Veterinary Infection Biology: Molecular Diagnostics and High-Throughput Strategies

534 Pages·2015·13.511 MB·English

by  Mónica V. Cunha, João Inácio (eds.)

Methods in
Molecular Biology 1247
Mónica V. Cunha
João Inácio Editors
Veterinary Infection
Biology: Molecular
Diagnostics and
High-Throughput
Strategies
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651

Veterinary Infection Biology:
Molecular Diagnostics
and High- Throughput Strategies
Edited by
Mónica V. Cunha
Instituto Nacional de Investigação Agrária e Veterinária, Lisbon, Portugal
Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisbon, Lisbon, Portugal
João Inácio
Instituto Nacional de Investigação Agrária e Veterinária, Lisbon, Portugal
School of Pharmacy and Biomolecular Sciences, University of Brighton, United Kingdom
Editors
Mónica V. Cunha João I nácio
Instituto Nacional de Investigação Instituto Nacional de Investigação
Agrária e Veterinária Agrária e Veterinária
Lisbon, Portugal Lisbon, Portugal
Centro de Biologia Ambiental School of Pharmacy and Biomolecular Sciences
Faculdade de Ciências, Universidade de Lisbon University of Brighton
Lisbon, Portugal United Kingdom
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-2003-7 I SBN 978-1-4939-2004-4 (eBook)
DOI 10.1007/978-1-4939-2004-4
Springer New York Heidelberg Dordrecht London
Library of Congress Control Number: 2014953901
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Foreword
Infectious diseases of domestic and wild animals have a tremendous impact on the economy
and public health worldwide. Sixty percent of the pathogens that cause diseases in humans
have their source in animals (whether domestic or wild), as do 75 % of emerging human
diseases and 80 % of the pathogens that potentially could be used in bioterrorism. Animal
diseases that are transmissible to humans (collectively known as zoonoses), such as avian
infl uenza, rabies, bovine tuberculosis, and brucellosis, represent a very relevant public
health threat worldwide, being imperative to prevent and/or control them. Likewise,
pathogens that are not zoonotic but have a negative impact on livestock production, and
the associated fi nancial income, should not be overlooked. Some estimates suggest that
world production of food animals is reduced by more than 20 % due to disease, which may
be particularly important in developing countries where the unavailability of animal protein
is socially impacting and inevitably exacerbates infectious diseases risk.
The World Organization for Animal Health (OIE) was created in 1924 with the aim of
controlling the international spread of infectious animal diseases, but currently, over and
above this original mission, the new mandate is “t o improve animal health worldwide .” The
OIE builds its expertise on a global network of Reference Laboratories and Collaborating
Centers that play an essential role in prevention, detection, surveillance, and control of
animal diseases worldwide. Reference Laboratories serve as centers of scientifi c and techni-
cal expertise for offi cial listed diseases and have particular responsibility for carrying out
confi rmatory diagnostic tests for these diseases. Collaborating Centers are centers of exper-
tise in key competences related to the management of a particular animal health issue, such
as epidemiology, diagnosis, risk analysis, welfare, or veterinary training. This global network
of excellence enables OIE to remain at the forefront of world veterinary scientifi c expertise
and successfully carry out its activities, providing authoritative scientifi c opinions and advice
on key topics, such as animal health and welfare and diagnostic techniques. Moreover, the
OIE is involved in the preparation of standards on diagnostic assays and their offi cial valida-
tion which are published in the OIE Terrestrial Manual and Aquatic Manual and updated
annually by the World Assembly of the Delegates of the OIE (available from w ww.oie.int ) .
The achievements of biotechnology are signifi cantly contributing to the development
of novel, rapid, and powerful diagnostic assays for animal diseases, namely based on molec-
ular approaches, such as standard and real-time polymerase chain reaction and isothermal
nucleic acid amplifi cation methods. The recent advent of high-throughput sequencing
technologies is also boosting the prompt detection of all microbes in a sample, uncovering
novel pathogens and signifi cantly advancing veterinary diagnostic microbiology. Furthermore,
the analysis of single nucleotide and large sequence polymorphisms in the genome of
pathogens provides novel information on their traits, such as virulence and antimicrobial
resistance determinants, and supports epidemiological studies. Outstandingly, biotechnol-
ogy is enabling the development of diagnostic kits that can ultimately be used in point-of-
decision settings, away from centralized laboratories to assist in local decision- making, for
instance during an outbreak. OIE is aware of the opportunities and challenges that these
novel molecular-based approaches bring to veterinary diagnosis and several OIE Reference
v
vi Foreword
Laboratories and Collaborating Centers are also dedicated to Research and Development
activities on these fi elds. In this context, the present Springer’s book on the use of molecu-
lar biology strategies in veterinary laboratory practice showcases the versatility of the veteri-
narian profession in meeting the challenges posed by the continuous advance of science,
namely in the biotechnology fi eld. The editors have succeeded in bringing together an
impressive group of renowned collaborating authors, primarily veterinary doctors and
researchers of veterinary science, from institutions with established and prized expertise in
the fi elds of molecular biology and veterinary diagnostics, including several OIE Reference
Laboratories and Collaborating Centers. This book provides therefore an excellent and
authoritative overview of molecular biology strategies for pathogen detection and charac-
terization, along with the most recent technological innovations and their potential to
reconstruct transmission chains and to disclose pathogen biology, evolution, and interac-
tion with the host. Beyond the techniques, the book also discusses the integration of these
new molecular approaches in the framework of veterinary practice and animal health
management. In recognition of the challenge faced by the public and private components
of Veterinary Services and all veterinarians to improve the animal health status worldwide,
this book may aid veterinary laboratories in setting up molecular diagnosis valences and is
a valuable resource to veterinary doctors and laboratory technicians, researchers, and
students of veterinary medicine and science interested in knowing more about these
challenging, but promising molecular strategies to unravel animal infectious diseases.
Director General B ernard Vallat
World Organization for Animal Health (OIE)
Prefa ce
Infectious diseases of animals represent a signifi cant economic burden to economies world-
wide and may raise relevant Public Health concerns. Molecular diagnostics has emerged as
the fastest growing and trending segment of the in vitro diagnostics industry and seems also
promising in the veterinary sector, providing novel and powerful tools that enable the fast
and accurate diagnosis of animal diseases.
In this book, we provide an overview of molecular biology tools for pathogen detection
and characterization, along with potential applications to disclose pathogen biology and
interaction with the host. In Part I, biobanking, biosafety and good laboratory practices,
biological specimen collection and processing, quality assurance and control, and validation
of molecular diagnostic assays for veterinary use are concisely introduced as a basis for the
molecular strategies enclosed in protocol sections. The signifi cance and integration of
molecular biology methods in the framework of veterinary practice are discussed, along
with a SWOT analysis presenting our view on the advantages, limitations, opportunities
and weaknesses, or challenges, of these approaches. The rationale is on the techniques and
applications rather than the pathogen or disease models. Part II is dedicated to the molecu-
lar detection and identifi cation of animal pathogens using a wide range of established tech-
niques and covering, also, emerging diagnosis approaches. A brief overview of the advances
on nanoscience and microfl uidics is provided, including a discussion on how the recent
developments in these research fi elds may be translated into fi eld deployable biosensors.
Part III addresses genotyping tools for assessing the genetic landscape and epidemiology of
pathogens. Part IV introduces integrative omics and high-throughput technologies as pow-
erful research tools, yielding massive amounts of information that may ultimately improve
the control and management of infectious diseases. We strived to span a broad range of
molecular approaches, from simple and affordable to emerging and sophisticated, which we
anticipate will be useful for veterinary doctors and laboratory technicians, researchers, and
students of veterinary medicine and science.
Lisbon, Portugal M ónica V. Cunha
João I nácio
vii

Acknowledgements
The editors were supported by Fundacão para a Ciência e Tecnologia (FCT, Portugal)
through projects PTDC/CVT/111634/2009 (JI) and PTDC/CVT/117794/2010 and
in the framework of Projecto 3599—Promover a Produção Científi ca e Desenvolvimento
Tecnológico e a Constituição de Redes Temáticas (MVC). Alice Santos (INIAV IP, Lisbon,
Portugal) is acknowledged for the cover image artwork. The authors of Chap. 17 are
acknowledged for providing the fl uorescence microscopy image used in the artwork.
ix