Preparatory Work for the Future Development of Scientific Opinions on Animal Health

This final report summarizes the results of two reviews and a scoping study related to Canine leishmaniosis (CanL). Three objectives were addressed in this project. Objective 1 was to summarize relative sensitivity and specificity estimates of assays used to detect infection in dogs with Leishmania infantum in studies of naïve dogs in areas where Leishmania infantum infection is endemic. Objective 2 was to summarize data available to estimate the prevalence of parasitological cure (failure to detect organism) after a 12-month follow-up period in animals treated with meglumine antimoniate, miltefosine, and allopurinol or combinations of these drugs for canine leishmaniosis. Objective 3 was to assess diagnostic test characteristics of PCR assays and serological assays (ELISA or IFAT) from studies that use experimental models of Canine leishmaniosis. The same comprehensive search was used for all objectives. The searches yielded 7,405 records. After duplicates were removed, 3,865 records remained. Of these, 243 were broadly identified as diagnostic test evaluation studies and at the 2nd level of screening 18 were considered longitudinal studies. The 18 references were then assessed based on the full text and 7 were considered relevant to the review. The assays assessed by these studies were PCR on skin, buffy coat, bone marrow, blood and conjunctiva, and IFAT and ELISA. For objective 2, 40 potentially relevant records were identified as treatment comparison studies. After full-text screening, 13 studies were included in the review. The treatments varied greatly, and few comparative efficacy estimates were provided. No treatment was associated with 100% cure after 180 days follow-up. For objective 3, 513 citations were identified and the full texts of 169 articles were obtained. Sixty-two articles described at least one of the assays requested (PCR, ELISA or IFAT) and 18 articles described the use of a PCR and either ELISA and/or IFAT

Systematic Review of the Effect of Perch Height on Keel Bone Fractures, Deformation and Injuries, Bone Strength, Foot Lesions and Perching Behavior

This report provides a summary of four systematic reviews on the impact of perch height on laying hen keel bone fractures, deformation and injuries, bone strength, foot lesions and perching behavior. After conducting a scoping review and identifying outcomes of interest, the review protocols were developed. An extensive literature search was conducted in information sources such as CABI, PUBMED and relevant conference proceedings. 1518 abstracts were assessed for relevance and 9 studies reported perch use and 1 reported keel injuries. No studies reported summary effect sizes; therefore it was not possible to conduct a meta-analysis. In lieu of a formal meta-analysis, a descriptive analysis was conducted, which plotted reported perch height against metrics of perch use. This descriptive analysis was not able to account for lack of independence, differences in sample size and other importance sources of heterogeneity such as cage height. The descriptive analysis suggested a positive association with metrics that measured perch use and height, i.e., increased usage was associated with increased height

A Geographically-Restricted but Prevalent Mycobacterium tuberculosis Strain Identified in the West Midlands Region of the UK between 1995 and 2008

Background: We describe the identification of, and risk factors for, the single most prevalent Mycobacterium tuberculosis strain in the West Midlands region of the UK.Methodology/Principal Findings: Prospective 15-locus MIRU-VNTR genotyping of all M. tuberculosis isolates in the West Midlands between 2004 and 2008 was undertaken. Two retrospective epidemiological investigations were also undertaken using univariable and multivariable logistic regression analysis. The first study of all TB patients in the West Midlands between 2004 and 2008 identified a single prevalent strain in each of the study years (total 155/3,056 (5%) isolates). This prevalent MIRU-VNTR profile (32333 2432515314 434443183) remained clustered after typing with an additional 9-loci MIRU-VNTR and spoligotyping. The majority of these patients (122/155, 79%) resided in three major cities located within a 40 km radius. From the apparent geographical restriction, we have named this the "Mercian" strain. A multivariate analysis of all TB patients in the West Midlands identified that infection with a Mercian strain was significantly associated with being UK-born (OR = 9.03, 95% CI = 4.56-17.87, p 65 years old (OR = 0.25, 95% CI = 0.09-0.67, p < 0.01). A second more detailed investigation analyzed a cohort of 82 patients resident in Wolverhampton between 2003 and 2006. A significant association with being born in the UK remained after a multivariate analysis (OR = 9.68, 95% CI = 2.00-46.78, p < 0.01) and excess alcohol intake and cannabis use (OR = 6.26, 95% CI = 1.45-27.02, p = .01) were observed as social risk factors for infection.Conclusions/Significance: The continued consistent presence of the Mercian strain suggests ongoing community transmission. Whilst significant associations have been found, there may be other common risk factors yet to be identified. Future investigations should focus on targeting the relevant risk groups and elucidating the biological factors that mediate continued transmission of this strain

Information retrieval for systematic reviews in food and feed topics: a narrative review

Introduction Systematic review methods are now being used for reviews of food production, food safety and security, plant health, and animal health and welfare. Information retrieval methods in this context have been informed by human healthcare approaches and ideally should be based on relevant research and experience. Objective This narrative review seeks to identify and summarise current research-based evidence and experience on information retrieval for systematic reviews in food and feed topics. Methods MEDLINE (Ovid), Science Citation Index (Web of Science) and ScienceDirect (http://www.sciencedirect.com/) were searched in 2012 and 2016. We also contacted topic experts and undertook citation searches. We selected and summarised studies reporting research on information retrieval, as well as published guidance and experience. Results There is little published evidence on the most efficient way to conduct searches for food and feed topics. There are few available study design search filters, and their use may be problematic given poor or inconsistent reporting of study methods. Food and feed research makes use of a wide range of study designs so it might be best to focus strategy development on capturing study populations, although this also has challenges. There is limited guidance on which resources should be searched and whether publication bias in disciplines relevant to food and feed necessitates extensive searching of the grey literature. Conclusions There is some limited evidence on information retrieval approaches, but more research is required to inform effective and efficient approaches to searching to populate food and feed reviews

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution

Media industries and engagement: A dialogue across industry and academia

This article focuses on media engagement within the industry. The article takes the form of a dialogue between industry and academic researchers involved in a collaborative project on production and audience research on engagement (funded by the Wallenberg Foundation and in collaboration with Endemol Shine Group). Speakers from the film and television industry, and academic researchers working on media engagement, discuss how engagement is multifaceted, working across political and public spheres, policy and industry sectors, audiences and popular culture

The efficacy of teat sealants in dairy cows at dry-off to prevent new intra-mammary infections during the dry-period or clinical mastitis during early lactation: A protocol for a systematic review

Rationale: The majority of antibiotic use in the dairy industry is for intramammary infections (IMI), with a large portion of this aimed at treating and preventing IMI during the dry period (Lam et al., 2102). During dry off, formation of the teat-canal keratin plug plays an important role in susceptibility to IMI (Huxley et al., 2002), but there is wide variation between cows on time to complete closure of the teat-canal, or indeed if closure occurs at all (Dingwell et al., 2003). In heifers, pre-partum IMI is an important risk factor for the development of clinical mastitis in early lactation, and the impact of this disease on future udder health and productivity is far greater than in multiparous animals (Piepers et al., 2009). Moreover, the incidence of clinical mastitis at freshening in heifers is roughly double that of multiparous cows (Ali Naqvi et al., 2018). Teat sealants provide a non-antibiotic strategy to prevent IMI in the pre-calving period, which is of increasing importance due to concern for antimicrobial use and its relationship with the development of antimicrobial resistance (WHO, 2015). Understanding the efficacy of these products is essential to optimizing their use in order to decrease reliance on antibiotics for both treatment and prevention. Systematic reviews of randomized controlled trials in these areas will yield the highest level of evidence for efficacy of treatment under field conditions (Sargeant and O’Connor, 2014). Establishing the efficacy of teat sealants at dry-off, and pre-partum in heifers, to reduce the incidence of both clinical mastitis and/or IMI, will serve to improve decision makers’ ability to engage in effective stewardship of antibiotics thorough the strategic use of non-antibiotic alternatives

The efficacy of antibiotic treatments in dairy cows at dry-off to prevent new intramammary infections during the dry-period or clinical mastitis during early lactation: A protocol for a systematic review

Rationale: The majority of antibiotic use in the dairy industry is for the treatment and prevention of intramammary infections (IMI); in the Netherlands, approximately 60 % of all antimicrobial use in dairy is for this purpose, with two-thirds being dry cow therapy (Lam et al., 2012). In the United States, over 90 % of dairy cows receive dry cow therapy after every lactation (USDA-APHIS, 2016), with the goal of treating or preventing IMI during the dry period. These infections are strongly associated with risk of development of clinical mastitis in the first two weeks post-calving, which represents the highest risk period for this disease (Green et al., 2002). To combat this, blanket dry cow therapy (intramammary antimicrobial treatment of all quarters of all cows after the last milking of the lactation) was recommended for decades as part of a comprehensive strategy to reduce IMI in the dry period (Neave et al., 1969), and has been widely adopted in North America and the United Kingdom (Ruegg, 2017). Although cow2 level selective dry cow therapy has been in use in some regions for several decades (Schultze, 1983), interest has more recently increased worldwide, in part driven by concern for antimicrobial use and its relationship with the development of antimicrobial resistance between species (WHO, 2015), including nation-specific regulations (Santman-Berends et al., 2016). Selective dry cow therapy has been employed because it is a means to rapidly reduce the amount of antimicrobials used in dairy cattle (Vanhoudt et al., 2018), rather than because it is known to contribute importantly to antimicrobial resistance (Oliver et al., 2011). With a greater concern for prudent antibiotic use in the dairy industry, it is important that decision making with regards to dry cow therapy at both the cow and herd levels be evidencebased. Choosing ineffective antibiotics, or using antibiotic when not warranted, unnecessarily contributes to use while having little impact on controlling disease, which has substantial bearing to both profitability and animal welfare (Leslie & Petersson-Wolfe, 2012). Systematic reviews of randomized controlled trials yield the highest level of evidence for efficacy of treatment under field conditions (Sargeant and O’Connor, 2014), and comparative efficacy can be examined using network meta-analysis for multiple comparisons. Establishing the efficacy of both cow-level antibiotic therapy and herd-level dry cow antibiotic protocols for the prevention of IMI will serve to improve decision makers’ ability to engage in effective stewardship of antibiotics

Promotion of testa rupture during garden cress germination involves seed compartment-specific expression and activity of pectin methylesterases

Pectin methylesterase (PME) controls the methylesterification status of pectins and thereby determines the biophysical properties of plant cell walls, which are important for tissue growth and weakening processes. We demonstrate here that tissue-specific and spatiotemporal alterations in cell wall pectin methylesterification occur during the germination of garden cress (Lepidium sativum). These cell wall changes are associated with characteristic expression patterns of PME genes and resultant enzyme activities in the key seed compartments CAP (micropylar endosperm) and RAD (radicle plus lower hypocotyl). Transcriptome and quantitative real-time reverse transcription-polymerase chain reaction analysis as well as PME enzyme activity measurements of separated seed compartments, including CAP and RAD, revealed distinct phases during germination. These were associated with hormonal and compartment-specific regulation of PME group 1, PME group 2, and PME inhibitor transcript expression and total PME activity. The regulatory patterns indicated a role for PME activity in testa rupture (TR). Consistent with a role for cell wall pectin methylesterification in TR, treatment of seeds with PME resulted in enhanced testa permeability and promoted TR. Mathematical modeling of transcript expression changes in germinating garden cress and Arabidopsis (Arabidopsis thaliana) seeds suggested that group 2 PMEs make a major contribution to the overall PME activity rather than acting as PME inhibitors. It is concluded that regulated changes in the degree of pectin methylesterification through CAP- and RAD-specific PME and PME inhibitor expression play a crucial role during Brassicaceae seed germination