DOCSLIB.ORG

Bacterial Population Genetics in Infectious Disease

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Bacterial Population Genetics in Infectious Disease Bacterial Population Genetics in Infectious Disease Edited by D. Ashley Robinson Daniel Falush Edward J. Feil A John Wiley & Sons, Inc., Publication Bacterial Population Genetics in Infectious Disease Bacterial Population Genetics in Infectious Disease Edited by D. Ashley Robinson Daniel Falush Edward J. Feil A John Wiley & Sons, Inc., Publication Copyright © 2010 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6088, or online at http://www.wiley.com/go/permission. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations of warranties with respect to the accuracy or complete- ness of the contents of this book and specifi cally disclaim any implied warranties of merchantability or fi tness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profi t or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For more information about Wiley products, visit our web site at www.wiley.com. Library of Congress Cataloging-in-Publication Data Bacterial population genetics in infectious disease / editors, D. Ashley Robinson, Daniel Falush, and Edward J. Feil. p. ; cm. Includes bibliographical references and index. ISBN 978-0-470-42474-2 (cloth) 1. Pathogenic bacteria. 2. Bacterial genetics. 3. Population genetics. I. Robinson, D. Ashley. II. Falush, Daniel. III. Feil, Edward J. [DNLM: 1. Bacteria–genetics. 2. Bacterial Infections–genetics. 3. Genetic Variation. 4. Genetics, Population. QW 51 B1327 2010] QR201.B34B355 2010 616.07–dc22 2009039211 Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 In memory of Thomas S. Whittam Contents Foreword xi 3.5 Beyond the Tree Model 53 References 58 Preface xv Contributors xvii 4 Genetic Recombination and Bacterial Population Structure 61 4.1 Introduction 61 Part I Concepts and Methods in Bacterial 4.2 Constraints on LGT 62 Population Genetics 4.3 Infl uences of LGT on Sequence Analyses 65 1 The Coalescent of Bacterial 4.4 The Detection of Individual Populations 3LGT Events 66 1.1 Background and Motivation 3 4.5 The Estimation of Homologous 1.2 Population Reproduction Recombination Rates 74 Models 4 4.6 Properly Accounting for 1.3 Time and the Effective LGT During Sequence Population Size 5 Analyses 75 1.4 The Genealogy of a Sample 4.7 Questions Relating Directly of Size n 8 to LGT 76 1.5 From Coalescent Time to References 80 Real Time 9 1.6 Mutations 9 5 Statistical Methods for Detecting 1.7 Demography 11 the Presence of Natural Selection 1.8 Recombination and Gene in Bacterial Populations 87 Conversion 13 5.1 Introduction 87 1.9 Summary 17 5.2 Natural Selection 88 References 18 5.3 Statistical Methods for Detecting the Presence of 2 Linkage, Selection, and the Natural Selection 88 Clonal Complex 19 5.4 Statistical Methods for 2.1 Introduction—Historical Bacterial Populations 94 Overview 19 5.5 An Example 98 2.2 Recombination, Linkage, and 5.6 Discussion and Perspective 99 Substructure 20 References 100 2.3 Neutrality versus Selection 25 2.4 Clustering Techniques 29 6 Demographic Infl uences on References 33 Bacterial Population Structure 103 6.1 Bacterial Population Size 103 3 Sequence-Based Analysis of 6.2 Measures of Genetic Bacterial Population Structures 37 Diversity 104 3.1 Introduction 37 6.3 The Concept of Effective 3.2 Alignments 38 Population Size 106 3.3 Phylogenetic Methods 43 6.4 Inferring Past Demography from 3.4 Measures of Uncertainty 49 Genetic Sequence Data 111 vii viii Contents 6.5 Population Subdivision 112 9.4 Molecular Genotyping of B. 6.6 What is a Bacterial anthracis 172 Population? 114 9.5 Genotypes within the Anthrax 6.7 Conclusion 115 Districts in North America 174 References 116 9.6 Phylogenetic Resolution within the WNA Lineage 174 7 Population Genomics of Bacteria 121 9.7 Phylogeographic Resolution within the Ames Lineage 176 7.1 Introduction 121 9.8 Additional B. anthracis 7.2 Classical Bacterial Genotypes in North 122 Population Genetics America 177 131 7.3 The Genomics Era 9.9 Conclusions 178 7.4 Bacterial Population References 178 Genomics 132 7.5 Next-Gen Bacterial 10 Population Genetics Population Genomics 135 of Campylobacter 181 7.6 Next-Gen Genomics Technology 137 10.1 Introduction 181 7.7 Next-Gen Genomic Data 10.2 Human Infection 182 Analysis 141 10.3 Genetic Structure 183 7.8 Conclusions/Future 10.4 Models of Campylobacter Prospects 146 Evolution 187 References 147 10.5 Clades and Species 190 10.6 Conclusion 191 8 The Use of MLVA and SNP References 191 Analysis to Study the Population Genetics of Pathogenic Bacteria 153 11 Population Genetics of Enterococcus 195 8.1 Introduction 153 11.1 Introduction 195 8.2 MLVA and Other DNA 11.2 Antibiotic Resistance 196 Fragment-Based Methods 154 11.3 Vancomycin Resistance 197 8.3 SNP and DNA Sequence-Based 11.4 VRE: A Zoonosis or Not? 199 Methods 157 11.5 Population Structure and Genetic 8.4 Conclusion 162 Evolution: Similarities and References 163 Differences Between E. faecium and E. faecalis 199 11.6 What Is Driving GD in E. faecium and E. faecalis? 205 Part II Population Genetics of Select 11.7 The Accessory Genome of E. Bacterial Pathogens faecium and E. faecalis 208 11.8 Summary, Conclusions, and 9 Population Genetics of Bacillus: Future Perspectives 211 Phylogeography of Anthrax in References 212 North America 169 12 Population Biology of Lyme 9.1 Introduction 169 Borreliosis Spirochetes 217 9.2 History of Anthrax in North America 169 12.1 Introduction 217 9.3 The Anthrax Districts after 12.2 Genome Organization of LB 1944 171 Spirochetes 219 Contents ix 12.3 Genotyping of LB Spirochetes 15 Population Genetics of Salmonella: and Phylogenetic Tools 222 Selection for Antigenic Diversity 287 12.4 Population Biology and Evolution 15.1 Introduction 287 of LB Spirochetes 224 15.2 Generation Timescale 12.5 Do LB Species Exist? 236 Diversifi cation 292 12.6 Future Research Avenues 237 15.3 Antigenic Diversity References 239 in Salmonella 296 15.4 Why Are Diverse H and O Antigens Maintained 13 Population Genetics of in Salmonella? 301 Neisseria meningitidis 247 15.5 Conclusions 311 13.1 Introduction 247 References 311 13.2 A Brief History of Typing of Meningococci 247 16 Population Genetics 13.3 Species Separation 248 of Staphylococcus 321 13.4 Sampling Strategies 251 13.5 The Clonal Complexes of 16.1 Introduction 321 Meningococci 251 16.2 Overview of The Staphylococcal 13.6 Forces Shaping the Population Structure 322 Meningococcal 16.3 Staphylococcal Population Metalineage 256 Structure in Specifi c 13.7 Virulence, a Mysterious Disease Contexts 327 Trait 258 16.4 Origin and Maintenance of 13.8 Population Effect of Staphylococcal Genetic Meningococcal Vaccines 259 Variation 331 13.9 Antibiotic Resistance and 16.5 Macroevolutionary Meningococcal Lineages 260 Considerations and 13.10 Concluding Remarks 261 Concluding Remarks 335 References 261 References 336 Appendix 1—Diversity and Differentiation 342 14 Population Genetics of Pathogenic Escherichia coli 269 17 Population Genetics of Streptococcus 345 14.1 Introduction 269 14.2 E. coli Population Genetics: 17.1 Habitats, Transmission, Clonal or not Clonal? 270 and Disease 345 14.3 The E. coli Phylogenetic 17.2 Classical Strain Typing 347 Structure 273 17.3 Multilocus Sequence 14.4 The Evolutionary History of a Typing (MLST) Based on Host-Specifi c Obligate Pathogen: Housekeeping Genes 350 The Shigella and EIEC 17.4 Species Boundaries and Case Study 276 Gene Flow 354 14.5 What Makes You an 17.5 Niche-driving Genes 360 Opportunistic Pathogen? 278 17.6 Bacterial Population Dynamics 14.6 The Virulence Resistance and Selection 364 Trade-off 281 17.7 Machinery of Genetic Change, 14.7 Concluding Remarks 281 Revisited 371 References 282 References 371 x Contents 18 Population Genetics of Vibrios 379 18.4 V. vulnifi cus 392 18.5 Conclusions 397 18.1 Introduction 379 References 397 18.2 V. cholerae 382 18.3 V. parahaemolyticus 389 Index 403 Foreword W hen I joined the faculty at the University of Sussex in 1980 the distinguished evolutionary biologist John Maynard Smith despaired of microbiologists for their lack of interest in the population genetics of bacteria.
Load more

Recommended publications
  • Host Dispersal Shapes the Population Structure of a Tick-Borne Bacterial
    Host dispersal shapes the population structure of a tick-borne bacterial pathogen Ana Cláudia Norte, Gabriele Margos, Noémie Becker, Jaime Albino Ramos, Maria Sofia Núncio, Volker Fingerle, Pedro Miguel Araújo, Peter Adamík, Haralambos Alivizatos, Emilio Barba, et al. To cite this version: Ana Cláudia Norte, Gabriele Margos, Noémie Becker, Jaime Albino Ramos, Maria Sofia Núncio, et al.. Host dispersal shapes the population structure of a tick-borne bacterial pathogen. Molecular Ecology, Wiley, 2020, 29 (3), pp.485-501. 10.1111/mec.15336. hal-02990550 HAL Id: hal-02990550 https://hal-cnrs.archives-ouvertes.fr/hal-02990550 Submitted on 19 Nov 2020 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. Molecular Ecology Host dispersal shapes the population structure of a tick- borne bacterial pathogen Journal: Molecular Ecology Manuscript ID MEC-18-1428.R1 Manuscript Type: Original Article Date Submitted byFor the Review Only n/a Author: Complete List of Authors: Norte, Ana; University of Coimbra, MARE - Marine and Environmental Sciences Centre, Department of Life Sciences Margos, Gabriele; Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia Becker, Noemie; LMU Munich, Division of Evolutionary Biology, Faculty of Biology Ramos, Jaime; University of Coimbra, MARE - Marine and Environmental Sciences Centre, Department of Life Sciences Nuncio, Maria ; National Institute of Health Dr.
    [Show full text]
  • Lists of Names of Prokaryotic Candidatus Taxa
    NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code.
    [Show full text]
  • Multilocus Sequence Typing Von Borrelia Burgdorferi Sensu Stricto
    Multilocus Sequence Typing von Borrelia burgdorferi sensu stricto und Borrelia afzelii Stämmen aus Europa und den USA: Populationsstruktur, Pathogenität und Patientensymptomatik Sabrina Jungnick München 2018 Aus dem Nationalen Referenzzentrum für Borrelien am Bayrischen Landesamt für Gesundheit und Lebensmittelsicherheit in Oberschleißheim Präsident: Dr. med. Andreas Zapf Multilocus Sequence Typing von Borrelia burgdorferi sensu stricto und Borrelia afzelii Stämmen aus Europa und den USA: Populationsstruktur, Pathogenität und Patientensymptomatik Dissertation zum Erwerb des Doktorgrades der Medizin an der Medizinischen Fakultät der Ludwig-Maximilians-Universität zu München vorgelegt von Sabrina Jungnick aus Ansbach 2018 Mit Genehmigung der Medizinischen Fakultät der Universität München Berichterstatter: Prof. Dr. med. Dr. phil. Andreas Sing Mitberichterstatter: Prof. Dr. Sebastian Suerbaum Prof. Dr. Michael Hoelscher Prof. Dr. Hans – Walter Pfister Mitbetreuung durch den promovierten Mitarbeiter: Dr. med. Volker Fingerle Dekan: Prof. Dr. med. dent. Reinhard Hickel Tag der mündlichen Prüfung: 26.04.2018 Teile dieser Arbeit wurden in folgenden Originalartikeln veröffentlicht: 1. Jungnick S, Margos G, Rieger M, Dzaferovic E, Bent SJ, Overzier E, Silaghi C, Walder G, Wex F, Koloczek J, Sing A und Fingerle V. Borrelia burgdorferi sensu stricto and Borrelia afzelii: Population structure and differential pathogenicity. International Journal of Medical Microbiology. 2015. 2. Wang G, Liveris D, Mukherjee P, Jungnick S, Margos G und Schwartz I. Molecular Typing of Borrelia burgdorferi. Current protocols in microbiology. 2014:12C. 5.1-C. 5.31. 3. Castillo-Ramírez S, Fingerle V. Jungnick S, Straubinger RK, Krebs S, Blum H, Meinel DM, Hofmann H, Guertler P, Sing A und Margos G. Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto.
    [Show full text]
  • Evolutionary Ecology of Lyme Borrelia T ⁎ Kayleigh R
    Infection, Genetics and Evolution 85 (2020) 104570 Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid Review Evolutionary ecology of Lyme Borrelia T ⁎ Kayleigh R. O'Keeffe , Zachary J. Oppler, Dustin Brisson Department of Biology, University of Pennsylvania, Philadelphia, PA, USA ARTICLE INFO ABSTRACT Keywords: The bacterial genus, Borrelia, is comprised of vector-borne spirochete species that infect and are transmitted from Evolutionary ecology multiple host species. Some Borrelia species cause highly-prevalent diseases in humans and domestic animals. Borrelia Evolutionary, ecological, and molecular research on many Borrelia species have resulted in tremendous progress Transmission toward understanding the biology and natural history of these species. Yet, many outstanding questions, such as Ecological interactions how Borrelia populations will be impacted by climate and land-use change, will require an interdisciplinary approach. The evolutionary ecology research framework incorporates theory and data from evolutionary, eco- logical, and molecular studies while overcoming common assumptions within each field that can hinder in- tegration across these disciplines. Evolutionary ecology offers a framework to evaluate the ecological con- sequences of evolved traits and to predict how present-day ecological processes may result in further evolutionary change. Studies of microbes with complex transmission cycles, like Borrelia, which interact with multiple vertebrate hosts and arthropod vectors, are poised to leverage the power of the evolutionary ecology framework to identify the molecular interactions involved in ecological processes that result in evolutionary change. Using existing data, we outline how evolutionary ecology theory can delineate how interactions with other species and the physical environment create selective forces or impact migration of Borrelia populations and result in micro-evolutionary changes.
    [Show full text]
  • Contribution of the Outer Surface Proteins of Borrelia Burgdorferi S. I
    Contribution of the outer surface proteins of Borrelia burgdorferi tos. I.the pathogenesis of Lyme disease O • V AKADEMISK AVHANDLING som för avläggande av doktorsexamen i medicinsk vetenskap vid Umeå Universitet, offentligen kommer att försvaras på engelska språket i föreläsningssalen, byggnad 6L, Institutionen för Mikrobiologi, Umeå Universitet, fredagen den 7 oktober 1994, kl 09.00 av Maria Jonsson Umeå 1994 ABSTRACT Contribution of the outer surface proteins of Borrelia burgdorferi s.to L the pathogenesis of Lyme disease. Maria Jonsson, Department of Microbiology, Umeå University, Sweden. Borrelia burgdorferi s.is aI spirochete which causes the multisystemic disorder Lyme disease. As the borreliae lack toxin production, the pathogenicity is thought to involve, at least in part, molecules from the outer surface. Most Lyme diseaseBorrelia strains express two major outer surface lipoproteins, OspA (31 kD) and OspB (34 kD), on their surface. However, some strains lack the expression of OspA and OspB, but express a smaller 21 to 25 kD OspC protein instead. This thesis focuses on the importance of these proteins in the pathogenesis of Lyme disease. Biochemical and immunochemical studies of the OspA and OspB proteins from strains of various geographic origins show considerable differences in the apparent molecular weights and in their reactivities to monoclonal antibodies. The cloning and sequencing of the ospAB opérons from strains of different origins has demonstrated that the heterogeneity is found also at the DNA level Comparison of theospAB sequences allows the classification of the strains into three types, which coincide with the recent species designations, B. burgdorferi sensu stricto, B. afzelii and B.
    [Show full text]
  • Détection De Bactéries Pathogènes Dans Leur Vecteur, Les Tiques Dures (Acarien : Ixodidae )
    Thèse présentée devant L’Institut National Agronomique Paris-Grignon Pour l’obtention Du diplôme de Docteur Spécialité : microbiologie infectieuse Détection de bactéries pathogènes dans leur vecteur, les tiques dures (Acarien : Ixodidae ) Par Lénaïg Halos Directeurs de recherche : Professeur Henri-Jean Boulouis Docteur Muriel Vayssier-Taussat Soutenue le 27 septembre 2005 devant le jury composé de : Président : Professeur Jacques Guillot Rapporteur : Professeur Philippe Brouqui Rapporteur : Docteur Benoit Jaulhac Examinateur : Docteur Frédéric Beugnet Remerciements Aux membres du jury Au Professeur Jacques Guillot, pour me faire l’honneur de présider ce jury de thèse, pour la gentillesse et la disponibilité avec lesquelles il a accompagné toutes mes études depuis les premières heures vétérinaires aux travaux de recherche. Au Docteur Benoit Jauhlac pour avoir généreusement donné des extraits d’ADN de Borrelia sp., avoir eu l’amabilité d’accepter d’être un de mes rapporteurs et pour ses remarques précises et constructives. Au Professeur Philippe Brouqui pour avoir eu l’amabilité d’accepter d’être un de mes rapporteurs. Au Docteur Frédéric Beugnet pour l’intérêt qu’il a toujours porté à mon travail et pour avoir accepté de se joindre à ce jury. Au Professeur Henri Jean Boulouis Pour avoir dirigé cette thèse avec confiance et sympathie. Au Docteur Muriel Vayssier-Taussat Pour m’avoir guidée tout au long de ce travail, pour sa confiance, sa disponibilité et son dynamisme. 2 A toutes les personnes qui ont participé à ce travail en alliant professionnalisme et bonne humeur. A la Bartonella Dream Team pour avoir rempli son rôle d’équipe de rêve : pour les coups de pouces en cas de soucis, pour l’amélioration permanente de la collection de bouteilles vides et pour toutes les tranches de vie partagées : • A Corinne, pour m’avoir initiée à la mystique de la PCR et avoir pris l’auto-stoppeuse de Gagny pendant certains temps difficiles.
    [Show full text]
  • MOTILITY and CHEMOTAXIS in the LYME DISEASE SPIROCHETE BORRELIA BURGDORFERI: ROLE in PATHOGENESIS by Ki Hwan Moon July, 2016
    MOTILITY AND CHEMOTAXIS IN THE LYME DISEASE SPIROCHETE BORRELIA BURGDORFERI: ROLE IN PATHOGENESIS By Ki Hwan Moon July, 2016 Director of Dissertation: MD A. MOTALEB, Ph.D. Major Department: Department of Microbiology and Immunology Abstract Lyme disease is the most prevalent vector-borne disease in United States and is caused by the spirochete Borrelia burgdorferi. The disease is transmitted from an infected Ixodes scapularis tick to a mammalian host. B. burgdorferi is a highly motile organism and motility is provided by flagella that are enclosed by the outer membrane and thus are called periplasmic flagella. Chemotaxis, the cellular movement in response to a chemical gradient in external environments, empowers bacteria to approach and remain in beneficial environments or escape from noxious ones by modulating their swimming behaviors. Both motility and chemotaxis are reported to be crucial for migration of B. burgdorferi from the tick to the mammalian host, and persistent infection of mice. However, the knowledge of how the spirochete achieves complex swimming is limited. Moreover, the roles of most of the B. burgdorferi putative chemotaxis proteins are still elusive. B. burgdorferi contains multiple copies of chemotaxis genes (two cheA, three cheW, three cheY, two cheB, two cheR, cheX, and cheD), which make its chemotaxis system more complex than other chemotactic bacteria. In the first project of this dissertation, we determined the role of a putative chemotaxis gene cheD. Our experimental evidence indicates that CheD enhances chemotaxis CheX phosphatase activity, and modulated its infectivity in the mammalian hosts. Although CheD is important for infection in mice, it is not required for acquisition or transmission of spirochetes during mouse-tick-mouse infection cycle experiments.
    [Show full text]
  • Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages
    Curr. Issues Mol. Biol. 42: 409-454. caister.com/cimb Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages Ira Schwartz1*, Gabriele Margos2, Sherwood R. Casjens3, Wei-Gang Qiu4 and Christian H. Eggers5 1Department of Microbiology and Immunology, New York Medical College, Valhalla, NY USA, 2National Reference Centre for Borrelia and Bavarian Health and Food Safety Authority, Oberschleissheim, Germany, 3Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT USA, 4Department of Biological Sciences, Hunter College of the City University of New York, New York, NY USA 5Department of Biomedical Sciences, Quinnipiac University, Hamden, CT, USA *Corresponding author: [email protected] DOI: https://doi.org/10.21775/cimb.042.409 Abstract pathogenicity have been deduced, and comparative All members of the Borrelia genus that have been whole genome analyses promise future progress in examined harbour a linear chromosome that is about this arena. 900 kbp in length, as well as a plethora of both linear and circular plasmids in the 5-220 kbp size range. Introduction Genome sequences for 27 Lyme disease Borrelia The genus Borrelia forms a deeply separated lineage isolates have been determined since the elucidation within the Spirochaetes branch of the bacterial tree of of the B. burgdorferi B31 genome sequence in 1997. life (Paster et al., 1991). The organisms are The chromosomes, which carry the vast majority of genomically unique and not closely related to any the housekeeping genes, appear to be very constant other bacteria, including the other Spirochaetes. in gene content and organization across all Lyme Borrelia burgdorferi and Borrelia hermsii are disease Borrelia species.
    [Show full text]
  • Lyme Disease and Other Tick & Flea-Borne Infections
    WHAT YOU MAY NOT KNOW ABOUT BARTONELLA, BABESIA, LYME DISEASE AND OTHER TICK & FLEA-BORNE INFECTIONS IMPROVING TREATMENT SPEED, RECOVERY & PATIENT SATISFACTION James Schaller, MD, MAR and Kimberly Mountjoy, MS International University Infectious Disease Press Bank Towers • Newgate Center (305) 5150 Tamiami Trail North [Highway 41] Naples, Florida 34103 Copyright © 2012 James Schaller, MD All rights reserved. Cover Art: Nick Botner Lead Research and Research Study Acquisitions: Randal Blackwell Copy Editing by Kimberly Mountjoy, Lindsay Gibson, Jeremy Schaller and anonymous patients from all over the world Wholesale discount requires purchase of at least twenty copies and can be in five book units. Fax request to (239) 304-1987 and (239) 263-6760. Library of Congress Cataloging Data Schaller, J.L; Mountjoy, K. ISBN: 978098408895942 What you may not know about bartonella, babesia, lyme disease and other tick & flea-borne infections: improving treatment speed, recovery & patient satis- faction by J.L. Schaller and K. Mountjoy 1.Tick infections 2. Flea infections 3. Bartonella 4. Babesia 5. Lyme disease Manufactured in the United States of America First Edition To my beloved friends in USA prisons, with a hope we will end our leadership as the PRISON NATION, and lead in liberty and not inmate numbers. Let our nation return to timely trials, end cruel and unusual excessive sentences, allow the poor to have a good defense, and may our peace officers never exceed the facts. Let our prisons never have any element of torture— the time is already a torture. Contents Tick and Flea Infection Emerging Medicine ............................................... 1 What do we do with people who still feel ill after a treatment with doxycycline at the approved dose? ......................................................
    [Show full text]
  • The Genus Borrelia Reloaded
    RESEARCH ARTICLE The genus Borrelia reloaded 1☯ 2☯ 3 1 Gabriele MargosID *, Alex Gofton , Daniel Wibberg , Alexandra Dangel , 1 2 2 1 Durdica Marosevic , Siew-May Loh , Charlotte OskamID , Volker Fingerle 1 Bavarian Health and Food Safety Authority and National Reference Center for Borrelia, Oberschleissheim, Germany, 2 Vector & Waterborne Pathogens Research Group, School of Veterinary & Life Sciences, Murdoch University, South St, Murdoch, Australia, 3 Cebitec, University of Bielefeld, Bielefeld, Germany ☯ These authors contributed equally to this work. * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 The genus Borrelia, originally described by Swellengrebel in 1907, contains tick- or louse- a1111111111 transmitted spirochetes belonging to the relapsing fever (RF) group of spirochetes, the Lyme borreliosis (LB) group of spirochetes and spirochetes that form intermittent clades. In 2014 it was proposed that the genus Borrelia should be separated into two genera; Borrelia Swellengrebel 1907 emend. Adeolu and Gupta 2014 containing RF spirochetes and Borre- OPEN ACCESS liella Adeolu and Gupta 2014 containing LB group of spirochetes. In this study we conducted Citation: Margos G, Gofton A, Wibberg D, Dangel an analysis based on a method that is suitable for bacterial genus demarcation, the percent- A, Marosevic D, Loh S-M, et al. (2018) The genus Borrelia reloaded. PLoS ONE 13(12): e0208432. age of conserved proteins (POCP). We included RF group species, LB group species and https://doi.org/10.1371/journal.pone.0208432 two species belonging to intermittent clades, Borrelia turcica GuÈner et al. 2004 and Candida- Editor: Sven BergstroÈm, Umeå University, tus Borrelia tachyglossi Loh et al. 2017. These analyses convincingly showed that all groups SWEDEN of spirochetes belong into one genus and we propose to emend, and re-unite all groups in, Received: May 4, 2018 the genus Borrelia.
    [Show full text]
  • A Bibliography of Selected References for Researchers and Academicians Dedicated to Tick and Flea-Borne Infection Science
    A Bibliography of Selected References for Researchers and Academicians Dedicated to Tick and Flea-borne Infection Science J.L. Schaller and K. Mountjoy INTERNATIONAL ACADEMIC INFECTION RESEARCH PRESS Bank Towers • New Gate Center (305) Highway 41 [Tamiami Trail North] Naples, FL 34103 Copyright © 2011 James Schaller, MD, MAR All Rights Reserved. Cover Design: Nick Botner (Kaze Studies) Research: Randall Blackwell, Lindsay Gibson, Kimberly Mountjoy Library of Congress Cataloging Data Schaller, J. L; Mountjoy, K. A bibliography of selected references for researchers and academicians dedicated to tick and flea-borne infection science by J.L. Schaller and K. Mountjoy ISBN 978-0-9840889-3-5 1. Tick infections 2. Flea infections 3. Bibliography Note on Citation Style The style of these references varies. Making them uniform would not add to the ability to locate a citation. Most were left as they appeared when uncovered from a wide range of locations. Manufactured in the United States of America First Edition Dedicated to researchers, physicians and healers willing to serve the “untreatable,” and who study without ceasing… To those healers who accept patients “no one else can help,” who read with a ferocious passion, hoping for an insight to save just one person— anywhere on the earth. You are my true brothers and sisters in the medical arts. Thank you for your friendships and lessons. (JS) And to my co-author Kimberly Mountjoy— a wise scientist, scholar and caretaker. Tick and Flea Infection Bibliography 1 Abbas HM, Brenes RA, Ajemian MS, Scholand SJ. Successful conservative treatment of spontaneous splenic rupture secondary to Babesiosis: a case report and literature review.
    [Show full text]
  • Prevalence of Borrelia Burgdorferi Sensu Lato in Ixodes Ricinus Ticks in Scandinavia
    Prevalence of Borrelia burgdorferi sensu lato in Ixodes ricinus ticks in Scandinavia Rikke Rollum Thesis for the Master’s degree in Molecular Biosciences 60 study points Department of Molecular Biosciences Faculty of Mathematics and Natural Sciences UNIVERSITY OF OSLO 2014 II © Rikke Rollum 2014 Prevalence of Borrelia burgdorferi sensu lato in Ixodes ricinus ticks in Scandinavia Supervisors: Vivian Kjelland (UiA), Hans Petter Leinås (UiO), Audun Slettan (UiA) http://www.duo.uio.no/ Print: Reprosentralen, University of Oslo III IV Acknowledgements This master thesis was partly funded by the ScandTick project, which is a transnational project in Scandinavia devoted to ticks and tick-borne diseases. The laboratory work was conducted at the Department of Natural Sciences at the University of Agder (UiA) as an external thesis from the University of Oslo (UiO). I want to acknowledge all the people at UiO and UiA who have guided and helped me during my thesis. Vivian Kjelland (UiA), my supervisor, who gave me the opportunity to use her lab and for always being helpful, thorough and positive, which I really appreciate. You have inspired me to explore my opportunities, build connections and to be more confident and independent – Thank you! Audun Slettan (UiA), my co-supervisor, for always having a cheerful attitude and keeping my courage up when things did not go exactly as planned. I am also grateful to Hans Petter Leinaas (UiO), my co-supervisor, who have guided me in the writing process and for not letting me get carried away in fun facts. I would also like to thank Lars Korslund (UiA), who have helped me to understand and interpret the value of my results from a statistical point of view.
    [Show full text]