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Antonio Freitas Duarte •
Luís Lopes da Costa
Editors
Advances in Animal Health,
Medicine and Production
A Research Portrait of the Centre
for Interdisciplinary Research in Animal
Health (CIISA), University of Lisbon,
Portugal
123
Editors
Antonio Freitas Duarte Luís Lopes da Costa
Faculty of Veterinary Medicine Faculty of Veterinary Medicine
University of Lisbon University of Lisbon
Lisbon, Portugal Lisbon, Portugal
ISBN 978-3-030-61980-0 ISBN 978-3-030-61981-7 (eBook)
https://doi.org/10.1007/978-3-030-61981-7
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Foreword
The Centre for Interdisciplinary Research in Animal Health–CIISA, the research
centre of the Faculty of Veterinary Medicine of the University of Lisbon, has
recently commemorated its 25-Year Jubilee. Having emerged as a R&D unit to
stimulate and coordinate the research activities at the Faculty of Veterinary
Medicine of the University of Lisbon (FMV-UL), its mission evolved, and pre-
sently, CIISA coordinates research at multiple institutions, within national net-
works. Developing fundamental and applied research in the areas of animal,
veterinary and biomedical sciences, it integrates research performed at the major
Portuguese institutes acting in the animal sciences and animal health fields.
To carry out this role, CIISA extended its networks to integrate R&D institutions
spread throughout the country, including universities, polytechnic institutes,
research institutes, national state laboratories, pharmaceutical, biotechnology and
food producing industries, private enterprises, cooperatives, producer’s associations
and other non-profit organizations. This allowed the rational use of research
infrastructures and resulted in a high level of internationalization, arising from an
impressive number of collaborations with foreign laboratories.
Over the years, CIISA has shown a steadily increasing trend in scientific indi-
cators and most importantly in the quality and impact of its outputs at the scientific,
economic and societal levels. This is the result of the combined efforts of a highly
motivated, committed and dynamic team, including CIISA’s coordination, labora-
tory leaders and principal investigators, postdocs, PhD and master students, tech-
nicians and administrative staff. This book showcases the latest developments in the
state-of-the-art research carried out a CIISA.
Antonio Freitas Duarte
Luís Lopes da Costa
v
Contents
Animal Science
Ruminants’ Welfare Assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
G. Stilwell, A. Vieira, E. Can, C. Krug, S. Saraiva, M. Battini,
and S. Mattiello
Pain Management for Ruminants During Common Farm Husbandry
Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
G. Stilwell, P. Windsor, and D. M. Broom
Genetic Diversity and Structure of Iberoamerican Livestock Breeds . . . 52
L. T. Gama, A. M. Martinez, C. Ginja, J. Cañon, I. Martin-Burriel,
M. A. Revidatti, M. N. Ribeiro, J. Jordana, O. Cortes, N. Sevane,
V. Landi, J. V. Delgado, and the BIOBOVIS, BIOPIG, BIOHORSE,
BIODONKEY, BIOGOAT and BIOVIS consortia
Genetics of Carcass and Meat Quality Traits in Iberian Pigs . . . . . . . . . 69
M. C. Bressan, J. Almeida, A. Amaral, C. Bettencourt, J. Santos-Silva,
O. Moreira, R. Bessa, and L. T. Gama
The Fine Structure of the Cellulosome Defines the Intricacies
of Carbohydrate Deconstruction in the Mammalian Gut . . . . . . . . . . . . 87
P. Bule, S. Najmudin, J. Brás, V. Pires, V. Fernandes, A. Sequeira,
K. Cameron, A. Leitão, J. A. M. Prates, L. M. A. Ferreira, V. D. Alves,
and C. M. G. A. Fontes
Exogenous Enzymes Improve the Nutritive Value of Cereal-Based
Diets for Monogastric Animals Through Different
Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
V. Cardoso, T. Ribeiro, V. Fernandes, C. Guerreiro, M. Centeno, V. Pires,
P. Ponte, A. Goyal, S. Najmudin, V. D. Alves, J. A. M. Prates,
L. M. A. Ferreira, and C. M. G. A. Fontes
vii
viii Contents
Cistus ladanifer L. in Ruminant Diets – A Sustainable Approach
to Improve the Feed Nutritional Value and the Quality of Edible
Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
E. Jerónimo, M. T. Dentinho, O. Guerreiro, A. Francisco, D. Soldado,
S. P. Alves, J. Santos-Silva, and R. J. B. Bessa
Ameliorating Pork Marbling and Quality with Novel Feeding
Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
M. S. Madeira, C. M. Alfaia, P. A. Lopes, J. Pestana, D. Coelho,
C. M. G. A. Fontes, and J. A. M. Prates
Growth and Development of the Lusitano Foal on Extensive
Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
M. J. Fradinho, R. J. B. Bessa, R. M. Caldeira, and G. Ferreira-Dias
Assisted Reproductive Technologies (ART) Directed to Germplasm
Preservation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
R. M. L. N. Pereira, C. C. Marques, J. Pimenta, J. P. Barbas,
M. C. Baptista, P. Diniz, A. Torres, and L. Lopes-da-Costa
Tropical Livestock Development: Mitigating Seasonal Weight Loss
and Health Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
L. A. Cardoso, A. Almeida, S. van Harten, and S. Zúquete
Animal Health, One Health
The Gut Microbiome and Antimicrobial Resistance in Companion
Animals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
A. Belas, C. Marques, and C. Pomba
Antimicrobial Resistance Trends in Dogs and Cats with Urinary
Tract Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
C. Marques, A. Belas, and C. Pomba
The Public Health Risk of Companion Animal to Human
Transmission of Antimicrobial Resistance During Different Types
of Animal Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
C. Pomba, A. Belas, J. Menezes, and C. Marques
Antibacterial Alternatives in the Scope of One Health . . . . . . . . . . . . . . 279
M. Oliveira, I. Serrano, and L. Tavares
Domestic, Wildlife and Environmental Virology:
Molecular Epidemiology and Serological Surveillance . . . . . . . . . . . . . . 288
A. Duarte, M. C. Bento, S. Gil, and L. Tavares
Contents ix
Leishmaniosis: New Insights in a Changing World . . . . . . . . . . . . . . . . 301
G. Alexandre-Pires, M. Santos, M. A. Rodrigues, M. A. Pereira, J. Gomes,
S. A. Diaz, L. Gomes, A. Basso, A. Reisinho, J. Gomes, R. Leal,
J. Correia, A. Bolas, J. Meireles, G. Santos-Gomes,
and I. Pereira-da-Fonseca
Vectors and Vector Borne Diseases: Morphological and Molecular
Diagnosis, Risk Assessment, Population Genetics and Control
Strategies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
D. W. Ramilo, A. M. Alho, J. Gomes, M. Santos, A. S. Santos,
M. Santos-Silva, G. Alexandre-Pires, J. Meireles, A. Tomás, S. Zúquete,
A. Amaro, S. Belo, M. Schnyder, P. Deplazes, M. T. Rebelo,
L. Madeira-de-Carvalho, and I. Pereira-da-Fonseca
Distribution, Major Epidemiological Features and Control of Equid
Gastrointestinal Parasites in Mainland Portugal . . . . . . . . . . . . . . . . . . 344
A. S. Lopes, B. Melo-Franco, T. Nunes, S. Sousa, P. Fabrica, B. São-Braz,
and L. Madeira-de-Carvalho
Veterinary Medicine
From Villains to Heroes: Insights into the Antagonizing Functions
of Prion like Genes and Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
J. Pimenta, L. Lopes-da-Costa, C. C. Marques, J. P. Barbas,
M. C. Baptista, and R. M. L. N. Pereira
Unraveling Notch Signaling in Reproductive
Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389
D. Murta, E. Silva, A. Trindade, D. Henrique, A. Duarte,
and L. Lopes-da-Costa
Endothelial Dll4/Notch Signaling as a Target for Cancer
and Wound Healing Therapy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
A. Trindade, D. Djokovic, L. Mendonça, M. Badenes, L. Lopes-da-Costa,
and A. Duarte
Feline Mammary Carcinoma: Past, Present and Future . . . . . . . . . . . . 419
A. Gameiro, F. Almeida, M. Soares, J. Correia, and F. Ferreira
Novel Diagnostic and Therapeutic Immunologic Strategies
to Overcome Infectious, Oncologic and Neurodegenerative
Disorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 436
F. Aires-da-Silva, J. Dias, S. I. Aguiar, F. Marques, A. André, S. Gil,
and L. Tavares
Trends in Translational Medical Research: Companion Animal
Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 460
L. A. Mestrinho, E. Delgado, M. Lourenço, and M. Niza
x Contents
Neuroprotection in Glaucoma – Is Erythropoietin the Solution? . . . . . . 475
A. P. Resende, B. R. Silva, B. São-Braz, and E. Delgado
No Room to Breathe: Airway Conditions Affecting the Equine
Athlete . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485
P. Tilley, J. Simões, V. Pessoa, R. Fonseca, and J. P. Sales-Luis
The Role of Uteropathogenic Escherichia Coli in the Development
of Canine Pyometra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 510
E. Silva, M. F. Silva, S. Henriques, P. Diniz, C. Carneiro,
L. Lopes-da-Costa, and L. Mateus
What Goes Wrong from a Mare Healthy Endometrium
to Endometrosis? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 528
G. Ferreira-Dias, M. R. Rebordão, A. M. Galvão, R. Roberto-da-Costa,
A. Amaral, C. Fernandes, P. Pinto-Bravo, S. Morazzo, G. Alexandre-Pires,
K. Lukasik, A. Szóstek-Mioduchowska, and D. J. Skarzynski
Pregnancy Toxaemia in Small Ruminants . . . . . . . . . . . . . . . . . . . . . . . 541
P. B. A. Simões, R. Bexiga, L. P. Lamas, and M. S. Lima
Historical Note
CIISA: A 25 Year Old Young Adult… or… A Dream on Veterinary
Science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 559
Luis Tavares and All Researchers Working in CIISA 1992–2018
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 573
Animal Science
Ruminants’ Welfare Assessment
G. Stilwell1(B) , A. Vieira2 , E. Can3 , C. Krug4 , S. Saraiva5 , M. Battini6 ,
and S. Mattiello6
1 Animal Behaviour and Welfare Research Laboratory, Centre for Interdisciplinary Research in
Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
[email protected] 2 Centre for Management Studies of Instituto Superior Técnico (CEG-IST),
University of Lisbon, Lisbon, Portugal
3 Division of Agricultural and Environmental Sciences,
University of Nottingham, Nottingham, UK
4 Faculty of Epidemiology and Population Health, London School of Hygiene
and Tropical Medicine, London, UK
5 School of Agrarian and Veterinary Sciences, DCV, CECAV, Centre of Animal and Veterinary
Science, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
6 Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
Abstract. Most consumers expect welfare to be part of the core of animal pro-
duction and will avoid products which they view as not fulfilling minimum condi-
tions. But even if consumers did not object to poor animal welfare, there is more
than enough evidence that promoting welfare corresponds to better performance
and higher quality products. Thus, there are plenty of reasons vindicating welfare
assessment of farm animals. Welfare is a multidimensional concept enclosing both
physical and mental components, so assessment has to address its full complexity
to be credible and fair. To achieve this, assessment protocols should include valid
and reliable indicators pertaining the real welfare of all the animals in a group. The
protocols should also include easily measured indicators to guarantee its feasibil-
ity in farm conditions. CIISA’s Animal Behaviour and Welfare Research Lab has
been involved in both the developing and the application of welfare assessment
protocols in ruminants. As part of the AWIN project, CIISA built, together with
the University of Milan research team, an assessment protocol for dairy goats. It
was also the first to apply the Welfare Quality® protocol to Portuguese intensive
dairy farms and to introduce changes to these protocols so that they could be used
in ruminants at pasture.
Keywords: Pain · Nociception · Analgesia · Welfare · Ruminants
1 Animal Welfare – Definition(s)
Social concern with animal welfare and the moral status of animals has been present
in different civilizations and cultures, evolving over time alongside science, namely
© Springer Nature Switzerland AG 2020
A. Freitas Duarte and L. Lopes da Costa (Eds.): Advances in Animal Health,
Medicine and Production, pp. 3–26, 2020.
https://doi.org/10.1007/978-3-030-61981-7_1
4 G. Stilwell et al.
through well-established disciplines, such as ethics, farming, medicine and policy (Stil-
well 2014). However, for centuries the main purpose of animal breeding was directed
at increasing product quantity, without caring much about quality and, above all, ignor-
ing animal welfare. The interest towards animal welfare arose after the last Great War,
and coincided with a higher level of economic well-being, significant advances in sci-
ence and technology, the decrease in rural population and the consequent intensification
of animal production. This interest was initially stimulated by the release of the book
“Animal machine”, written by Ruth Harrison and published in the United Kingdom in
1964, that received great attention from consumers and from the public, who became
aware of the conditions in which animals were bred in intensive systems. These opin-
ion movements prompted the British government to set up a commission, presided over
by Professor Brambell, with the aim of investigating the welfare of intensively bred
animals. The Brambell Committee (1965) proposed the famous Five Freedoms (later
adopted and developed by FAWC 2009) which should be ensured so as to allow animals
to live “a life worth living”: 1) freedom from thirst, hunger and malnutrition; 2) freedom
from physical and thermal discomfort; 3) freedom from illness and pain; 4) freedom to
exhibit “normal” behaviour; 5) freedom from fear and distress. This was one of the first
steps towards the design of a scientifically based framework to evaluate farm animal
welfare.
Along the process of establishing “animal welfare” as a new branch of science, three
different views developed (Fraser 2008): one emphasizes the affective state, one the
biological function, and one selects natural living as the more fundamental measure. The
first view highlights the feelings, emotions, or affective states of the animal. The second
focuses on health, growth, and productivity of animals. Finally, the third view is centred
on the idea that animals should be able to express their normal behaviour in a natural
environment, and is referred to as the “naturalness” approach. Although these three views
comprise quite different areas when assessing welfare, they constitute complementary
starting points for identifying and solving animal welfare problems, often leading to
similar conclusions (Fraser et al. 1997; Fraser 2008). However, notwithstanding all the
(admirable) scientific work done within the last five decades, no universally established
definition of animal welfare has emerged (Green and Mellor 2011; Keeling et al. 2011).
As highlighted by Broom (2007), an agreement should be reached on the definition of the
concept of animal welfare for standardization in scientific papers, in legal documents,
and in public statements or discussions. Lack of precision in the definition opens space
for distortion, misrepresentation and exaggeration, which are of no value to animals,
farmers or even consumers.
In short, we can say that animal welfare is a multidimensional concept, defined as a
state of complete mental and physical health through which the animal lives in harmony
with its environment. It is important to point out that multidimensional means we cannot
forget, devalue or replace components, at least without a very valid reason. Accordingly,
welfare reflects and is a reflection of how an animal functions, how it feels and how it
performs. It seems logical to integrate all that composes an animal and that differentiates
it from non-living things, to reach the definition of welfare. Thus, the idea of an holistic
welfare is elegantly conveyed in one of its most accepted definitions: welfare is the state
of the individual as regards its attempts to cope with its environment (Broom 1986).
Ruminants’ Welfare Assessment 5
However, assessing how rich or how poor is the welfare of an animal, and especially
of those living in large groups, is not an easy task because: there are specific needs;
large populations conceal individual difficulties; farm animals very frequently adapt or
disguise signs; subclinical problems take time to arise; animals may not be familiarized to
artificial settings, etc. Moreover, certain dimensions will understandably be prioritized by
some according to their view of what reflects good quality of life. For example, producers
will say that performance is the key sign, veterinarians will perhaps choose absence of
disease and pain, while ethologists will select the expression of natural behaviour.
So the important questions remain. Are domestic animals in farms always subjected
to conditions which invariably will lead to poor welfare? Is ensuring natural surroundings
and the exhibition of normal behaviours sufficient? Are certain needs more important
than others? How can we measure the welfare of each individual (or at least of the
vast majority) living in a farm? How can we avoid anthropomorphic vision to distort our
observations? How can we make welfare evaluation reliable and credible to stakeholders
and society in general?
Because there are no clear answers, it is crucial to be able to assess farm animal
welfare in a scientific, multidimensional, objective and unbiased way. This should be the
aim of a welfare assessment protocol and has been the drive of some of the investigation
carried out by the Animal Behaviour and Welfare Research Lab at CIISA.
2 Why and How Should We Assess Animal Welfare?
There are four areas benefiting from methodical and meticulous animal welfare assess-
ment: research, monitor legislation compliance (non-voluntary), voluntary certification
schemes and as advisory/management tool aimed at improving health, welfare and
performance (Johnsen et al. 2001; Main et al. 2001; Sørensen et al. 2001; Main 2009).
Welfare certification and welfare legislation are now unstoppable because sustain-
ability, animal welfare and environmental concerns have increased consumers’ interest
in knowing how, where and by whom food is produced and handled from “farm to fork”.
Even if farmers do not always agree, food animal production will probably be unmain-
tainable in the future if these demands are not addressed. The market will make sure
of that. So, in response to society request, mandatory or voluntary assurance schemes
have multiplied all over the world in order to guarantee the marketing of high quality
animal products, in terms of health, safety and respect for animal welfare (Barnett et al.
2009). Assessment protocols have also shown to be superlative management tools for
veterinarians and producers, being used to identify subclinical problems or causes for
subperformance.
Hence, welfare assessment protocols should be considered one of the pillars of
modern, profitable, efficient and sustainable farming.
3 On-Farm Animal Welfare Assessment
At the end of the XX Century many researchers all around Europe started to concen-
trate their efforts on setting up methods for on-farm welfare assessment. Several animal
welfare monitoring systems were developed, such as an ethical account of farming in
6 G. Stilwell et al.
Denmark (Sørensen et al. 2001). However, the first real assessment schemes were the
TGI 35L and TGI 200 (Animal Need Index) for the certification of organic farms in
Austria (Bartussek et al. 2001) and Germany (Sundrum et al. 1994), respectively. These
schemes were based exclusively on the assessment of housing structures and manage-
ment (e.g., space, ventilation, stocking density, feeding regime, milking procedures). We
then assisted to the proposition in different European countries of several other assess-
ment schemes, using a wide range of approaches, essentially based on resources and
management, but sometimes combined with animal-based measures, such as disease
prevalence and mortality.
The high number of different attempts carried out in several countries to measure
animal welfare lead to the need of harmonising the research in this field at European
level. This gave origin to the European Action 846 of the COST Framework “Measuring
and monitoring farm animal welfare” (Blokhuis et al. 2003). From this action derived the
EU project “Welfare Quality® (WQ® ): science and society improving animal welfare in
the food quality chain” (2004–2010), the largest yet European project on animal welfare.
The aim of the project was to set up welfare assessment schemes and specific practical
strategies to improve the welfare of farmed animals, meeting the needs of society and
market demands. The WQ® project updated the Five Freedoms, subdividing them into
12 criteria grouped into four distinct but complementary principles, allowing to describe
in a comprehensive way all the aspects necessary to guarantee high animal welfare
standards. These criteria and principles were expanded, leading to the development of
protocols for the evaluation of dairy and meat cattle, pigs, broilers and hens’ welfare.
All these protocols were mainly focused on animal-based indicators.
Similarly, the “Animal Welfare Indicators” (AWIN) EU project (from 2011 to 2015)
aimed at developing, integrating and disseminating animal-based welfare indicators,
including pain, in goats, sheep, horses, donkeys and turkeys, addressing the same prin-
ciples and criteria proposed by the WQ® . The project generated five welfare assessment
protocols, with CIISA being most closely involved in the developing of the dairy goat
protocol (AWIN 2015; Battini et al. 2015a; Battini et al. 2016; Can et al. 2016), in
collaboration with the University of Milan (Italy), and also in the validation of pain
indicators, such as in lameness in goats (see paper on pain assessment in this book).
A strongly characterizing aspect of both WQ® and AWIN projects lies on the close
involvement of stakeholders: representatives of agricultural associations, animal rights
activists and consumers, breeders, processors, technicians and operators of large-scale
retail trade were systematically invited to meetings of experts, namely for the selection
and development of the indicators to be used. Their contribution was essential for the
development of the final protocols and contributed to the wide acceptance of these
protocols.
4 Which Indicators Should We Use?
Because approaches centred only on particular aspects of welfare (e.g. behaviour, emo-
tional state, health or performance) may fail to give a full overview of a farm (Web-
ster et al. 2004), the diverse measures should be combined and integrated into a com-
prehensive assessment protocol (Blokhuis et al. 2003; Botreau et al. 2007a; De Vries
Ruminants’ Welfare Assessment 7
et al. 2014). Various studies and welfare assessment schemes have adopted different
approaches throughout the last decades.
It is not surprising that the first assessment tools included only resource-based mea-
sures, because they are often easier and quicker to record, and their intra- and inter-
observer reliability is usually very high. For example, if we assume that a certain envi-
ronmental temperature is adequate for the welfare of a certain species, it would be easy
to measure it using a thermometer, and the result would probably be the same for dif-
ferent assessors. However, individuals of the same species can adapt differently to the
situation in which they live, according to their individual coping abilities; consequently,
their welfare cannot be assessed only through environmental and management factors,
but will depend on how each subject will be able to adapt to that situation.
In line with these considerations, the measures selected for WQ® and AWIN proto-
cols were focused almost exclusively on animal-based indicators (e.g. behaviour mea-
sures, productivity, health issues). This is in agreement with the “Statement on the use
of animal-based measures to assess the welfare of animals” published by the European
Food Security Authority (EFSA). In this publication the use of animal-based indicators
is promoted to allow for the identification of real situations of poor welfare, whereas
resource-based indicators such as management, structures or practices, are considered
as “risk factors” that may reduce welfare if animals cannot adapt to them (EFSA 2012).
Each indicator can provide information on a specific criteria, or sometimes even on
more than one criterion. For example, hair coat condition in goats can be indicative of
both appropriate nutrition and absence of disease (Battini et al. 2015), and can be useful
for a quick general screening. However, if an overall and detailed assessment has to be
carried out, then a range of animal-based indicators that cover all principles and criteria
should be selected. Obviously, if we need to assess specific issues or answer specific
questions, we should select the most appropriate indicator(s) for our context (Botreau
et al. 2007a; Main 2009). Several indicators have been established for almost all farmed
species, but they have only been validated under specific situations. This means that they
may not be valid, reliable and feasible if applied in different contexts. Unfortunately, the
majority of the existing indicators have been tested only for the most common breeds,
often in intensive rearing conditions. Many of them may also be relevant to other breeds
and farming (especially extensive and free-ranging) conditions; however, they should
be used with care, and the development and testing of specific indicators for each breed,
animal category, farming system, season, etc., should be encouraged, in order to ensure
valid results.
5 Building a Welfare Assessment Protocol Step by Step
5.1 Selecting Indicators – Validity, Reliability, Feasibility
Animal welfare is a science constantly growing and everyday new papers containing
potentially promising indicators are published. However, are these indicators valid in
all circumstances? Or reliable? Or feasible? Building a welfare assessment protocol is a
complex work requiring that all the indicators follow these specific attributes.
Validity tells us the extent to which an indicator measures what it is supposed to
measure. This attribute is particularly relevant because it defines the usefulness of an
8 G. Stilwell et al.
indicator. However, valid indicators are not useful if not reliable. Reliability is the extent
to which a measurement is repeatable and consistent and it can be further divided into
(Martin and Bateson 2007):
– Intra observer reliability, the agreement between successive observations of the same
individual or group by a single observer, based on statistical significance of correla-
tions (P < 0.05) or to Kendall’s coefficient of concordance (>0.7). According to time
between measurements, reliability may be classified as short-(1–7 days), medium-
(1 week to 1 month), or long-term reliability (>1 month); Test-retest reliability, the
agreement between observations performed on the same individual on at least two dif-
ferent occasions (Scott et al. 2007). A case of test–retest reliability is the consistency
over time, where results represent a long-term farm condition.
– Inter observer reliability, the agreement between different observers during a simul-
taneous observation, based on statistical significance of correlations (P < 0.05) or to
Kendall’s coefficient of concordance (>0.7).
It is paramount that indicators are valid and reliable, but there is yet another essen-
tial attribute that allows the protocol to be successfully applied on farm. This attribute
is feasibility. Feasibility is the practical chance of using the indicator during on-farm
assessment and its’ grade should be previously defined because it depends on the objec-
tive, the farm conditions and on other potential limitations (Knierim and Winckler 2009).
For example, attention should be paid to time constraints as it has been pointed out that
any on-farm welfare protocol should take less than 2 h/farm and less than 5 min/animal
(EFSA 2012). Furthermore, it was previously defined that indicators should not require
further processing after collection (e.g., laboratory analysis). Collection of indicators
should also be straightforward and inexpensive, as cost may be one other important con-
straint. Last, but not least, the whole protocol should be accepted by stakeholders and
farmers, therefore it should not: require more than one evaluator; alter the farm routine
(e.g., affecting feeding or milking time); over-run biosecurity rules; require a specific
location to be recorded (e.g., moving animals to a test arena); cause stress to the animals
(e.g., isolation, fear); or, require individual identification of the animals. Also, it should
be easily applied to all animals or to a representative sample of the herd (Battini et al.
2015c).
5.2 Testing Prototypes and Training Assessors
As a starting point for the development of a welfare assessment protocol for farm animals,
experts should review the relevant scientific literature to select promising animal-based
indicators. A screening period involving experts and researchers should follow in order
to address potential lack of data regarding validity, reliability, and feasibility of some
indicators (Battini et al. 2015a; Fig. 1). When validity is questionable, specific validation
studies should be designed and performed.
For each of the indicators finally elected, specific interactive learning material should
be prepared and used to provide a common training to all future assessors. From our
experience, the learning material should consist of a PowerPoint file starting with a brief
description of the indicator, followed by a detailed explanation of the assessing and
Ruminants’ Welfare Assessment 9
Fig. 1. Characteristics and process to identify promising animal-based indicators (Battini et al.
2015).
scoring procedures. Pictures and video-clips should be given as examples in order to
simulate on-farm conditions and therefore improve the understanding and assessment
of the indicator. At the end of the learning process, the level of knowledge should be
tested to determine if the assessors are ready to perform the farm visits. In the case of the
AWIN protocol, this preliminary phase was followed by a one-week training period at
the FMV-UL, which included both theoretical and practical sessions on farm, to ensure
similar level of training among assessors.
In order to facilitate and speed gathering and analysis of data collected during on-
farm inspections, a digitalized data collection system can be used, adapting an Open
Data Kit (ODK), a free and open-source set of tools that manages mobile data collection
solutions, developed by the University of Washington’s Department of Computer Sci-
ence and Engineering. This system also automatically records the time needed to assess
each indicator, providing important information about the feasibility of the prototype
(Battini et al. 2015d). The use of ODK system was a milestone for the development of
the AWINGoat app, freely available on Google Play Store. This app was specifically
designed to guide the user step-by-step when collecting data during the farm visit and
to provide an immediate visual output with the results of the assessment. AWINGoat
can be used by veterinarians and technicians in their everyday practice. The real-time
output can facilitate dialogue with farmers, suggesting actions to improve the welfare of
animals. Farmers can use the app to compare the welfare status of their animals to that
of those on farms with similar husbandry or management systems, and furthermore can
easily identify causes for sub-performance.
5.3 Common Problems and Constraints
Herd size is one of the main constraints when assessing production animals that are
group-housed. The high number of animals may demand a lot of time for the evalu-
ation, or data collection may become too complicated due to problems in separating
10 G. Stilwell et al.
and restraining a large number of animals. This is particularly true when performing
individual-level assessment. Whenever possible, locking the animals (e.g. at the feeding
rack or in a race) is the preferable way to restrain animals for examination, but if farmers
agree, an alternative location can be the milking parlour to where dairy animals can be
moved to outside milking hours. In the case of the AWIN prototype protocol testing, it
was clear that manually restraining goats in the pen was unfeasible because it caused too
much stress to the animals, put the assessors safety at risk and frequently required the
help of the farmer. This is also an issue when working with cattle and especially beef
cattle not used to humans’ proximity. That is the reason restraining and handling are not
included in the large ruminants’ protocols.
The herd size and species behaviour can also influence the collection of some group-
level indicators: an example is the decision to use the latency to the first contact test to
evaluate the human-dairy goat relationship rather than choosing the avoidance distance
test in the pen, that is commonly used in other species (e.g., dairy cows). In the avoidance
distance test the assessor enters the pen and, slowly walking, approaches each animal
in order to test its reaction to human. Even if accidents have never been reported, goats
may start running around making it difficult to conduct the test on individual animals
(especially in large groups), and to individually mark animals (ear tags in goats often
are not big enough to be read at a distance as in cows).
Irrespective of the indicators selected, assessing large herds may pose some flowing
related issues, namely the time needed to finish the assessment. For this reason, an
effective sampling strategy is usually required. Both the WQ and the AWIN protocols
were developed taking into account this aspect and both include a table that will advise
on the size of the sample taking into account the dimension of the population (Welfare
Quality 2009; AWIN 2015).
The protocol success implies that observers are well trained and know the normal and
abnormal behaviour of the particular species. Most of the indicators are quantitative, but
some problems can be found when qualitative indicators are used. Qualitative Behaviour
Assessment (QBA) is a scientific method conceived to evaluate the emotional state of
farm animals using the judgement of observers of animals’ behaviour and body language.
QBA requires experienced assessors, as they must be able to properly interpret and
recognize, e.g. aggressive vs. play behaviour or relaxed vs. bored animals. An exhaustive
training can overcome the limits due to lack of experience with a particular species,
however this is usually very time consuming, affecting the practicability of a protocol.
6 CIISA’s Work with Farm Animal Welfare Assessment Protocols
As mentioned before, CIISA has been deeply involved in building and applying cattle
and goat welfare assessment protocols. The CIISA’s Behaviour and Welfare research
teams not only applied validated protocols to Portuguese dairy cow farms, in this way
helping to understand the welfare status of production animals in our country, but also
developed and tested adaptations of the protocol to other production systems. As will be
shown in the few examples below, CIISA has acquired strong expertise in farm animal
welfare assessment.
