Caister Academic Press Yersinia Systems Biology and Control Edited by Elisabeth Carniel Yersinia Research Unit National Reference Laboratory and WHO Collaborating Center for Yersinia Institut Pasteur Paris France and B. Joseph Hinnebusch Rocky Mountain Laboratories National Institute of Allergy and Infectious Diseases National Institutes of Health Hamilton, MT USA caister.com/yersinia
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Caister Academic Press
YersiniaSystems Biology and Control
Edited by
Elisabeth CarnielYersinia Research UnitNational Reference Laboratory and WHO Collaborating Center for YersiniaInstitut PasteurParisFrance
and
B. Joseph HinnebuschRocky Mountain LaboratoriesNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthHamilton, MTUSA
British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library
ISBN: 978-1-908230-05-8
Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or publisher. The author and publisher do not assume responsibility for the validity of any products or procedures mentioned or described in this book or for the consequences of their use.
All rights reserved. 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 or otherwise, without the prior permission of the publisher. No claim to original U.S. Government works.
Cover design adapted from Figure 2.2.
Printed and bound in Great Britain
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Contents
Contributors v
Preface ix
1 Transcriptional Profiling of the Yersinia pestis Life Cycle 1B. Joseph Hinnebusch, Florent Sebbane and Viveka Vadyvaloo
2 Yersinia pseudotuberculosis Gene Expression in Plasma 19Michael Marceau and Michel Simonet
3 Host Transcriptome Responses to Yersinia pestis Infection 43Zongmin Du and Ruifu Yang
4 Transcriptional Profiling of Yersinia enterocolitica–Host Cell Interactions 59Reinhard Hoffmann, Ekaterina Lenk and Jürgen Heesemann
5 Proteome Analysis of Yersinia pestis and the Mammalian Host Response to Yersinia pestis Infection 69Rembert Pieper and Scott N. Peterson
6 Yersinia pestis Metabolic Network 83Ali Navid and Eivind Almaas
7 Plague Treatment and Resistance to Antimicrobial Agents 109Marc Galimand and Patrice Courvalin
8 Enteropathogenic Yersinia: Antibiotic Resistance and Susceptibility of Yersinia enterocolitica and Yersinia pseudotuberculosis 115Jeanette N. Pham
9 Acellular Vaccines Against Plague 123E. Diane Williamson and Petra C.F. Oyston
10 Live Vaccines Against Plague and Pseudotuberculosis 143Christian E. Demeure
11 North American Plague Models of Enzootic Maintenance, Epizootic Spread, and Spatial and Temporal Distributions 169Rebecca J. Eisen and Kenneth L. Gage
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Contentsiv |
12 Surveillance and Control of Plague 183Jean-Marc Duplantier
13 Tracing of Enteropathogenic Yersinia 201Maria Fredriksson-Ahomaa
14 Surveillance and Control of Enteric Yersinioses 217Truls Nesbakken
Index 239
Colour plate A1
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Preface
Systems biology, made possible by advances in biotechnology and bioinformatics during the last decade, is becoming an increasingly prominent methodology in infectious disease research. Systems biology can mean different things to different people, but at its core is a com-prehensive, integrative, and quantitative analysis of all components of a biological system, such as an intact cell, organism, or community. The ambitious ultimate goal of systems biology is to understand how all the components interact to enable the system to function successfully in different conditions; for example, how a host responds to infection and how a microbe adapts to survive within its host or in an external eco-system. Deciphering these dynamic biological networks is expected to disclose new molecular targets for disease control strategies. The first part of this book reviews some of the pioneering
applications of systems biology to study host-pathogen interactions of the medically important Yersinia species. The eventual synthesis of these and future analyses should provide a more holis-tic perspective of Yersinia infection mechanisms. The epidemiology and control of plague and yersiniosis is a second focus of the book. Interest-ingly, infectious disease ecology has historically relied on systems analysis, in which the pathogen is but one component of a complex ecosystem. Discovery of the important elements of the ecosystem and characterizing the interactions that lead to disease outbreaks in a population represents another level of systems biology that is critical for effective public health surveillance and control measures. We thank Annette Griffin and Horizon Scientific Press for the opportunity to organize this volume and all of the authors for their outstanding contributions.
VaccineAerosol 113, 128, 129, 132, 134, 144, 145, 149AFLP 207Ail 10, 12, 15–17, 40, 69, 73, 75, 76, 78, 81, 202, 205, 214Alexandre Yersin 144Alpha-ketoglutarate dehydrogenase 35Alum 126, 160Amikacin 113, 115. See also AntibioticAminoglycosides 110, 111, 113–115, 119. See also
AntibioticAmoxicillin-clavulanate 116–118. See also AntibioticAmoxi-clav see amoxicillin-clavunalateAmpicillin 110, 111, 115–121. See also AntibioticAnimal 2, 19, 26, 43–47, 53, 54, 110, 123, 125–127,
Analysis of variance 21, 23, 29, 36, 39, 41ANOVA see Analysis of varianceAnti F1 antibodies 161, 190. See also F1 antigenAntiapoptotic genes 64Anti-bactericidal peptides 150. See also Bacteriocin
Calcium 37, 40, 49, 77, 78, 81, 91, 94, 102–104, 106, 141Canada 117, 176, 203, 218–220, 236Carbapenem 119, 120. See also AntibioticCarnivore 189, 190, 195. See also AnimalsCase–control studies 208, 218Caspase 46, 133, 142, 167CCP see Critical control pointCD14 47, 48, 53, 61, 63Cefotaxime 116, 117, 119–121. See also AntibioticCeftriaxone 119, 120. See also AntibioticCephalosporinase 115. See also AntibioticCephalosporins 110, 111, 115, 116, 119, 120. See also
AntibioticChemokines 44–46, 48, 51, 53, 60, 61Chloramphenicol 106, 109–111, 115, 119. See also
CIN 190, 204Ciprofloxacin 110, 113–115, 117, 119, 120. See also
AntibioticCitrobacter freundii 116Class A β-lactamase 115, 116, 118. See also AntibioticClass C 115, 116. See also AntibioticClavulanate 117–119. See also AntibioticClinical trials 123, 125, 131, 156, 163Comparative transcriptomics 5Complement
HHACCP see Hazard analysis critical control pointHaffkine 144, 145. See also VaccineHazard analysis critical control point 222, 224, 230HeLa cells 42, 64Hemin storage 16, 17, 23, 104, 106
conjugative plasmid 111, 113, 114, 144IncA/C 109, 111–114. See also AntibioticIncP 111, 114. See also AntibioticpCD1 see pYVpFra see pFrapIP1202 111, 112. See also AntibioticpIP1203 109, 112. See also AntibioticpMT1 see pFrapPCP1 see pPlapYV see pYVR751 111, 114RSF1010 111, 114
Plasminogen activator see pPlapMT1 see pFraPneumonic plague see PlaguePolyamine biosynthesis 101Polysaccharide 78, 101
proteome 15, 27, 37, 38, 69–73, 77, 78, 80–82PRRs see Pattern recognition receptorsPsaA see pH6 antigenPTS see Phosphotransferase systemsPulsed-field gel electrophoresis 201, 206–211. See also
Trap 70, 189, 190, 194Tristetraprolin 61, 67TTP see TristetraprolinTTSS see Type III secretion systemTwo-dimensional gel electrophoresis 70Type III secretion system 17, 37, 38, 44, 55, 76, 106, 124,
Figure 3.1 Y. pestis–host interaction revealed by the transcriptional responses after exposure to Y. pestis. The dynamics of bacterial load (red line) and PMNs numbers in lung tissue (blue line) are shown at different time points post infection. The clustered gene expression data of Y. pestis and of lung tissue of infected mice
are shown in the solid line frame and the dotted line frame, respectively. Red represents the up-regulation
and green represents the down-regulation of specific genes. This figure is drawn according to the results of Liu et al. (2009).
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Colour plateA2 |
Figure 4.1 Serial cryosections of mouse spleen collected three days after intraperitoneal infection with
Y. enterocolitica O:8 (from C57BL/6 mouse carrying the CX3CR1-EGFP reporter gene expressed by a
subpopulation of DCs and macrophages). Five abscess-like lesions/Y. enterocolitica microcolonies are
shown. Left: Y. enterocolitica patches: pink; neutrophils (Ly6G+): red; CX3CR1-positive cells: green. Right: Y. enterocolitica patches: pink; B lymphocytes (white pulp): red; CX3CR1-positive cells: green (Lenk, 2011).