Modern Techniques for Pathogen Detection E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 648

Veröffentlichungsjahr: 2015

Beschreibung

This outstanding overview sets a new standard for a methods book on pathogen detection. The first chapter provides an outline of currently used routine methods, including their background, strengths and weaknesses, as well as comparing them to newer methods. The following chapters then cover novel methods already in wide use and which are still more experimental for routine purposes.
An invaluable resource for all medical laboratories and clinical institutions dealing with infectious diseases.

Leseprobe

Table of Contents

Cover

Related Titles

Title Page

Copyright

Preface

List of Contributors

Chapter 1: Unmet Medical Needs in Life-Threatening Infections – Caring for the Critically Ill

1.1 Life Threatening Infections and Sepsis – Defining the Problem

1.2 Sepsis as a “Hidden Healthcare Disaster”

1.3 Microorganisms and Types of Infection Triggering Sepsis

1.4 Emerging Problems Related to Resistance in Bacterial Infections

1.5 The Role of Fungi and Viruses

1.6 The Need for New Approaches in Diagnostics of Life-Threatening Infection and Sepsis

1.7 Rapid and Sensitive Culture-Independent Strategies to Identify Blood Stream Infection

1.8 Beyond Infection – Profiling the Immune Response of the Septic Host

1.9 Host Factors Contributing to Pathogenesis of Sepsis

References

Chapter 2: Identification Methods – An Overview

2.1 Taxonomy of Pathogenic Organisms

2.2 Microscopic Methods

2.3 Culture-Based Methods

2.4 Nucleic Acid-Based Techniques

2.5 Serology

2.6 Conclusions and Perspectives

References

Chapter 3: Nucleic Acid Amplification Techniques

3.1 Introduction

3.2 The Basic PCR Protocol

3.3 Primer Design

3.4 Modified End-Point PCR Protocols

3.5 Non-PCR NAT: Isothermal Amplification Protocols

3.6 Quantitative PCR

3.7 Controls, Probing, and General Aspects of Result Interpretation

3.8 Preanalytics

3.9 Fields of PCR Application

3.10 Microbial Trace Detection in BSI, Ascites, and Synovial Fluids

3.11 Upcoming Routine Solutions – Dawn of Assay Automation

3.12 Conclusion and Perspective

Acknowledgment

References

Chapter 4: DNA Microarrays for Pathogen Detection

4.1 Introduction

4.2 DNA Microarrays for the Detection of Bacterial Pathogens

4.3 Antibiotic Resistance Detection

4.4 DNA Microarrays for Virus Diagnostics

4.5 DNA Microarrays for Detection of Fungal Pathogens

4.6 DNA Microarrays for Parasite Diagnostics

4.7 Conclusion an Outlook

References

Chapter 5: MALDI-ToF

5.1 Introduction

5.2 MALDI-ToF Technology

5.3 Bacterial Identification Using Mass Spectrometry

5.4 Culture-Independent Rapid Identification of Clinical Pathogens

5.5 Antibiotic Susceptibility Testing Using Mass Spectrometry

References

Chapter 6: IR and Raman Spectroscopy for Pathogen Detection

6.1 Introduction

6.2 Bulk Analysis

6.3 Excitation with Visible Wavelengths

6.4 UV-Resonance Raman Spectroscopy

6.5 Single-Cell Analyses

6.6 Conclusion and Outlook

References

Chapter 7: FISH

7.1 Introduction

7.2 FISH Techniques

7.3 Clinical Implications of PNA FISH

7.4 Summary and Outlook

References

Chapter 8: Conclusions

Index

End User License Agreement

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Guide

Cover

Table of Contents

Preface

Begin Reading

List of Illustrations

Figure 1.1

Figure 1.2

Figure 1.3

Figure 1.4

Figure 1.5

Figure 2.1

Figure 2.2

Figure 2.3

Figure 2.4

Figure 2.5

Figure 2.6

Figure 3.1

Figure 3.2

Figure 3.3

Figure 3.4

Figure 3.5

Figure 3.6

Figure 4.1

Figure 4.2

Figure 4.3

Figure 4.4

Figure 5.1

Figure 5.2

Figure 5.3

Figure 5.4

Figure 5.5

Figure 5.6

Figure 6.1

Figure 6.2

Figure 6.3

Figure 6.4

Figure 6.5

Figure 6.6

Figure 6.7

Figure 6.8

Figure 6.9

Figure 6.10

Figure 6.11

Figure 6.12

Figure 7.1

Figure 7.2

Figure 7.3

Figure 7.4

List of Tables

Table 1.1

Table 1.2

Table 3.1

Table 3.2

Table 3.3

Table 4.1

Table 4.2

Table 4.3

Table 4.4

Table 4.5

Table 4.6

Table 4.7

Table 7.1

Related Titles

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2015

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2013

ISBN: 978-0-470-68318-7, also available in digital formats

Hillenkamp, F., Peter-Katalinic, J. (eds.)

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Edited by Jürgen Popp and Michael Bauer

Modern Techniques for Pathogen Detection

The Editors

Prof. Dr. Jürgen Popp

Friedrich-Schiller University Jena and Abbe Center of Photonics

Institute of Physical Chemistry

Helmholtzweg 4

07743 JenaandLeibniz Institute of Photonic Technology

Albert-Einstein-Straße 9

07745 Jena

Germany

Prof. Dr. Michael Bauer

Jena University Hospital

Department of Anesthesiology

and Intensive Care MedicineandCenter for Sepsis Control and Care (CSCC)

Erlanger Allee 101

07747 Jena

Germany

Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty can 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 authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.}

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication Data

A catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche Nationalbibliothek

The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.

© 2015 Wiley-VCH Verlag GmbH & Co. KGaA,

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Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley's global Scientific, Technical, and Medical business with Blackwell Publishing.

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

Print ISBN: 978-3-527-33516-9

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Preface

This book gives a comprehensive overview of the frontline research in pathogen detection. Infectious diseases caused by bacterial, viral, or fungal pathogens are one of the leading causes of death worldwide. In order to find the optimal treatment regime for the highly heterogeneous group of patients and to significantly reduce costs in medical care, novel tools that characterize the pathogenic microbes and the host-specific immune response are highly desired. Information about the phenotype and genotype of the germs help to accelerate quick and effective interventions, for example, the treatment of a sepsis patient with the right medication. Especially, within this context, the terms personalized medicine and pharmacogenomics, which define a stratified treatment for each individual patient, are of increasing importance. Due to a high variety in the responses of a patient panel to similar drug treatment regimes, which are caused by genetic and/or physiological variations among patients, the therapy has to be adapted to achieve highest efficiency and lowest side effects.

A plethora of analytical methods such as spanning microbiology, biochemistry, molecular biology, immunology, and biophysics are commonly applied for the detection of pathogens. Modern Techniques for Pathogen Detection informs in detail about various cutting-edge tools for pathogen identification. International scientists of the respective areas highlight recent emerging methods as well as improvements of conventional assays within individual chapters.

The management of life-threatening infections, especially sepsis, is covered, due to its importance, in a separate chapter of the book (Chapter 1). In the case of a sepsis suspicion, pathogen detection and administration of the appropriate drug combination should be performed as soon as possible. We stand at the beginning of a more personalized approach toward sepsis care. The novel developed analytical tools can facilitate an early and precise diagnosis of the pathogenic causatives of the severe infection concomitant, with profiling of their genetic status in terms of resistance to a certain antimicrobial therapy and finally also the monitoring of the treatment response.

Conventional techniques, involving microscopic or culture-based identification, enable the reliable detection of bacteria at low concentrations (Chapter 2). The morphological rating of bacteria from human patient samples combining microscopy with several classical or immunological staining techniques is an inherent part of everyday clinical practice. Beyond that, the gold standard in routine pathogen diagnostics is based on culture methods, which use selective growth media in combination with a multitude of biochemical tests. These tests are inexpensive and provide qualitative and quantitative information about the investigated pathogens. Culture-based techniques usually require an overnight incubation, thus the analysis time is extended to at least 1 day. In addition, the culture-based approach relies on the presence of culturable cells. Therefore, only the implementation of testing results from other assays provides the possibility to evaluate the pathogenic flora in case of non-culturable or slow-growing organisms.

In the last decades, molecular assays improved pathogen detection, leading to higher sensitivity, selectivity, and a significantly reduced sample-to-answer time. Nucleic acid-based techniques are discussed in detail in the relevant chapters (Chapters 3, 4, and 7). Great efforts were made to enable a simultaneous screening of several pathogens by means of multiplex nucleic acid amplification or microarray platforms. The trend to integrate automation in the molecular assay workflow has led to sample-to-answer times of several hours, depending on the employed diagnostic technique. Nevertheless, the results of PCR and microarray approaches should be critically rated in the clinical and microbiological context of the patients. An elegant assay is the direct specification of pathogens within a blood culture by means of fluorescence in situ hybridization (FISH). This approach is a follow-up staining method after the initial identification of Gram-positive or Gram-negative bacteria. A Quick-FISH testing platform can minimize the sample-to-answer time starting from Gram stain to 30 min. Of great importance is the fact that the inclusion of nucleic acid-based techniques into clinical routine depends on both the total hands-on-time and operator-friendly analysis platforms.

Furthermore, modern analytical methods, such as MALDI-TOF mass spectrometry, are discussed as a routine clinical microbiology laboratory for identification of infectious agents (Chapter 5). This fast evolving and increasingly applied technique allows the rapid and accurate identification of microorganism as well as antibiotic resistance markers based on specific biomarker signatures. Within this context, this pattern-matching process offers the balance between the time-consuming culture-based techniques and highly accurate nucleic acid-based techniques. Very promising tools for pathogen profiling are IR and Raman spectroscopic techniques, which are therefore also introduced within the book (Chapter 6). Their main advantage is given by the possibility of probing bacteria at single-cell level without any prior cultivation steps. IR and Raman spectroscopic techniques are successfully applied to identify bacteria by matching experimental molecular fingerprint information of single bacteria with reference members of the same biological species in preformed spectral databases by chemometrics. This pattern-matching approach is described for the direct classification and identification of infectious agents.

In summary, Modern Techniques for Pathogen Detection highlights state-of-the-art knowledge, emerging trends, and critical advices from experts for pathogen detection. We highly recommend the book to interdisciplinary working scientists at the nexus of fundamental research and clinical application, which plan to focus their research on further improvements that enable accurate and timely pathogen identification along with the respective antibiotic resistance information. The latter one is definitely the prerequisite to quickly adjust the right medication for a patient who suffers from severe microbial infection. A further crucial challenge for all the applied tools in terms of pathogen detection is the precise distinction of normal colonization and pathogenic invasion.

Last but not least, we would like to thank all the authors for the enjoyable cooperation that contribute to this book. The authors have a designated longtime expertise on their respective scientific area within the fast evolving field of microbial infection detection. Special thanks for their conscientious work, the abundance of patience, and the countless fruitful discussions. We would also thank the dedicated team of the publisher.

Michael BauerJürgen Popp

Jena, January 2015

List of Contributors

Till T. Bachmann

The University of Edinburgh

College of Medicine and Veterinary Medicine

Division of Infection and Pathway Medicine

Chancellor's Building

49 Little France Crescent

Edinburgh

EH16 4SB Scotland

UK

Michael Bauer

InfectoGnostics Forschungscampus Jena

Zentrum für Angewandte Forschung

Philosophenweg 7

07743 Jena

GermanyandJena University Hospital

Department of Anesthesiology and Intensive Care Medicine

Erlanger Allee 101

07747 Jena

GermanyandJena University Hospital

CSCC, Center for Sepsis Control and Care

Erlanger Allee 101

07747 Jena

Germany

Graeme N. Forrest

Portland Veterans Affairs Medical Center and Oregon Health and Science University

3710 SW US Veterans Hospital Rd

P3-ID, Portland

OR 97239

USA

Ralf Heinke

Institute of Physical Chemistry and Abbe Center of Photonics

Friedrich Schiller University Jena

Helmholtzweg 4

07743 Jena

Germany

Sandra Kloß

Institute of Physical Chemistry and Abbe Center of Photonics

Friedrich Schiller University Jena

Helmholtzweg 4

07743 Jena

Germany

Andreas Kortgen

Jena University Hospital

Friedrich-Schiller-University

Department of Anesthesiology and Intensive Care Medicine

Erlanger Allee 101

07747 Jena

GermanyandJena University Hospital

CSCC, Center for Sepsis Control and Care

Erlanger Allee 101

07747 Jena

Germany

Dragana Kusic

Institute of Physical Chemistry and Abbe Center of Photonics

Friedrich Schiller University Jena

Helmholtzweg 4

07743 Jena

Germany

Marc Lehmann

Jena University GmbH

Moldiax GmbH

Konrad-Zuse-Straße 1

07745 Jena

Germany

Bettina Löffler

University Hospital of Münster

Institute of Medical Microbiology

Domagkstr. 10

48149 Münster

Germany

Oliwia Makarewicz

Jena University Hospital

Center for Infectious Diseases and Infection Control

Erlanger Allee 101

07747 Jena

GermanyandJena University Hospital

CSCC, Center for Sepsis Control and Care

Erlanger Allee 101

07747 Jena

Germany

Claudia Stein

Jena University Hospital

Center for Infectious Diseases and Infection Control

Erlanger Allee 101

07740 Jena

Germany

Susann Meisel

Institute of Physical Chemistry and Abbe Center of Photonics

Friedrich Schiller University Jena

Helmholtzweg 4

07743 Jena

Germany

Jwan Mohammadi

Oregon Health and Science University

3181 SW Sam Jackson Park Rd, L-457

Portland

OR 97239

USA

Shahrzad Mohammadi

Portland Veterans A{f}{f}airs Medical Center and Oregon Health and Science University

3710 SW US Veterans Hospital Rd

P3-ID, Portland

OR 97239

USA

Ute Münchberg

Institute of Physical Chemistry and Abbe Center of Photonics

Friedrich Schiller University Jena

Helmholtzweg 4

07743 Jena

GermanyandJena School for Microbial

Communication

Friedrich Schiller University Jena

07743 Jena

Germany

Wolfgang Pfister

Jena University Hospital

Institute of Medical Microbiology

Erlanger Allee 101

07747 Jena

Germany

Mathias Pletz

Jena University Hospital

Center for Infectious Diseases and Infection Control

Erlanger Allee 101

07740 Jena

GermanyandJena University Hospital

CSCC, Center for Sepsis Control and Care

Erlanger Allee 101

07747 Jena

Germany

Sibyll Pollok

Abbe Center of Photonics

Friedrich-Schiller University Jena

Institute for Physical Chemistry

Helmholtzweg 4

07743 Jena

GermanyandLeibniz Institute of Photonic Technology Jena

Albert-Einstein-Straße 9

07745 Jena

GermanyandInfectoGnostics Forschungscampus Jena

Zentrum für Angewandte Forschung

Philosophenweg 7

07743 Jena

Germany

Jürgen Popp

Institute of Physical Chemistry and Abbe Center of Photonics

Friedrich Schiller University Jena

Helmholtzweg 4

07743 Jena

GermanyandLeibniz Institute of Photonic Technology Jena e. V.

Albert Einstein Straße 9

07745 Jena

GermanyandInfectoGnostics Forschungscampus Jena

Zentrum für Angewandte Forschung

Philosophenweg 7

07743 Jena

Germany

Petra Rösch

Institute of Physical Chemistry and Abbe Center of Photonics

Friedrich Schiller University Jena

Helmholtzweg 4

07743 Jena

Germany

Maya Rubtsova

M.V. Lomonosov Moscow State University

Department of Chemical Enzymology

Chemistry Faculty

Leninskie gori

119991 Moscow

Russia

Roland P.H. Schmitz

Center for Sepsis Control and Care (CSCC)

Department of Anesthesiology and Intensive Care Medicine

Jena University Hospital

Erlanger Allee 101

07747 Jena

Germany

Holger Schulze

The University of Edinburgh

College of Medicine and Veterinary Medicine

Division of Infection and Pathway Medicine

Chancellor's Building

49 Little France Crescent, Edinburgh

EH16 4SB Scotland

UK

Mervyn Singer

InfectoGnostics

Forschungscampus Jena

Zentrum für Angewandte Forschung

Philosophenweg 7

07743 Jena

GermanyandUniversity College London

Bloomsbury Institute for Intensive Care Medicine

Cruciform Building, Gower Street

WC1E 6BT, London

UK

Claudia Stein

Jena University Hospital

Center for Infectious Diseases and Infection Control

Erlanger Allee 101

07740 Jena

Germany

Stephan Stöckel

Abbe Center of Photonics

Friedrich Schiller University Jena

Institute of Physical Chemistry

Helmholtzweg 4

07743 Jena

Germany

Karina Weber

Abbe Center of Photonics

Friedrich-Schiller University Jena

Institute for Physical Chemistry

Helmholtzweg 4

07743 Jena

GermanyandLeibniz Institute of Photonic Technology Jena

Albert-Einstein-Straße 9

07745 Jena

GermanyandInfectoGnostics Forschungscampus Jena

Zentrum für Angewandte Forschung

Philosophenweg 7

07743 Jena

Germany

Stefan Zimmermann

Medical Microbiology and Hygiene

Department of Infectious Diseases

University Hospital Heidelberg

alternatively: Ruprecht Carl University Heidelberg

Im Neuenheimer Feld 324

69120 Heidelberg

Germany

1Unmet Medical Needs in Life-Threatening Infections – Caring for the Critically Ill

Michael Bauer Andreas Kortgen, and Mervyn Singer

1.1 Life Threatening Infections and Sepsis – Defining the Problem

The large number of infectious agents, complicated further by many varied pathogen- and host-specific characteristics, results in a broad spectrum of communicable diseases of which both prevention and control are challenging. While many infectious diseases are benign and are primarily treated in the community, severe infections may give rise to an urgent need to control the source of infection, to implement appropriate anti-infective therapy, and to provide supportive care to maintain homeostasis [1].

Under these conditions, the patient outcome from infection is determined not only by the invading pathogen which can be directly toxic and destructive to cells and tissues but also – or even primarily – by the host response. This host response may be inappropriately exaggerated, leading to severe tissue injury. Here, the effector molecules of immune cells, such as oxygen free-radicals and nitric oxide, cannot discriminate between microbial targets and host tissue [2]. Indeed, a novel concept has been proposed to describe the development of organ failure, that is, severe sepsis, as a disturbed “disease tolerance” where the eventual development of organ dysfunction is considered an inability to establish an appropriate equilibrium between direct pathogen damage and the ensuing host response (Figure 1.1) [3]. Patients with an uncontrolled focus of infection or an exuberant host response are particularly prone to develop organ dysfunction requiring care in a specialized “intensive care unit (ICU).” Such patients are referred to as septic (Figure 1.2).

Figure 1.1 Evolving concepts of sepsis as a “host defense failure disease.” The host response to invading pathogens requires a cytotoxic response that can result in a trade-off where tolerance of a pathogen may be associated with less organ injury.

Figure 1.2 Activation of the innate immune system as a “double-edged sword.” Activation of innate immunity reflects a prerequisite for defense and repair of a septic focus, such as a perforated viscus. However, this may lead to collateral damage if spillover of inflammatory mediators or release of activated cells into the systemic circulation occurs.