em Ciências. Área de concentração: Imunologia Orientadora: Profa. Dra. Lourdes Isaac Co-orientadora: Profa. Dra. Angela Silva Barbosa Versão original São Paulo 2014 Aos meus pais e minha querida avó, pelo amor incondicional. AGRADECIMENTOS Às minhas queridas orientadoras Dra. Lourdes Isaac e Dra. Angela Silva Barbosa pela grande amizade de todos esses anos, pela confiança em meu trabalho e neste projeto. Muitíssimo obrigada por tudo, sem palavras para agradecer tudo o que fizeram por mim! Às colombianas Mónica Castiblanco e Adriana Granados, amigas mais que especiais que me acompanharam em todos os momentos do doutorado. Ufa! Conseguimos meninas! À estagiária de iniciação científica Daniella Courrol que contribuiu em diversos experimentos desta tese. Sua alegria e motivação foram simplesmente fundamentais, Dani! Aos membros mais recentes do Laboratório de Complemento: Iris, Karina e Leandro, que são amigos queridíssimos e excelentes pessoas para se ter ao lado no dia a dia. Adoro vocês! À Marlene P. C. Florido e à Paula e pelos trabalhos técnicos, pela amizade e grande apoio, sempre. Aos pesquisadores e funcionários do Laboratório de Zoonoses Bacterianas da Faculdade de Medicina Veterinária da USP: Dr.