The Elephant in the Room: Recognition and Documentation of Personnel Practices That Confound Reproducibility.

The ability to apply findings from animal studies efficiently and effectively is predicated on an understanding of biology and pathobiology, how that biology relates to the human systems being modeled, and how the studies are conducted and reported. This overview discusses various factors in research within the animal environment (referred to as extrinsic factors) that the NIH now expects to be documented to foster replicability in science and expand interpretations of study outcomes. Specifically, an important extrinsic factor in research with animals is that of individual personnel who perform handling practices, participate in research interactions, and share an overall presence in the housing facility with animals, all of which can confound reproducibility efforts in biomedical science. An improved understanding of the influences and behaviors of animal research personnel on animal responses is critical with regard to research results and the interpretation of data collected from animal models of biomedical disease.

Generation, maintenance, and monitoring of gnotobiotic mice.

Gnotobiology has revolutionized the study of microbiota-host interactions. This protocol explains how to generate, maintain, and monitor gnotobiotic mice. Three monitoring methods are presented and compared: bacterial culture, microscopy to visualize the presence (or absence) of bacteria using Gram staining or DNA staining, and 16S rRNA gene amplification and sequencing. The generation and maintenance of gnotobiotic animals should be performed in a germ-free and gnotobiotic facility to guarantee sterility and precision of gnotobiotic conditions. For complete details on the use and execution of this protocol, please refer to McDonald et al., 2020.

Federation of European Laboratory Animal Science Associations recommendations of best practices for the health management of ruminants and pigs used for scientific and educational purposes.

Most ruminants and pigs used for scientific and educational aims are bred not for these purposes but in a farm environment. Given the wide range of diseases that these species might have, ensuring that the animals' health status is appropriate can be complex and challenging. The Federation of European Laboratory Animal Science Associations has previously published recommendations for the health monitoring of experimental colonies of pigs (1998) and, respectively, calves, sheep and goats (2000). Unfortunately, the uptake of those recommendations was poor and insufficiently reported in scientific publications. These new recommendations for best practice focus on the main species of ruminants (cattle, sheep and goats) and pigs. They provide general and specific information helpful for designing a health management programme for the suppliers and for the user establishments, as well as guidance on animal procurement. Critical thinking based on the fields of use of the animals is promoted, aiming to help in taking informed decisions rather than establishing an exhaustive exclusion list for pathogens. Implementing the best health and welfare management practices should be done under the guidance of a competent attending veterinarian, with expertise and sufficient authority to take the appropriate action, doubled by excellent communication skills. It is strongly recommended that the user establishment's veterinarian works in close collaboration with the supplier's veterinarian.

Assessable learning outcomes for the EU Education and Training Framework core and Function A specific modules: Report of an ETPLAS WORKING Group.

Article 23(2) of the European Union Directive 2010/63/EU, which regulates welfare provisions for animals used for scientific purposes, requires that staff involved in the care and use of animals for scientific purposes be adequately educated and trained before they undertake any such work. However, the nature and extent of such training is not stipulated in the Directive. To facilitate Member States in fulfilling their education and training obligations, the European Commission developed a common Education and Training Framework, which was endorsed by the Member States Competent Authorities. An Education & Training Platform for Laboratory Animal Science (ETPLAS) Working Group was recently established to develop further guidance to the Learning Outcomes in the Framework, with the objective to clarify the levels of knowledge and understanding required by trainees, and to provide the criteria by which these Learning Outcomes should be assessed. Using the Framework document as a starting point, assessment criteria for the Learning Outcomes of the modules required for Function A persons (carrying out procedures on animals) for rats, mice and zebrafish were created with sufficient detail to enable trainees, providers and assessors to appreciate the level of knowledge, understanding and skills required to pass each module. Adoption and utilization of this document by training providers and accrediting or approving bodies will harmonize introductory education and training for those involved in the care and use of animals for scientific purposes within the European Union, promote mutual recognition of training within and between Member States and therefore free movement of personnel.

Guidelines for best practice in placebo-controlled experimental studies on probiotics in rodent animal models.

In the absence of established best practice standards in the probiotic field for reducing the risk of bacterial transfer between experimental groups, we developed protocols and methods to ensure the highest quality and interpretability of results from animal studies, even when performed in non-conventional animal care facilities. We describe easily implementable methods for reducing cross-contamination during animal housing, behavioural testing, and euthanasia, along with highlighting protocols for contamination detection in experimental subjects and laboratory areas using qPCR. In light of the high cross-contamination risks between animals during experiments involving probiotics, constant vigilance in animal care and research protocols is critical to ensure valid and reliable research findings.

Zebrafish: Housing and husbandry recommendations.

This article provides recommendations for the care of laboratory zebrafish (Danio rerio) as part of the further implementation of Annex A to the European Convention on the protection of vertebrate animals used for experimental and other scientific purposes, EU Commission Recommendation 2007/526/EC and the fulfilment of Article 33 of EU Directive 2010/63, both concerning the housing and care of experimental animals. The recommendations provide guidance on best practices and ranges of husbandry parameters within which zebrafish welfare, as well as reproducibility of experimental procedures, are assured. Husbandry procedures found today in zebrafish facilities are numerous. While the vast majority of these practices are perfectly acceptable in terms of zebrafish physiology and welfare, the reproducibility of experimental results could be improved by further standardisation of husbandry procedures and exchange of husbandry information between laboratories. Standardisation protocols providing ranges of husbandry parameters are likely to be more successful and appropriate than the implementation of a set of fixed guidance values neglecting the empirically successful daily routines of many facilities and will better reflect the wide range of environmental parameters that characterise the natural habitats occupied by zebrafish. A joint working group on zebrafish housing and husbandry recommendations, with members of the European Society for Fish Models in Biology and Medicine (EUFishBioMed) and of the Federation of European Laboratory Animal Science Associations (FELASA) has been given a mandate to provide guidelines based on a FELASA list of parameters, 'Terms of Reference'.

Exploring the advantages and limitations of sampling methods commonly used in research facilities for zebrafish health inspections.

Examining zebrafish populations for the presence of disease is an integral component of managing fish health in research facilities. Currently, many different strategies are used for zebrafish fish health inspections, which is a scenario that may result in subjective and biased diagnostic evaluations. The goal of this study was to compare the success of pathogen detection between a sample size of randomly selected fish (n = 60) that provides 95% confidence in pathogen detection based on a presumed pathogen prevalence level ≥5%, and other subpopulations and sample numbers commonly submitted for diagnostic testing within a 1000 tank, 30,000 fish, recirculating research system. This included fish collected from a sump tank (n = 53), sentinel fish (n = 11), and fish that were found moribund or freshly dead (n = 18). Additionally, five fish from each subpopulation were collected for histopathologic examination. A second study used retrospective data to examine pathogen distribution between systems (n = 2-5) in multi-system facilities (n = 5) using a sample size of 60 fish per system. For the pathogens detected, results supported the use of representative sample numbers rather than smaller numbers of populations considered more at risk. The exception to this is for the moribund/mortality group, which may be a resource for targeted surveillance of select pathogens. Each system within multi-system facilities should be considered separate units in terms of fish health inspections and biosecurity. Development of these evidence-based standards for fish health inspections in zebrafish systems enhances fish welfare, provides identification of potentially zoonotic pathogens, and ensures scientific integrity and reproducibility of research results.

Genetic quality assurance and genetic monitoring of laboratory mice and rats: FELASA Working Group Report.

Genetic quality assurance (QA), including genetic monitoring (GeMo) of inbred strains and background characterization (BC) of genetically altered (GA) animal models, should be an essential component of any QA programme in laboratory animal facilities. Genetic quality control is as important for ensuring the validity of the animal model as health and microbiology monitoring are. It should be required that studies using laboratory rodents, mainly mice and rats, utilize genetically defined animals. This paper, presented by the FELASA Working Group on Genetic Quality Assurance and Genetic Monitoring of Laboratory Murines, describes the objectives of and available methods for genetic QA programmes in rodent facilities. The main goals of any genetic QA programme are: (a) to verify the authenticity and uniformity of inbred stains and substrains, thus ensuring a genetically reliable colony maintenance; (b) to detect possible genetic contamination; and (c) to precisely describe the genetic composition of GA lines. While this publication focuses mainly on mouse and rat genetic QA, the principles will apply to other rodent species some of which are briefly mentioned within the context of inbred and outbred stocks.

Pacing behaviour in laboratory macaques is an unreliable indicator of acute stress.

Pacing behaviour, the most frequent stereotypic behaviour displayed by laboratory rhesus macaques (Macaca mulatta) is often used as an indicator of stress. In this study, we investigated how reliable this welfare indicator is at detecting acute stress by testing the reaction of macaques to the stressful event of being exposed to an agonistic interaction between conspecifics housed in the same room but in a different cage. Pacing, agitated locomotion, and stress-related displacement behaviours were quantified before, during and after agonistic interaction exposure, based on video recordings of 13 socially-housed macaques in their home cage. Displacement behaviours increased after agonistic interaction exposure, confirming that the events were experienced as stressful by the focal individuals. The occurrence of pacing did not increase during or after the agonistic interactions. Instead, agitated locomotion increased during the agonistic interactions. These results suggest either, that pacing as an indicator of acute stress is prone to false negative results, increasing in some stressful situations but not others, or that agitated locomotion has been mistaken for pacing in previous studies and that pacing is in fact unrelated to current acute stress. Both interpretations lead to the conclusion that pacing is unreliable as an indicator of acute stress in laboratory rhesus macaques.

Review: Assessing fish welfare in research and aquaculture, with a focus on European directives.

The number of farmed fish in the world has increased considerably. Aquaculture is a growing industry that will in the future provide a large portion of fishery products. Moreover, in recent years, the number of teleost fish used as animal models for scientific research in both biomedical and ecological fields has increased. Therefore, it is increasingly important to implement measures designed to enhance the welfare of these animals. Currently, a number of European rules exist as requirements for the establishment, care and accommodation of fish maintained for human purposes. As far as (teleost) fish are concerned, the fact that the number of extant species is much greater than that of all other vertebrates must be considered. Of further importance is that each species has its own specific physical and chemical requirements. These factors make it difficult to provide generalized recommendations or requirements for all fish species. An adequate knowledge is required of the physiology and ecology of each species bred. This paper integrates and discusses, in a single synthesis, the current issues related to fish welfare, considering that teleosts are target species for both aquaculture and experimental models in biological and biomedical research. We first focus on the practical aspects, which must be considered when assessing fish welfare in both research and aquaculture contexts. Next, we address husbandry and the care of fish housed in research laboratories and aquaculture facilities in relation to their physiological and behavioural requirements, as well as in reference to the suggestions provided by European regulations. Finally, to evaluate precisely which parameters described by Directive 2010/63/EU are reported in scientific papers, we analysed 82 articles published by European researchers in 2014 and 2015. This review found that there is a general lack of information related to the optimal environmental conditions that should be provided for the range of species covered by this directive.

FELASA accreditation of education and training courses in laboratory animal science according to the Directive 2010/63/EU.

THE FOUR EU FUNCTIONS AND BEYOND: FELASA accredits courses that fulfil the requirements of Functions A, B, C and D as defined by EU Directive, Article 23, as well as for designated veterinarians and specialists in laboratory animal science. MODULARITY AND MOBILITY: Cohesive courses for Functions and for very specific topics are accredited, but flexibility and mobility are possible: a researcher can start his/her training with one FELASA accredited course and complete other modules with another. A course organizer will deliver a FELASA certificate relating to the successfully completed modules. ACCREDITATION PROCESS: The process consists of two major steps: (1) a review of full course documentation provided by the applicant will lead, if successful, to FELASA accreditation. The course is posted on the FELASA website as 'FELASA accredited' and the course provider can deliver FELASA certificates upon successful completion of the course; (2) successful accreditation is followed by an on-site course audit. In the case of a negative outcome of the audit, FELASA accreditation is withdrawn, the course is deleted from the list of FELASA accredited courses and FELASA certificates cannot be issued. To ensure that quality is maintained, continuation of accreditation requires regular revalidation.