Systematic reviews answer specific review questions by following structured steps and employing specific methods to reduce the risk of bias and to maximize transparency in the process of the review, and systematic review methodology differs from traditional narrative reviews in many ways. As a journal devoted to reviews, it is appropriate that Animal Health Research Reviews (AHRR) includes this approach to reviews of the literature. The aim of this special issue of AHRR was to illustrate the scope of articles that can be considered for submission to the systematic review section of this journal for prospective authors and readers.

Vaccination of calves in the face of maternal antibodies (IFOMA) often does not result in seroconversion as maternally derived immunity interferes with the activation of adequate antibody responses to vaccination; however, it can prime T and B cell memory responses that protect calves against clinical disease when maternal immunity has decayed. The activation of B and T cell memory responses in calves vaccinated IFOMA varies and is affected by several factors, including age, level of maternal immunity, type of vaccine, and route of administration. These factors influence the adequate priming of humoral and cell mediated immune responses and the outcome of vaccination. The failure to adequately prime immune memory after vaccination IFOMA could result in lack of clinical protection and increased risk of viremia and/or virus shedding.

Calves are highly dependent of colostrum (and antibody) intake because they are born agammaglobulinemic. The transfer of passive immunity in calves can be assessed directly by dosing immunoglobulin G (IgG) or by refractometry or Brix refractometry. The latter are easier to perform routinely in the field. This paper presents a protocol for a systematic review meta-analysis to assess the diagnostic accuracy of refractometry or Brix refractometry versus dosage of IgG as a reference standard test. With this review protocol we aim to be able to report refractometer and Brix refractometer accuracy in terms of sensitivity and specificity as well as to quantify the impact of any study characteristic on test accuracy.

Herein we describe a protocol for a systematic review of the evidence on whether point sources of anthropogenic effluent are associated with an increase in antibiotic resistance in the adjacent environment. The review question was based on the Population, Exposure, Comparator, Outcome, Study Design (PECOS) framework as follows: Is the prevalence or concentration of antibiotic resistant bacteria or resistance genes (O) in soil, water, air or free-living wildlife (P) higher in close proximity to, or downstream from, known or suspected sources of anthropogenic effluent (E) compared to areas more distant from or upstream from these sources (C)? A comprehensive search strategy was created to capture all relevant, published literature. Criteria for two stages of eligibility screening were developed to exclude publications that were not relevant to the question, and determine if the study used a design that permitted estimation of an association between a source and levels of resistance. A decision matrix was created for assessment of risk of bias to internal validity due to sample selection bias, information bias, and confounding. The goal of this protocol is to provide a method for determining the state of knowledge about the effect of point sources on antibiotic resistance in the environment.

Bioactive compounds from marine and terrestrial organisms have been used extensively in the treatment of many diseases in both their natural form and as templates for synthetic modifications. This review summarizes present knowledge about anthelmintic effects of the extracts of bioactive plants in Nigeria against helminth parasites of ruminants. Plants traditionally used in livestock production are discussed. The main focus is hinged on in vitro and in vivo activities of secondary plant metabolites against nematodes of livestock. This review provides insight into preliminary studies of medicinal plants, which can be investigated further to discover promising molecules in the search for novel anthelmintic drugs and nutraceuticals.

Natural bornavirus infections and their resulting diseases are largely restricted to horses and sheep in Central Europe. The disease also occurs naturally in cats, and can be induced experimentally in laboratory rodents and numerous other mammals. Borna disease virus-1 (BoDV-1), the cause of most cases of mammalian Borna disease, is a negative-stranded RNA virus that replicates within the nucleus of target cells. It causes severe, often lethal, encephalitis in susceptible species. Recent events, especially the discovery of numerous new species of bornaviruses in birds and a report of an acute, lethal bornaviral encephalitis in humans, apparently acquired from squirrels, have revived interest in this remarkable family of viruses. The clinical manifestations of the bornaviral diseases are highly variable. Thus, in addition to acute lethal encephalitis, they can cause persistent neurologic disease associated with diverse behavioral changes. They also cause a severe retinitis resulting in blindness. In this review, we discuss both the pathological lesions observed in mammalian bornaviral disease and the complex pathogenesis of the neurologic disease. Thus infected neurons may be destroyed by T-cell-mediated cytotoxicity. They may die as a result of excessive inflammatory cytokine release from microglia. They may also die as a result of a ‘glutaminergic storm’ due to a failure of infected astrocytes to regulate brain glutamate levels.

A meta-analysis was performed to derive prevalence estimates for Brucella spp., Mycobacterium spp. and Trypanosoma spp. in cattle in Tanzania using data derived from a systematic review of zoonotic hazards in cattle production systems. Articles published before 2012 reporting prevalence and considered at least moderate in quality were included in the analysis. Results showed high heterogeneity between studies, with wide ranges in the reported prevalence: Brucella (0.3–60.8%), Mycobacterium (0.1–13.2%) and Trypanosoma (0.82–33.3%). Overall meta-analytic mean prevalence estimates were 8.2% (95% CI 6.5–10.2), 1.28% (95% CI 0.35–4.58) and 10.3% (95% CI 6.20–16.70) respectively, for Brucella spp., Mycobacterium spp. and Trypanosoma spp. Time and region were predictors of variability of Brucella spp. prevalence, while diagnostic test was a strong predictor of Mycobacterium spp. prevalence, with higher prevalence estimates given by skin tests compared with post-mortem inspection. None of the studied factors were associated with prevalence of Trypanosoma spp. The small sample sizes, range of study locations, study designs and diagnostics used, contributed to high variability among prevalence estimates. Larger and more robust prevalence studies are needed to adequately support risk assessment and management of animal and public health threats.

Bornaviruses cause neurologic diseases in several species of birds, especially parrots, waterfowl and finches. The characteristic lesions observed in these birds include encephalitis and gross dilatation of the anterior stomach — the proventriculus. The disease is thus known as proventricular dilatation disease (PDD). PDD is characterized by extreme proventricular dilatation, blockage of the passage of digesta and consequent death by starvation. There are few clinical resemblances between this and the bornaviral encephalitides observed in mammals. Nevertheless, there are common virus-induced pathogenic pathways shared across this disease spectrum that are explored in this review. Additionally, a review of the literature relating to gastroparesis in humans and the control of gastric mobility in mammals and birds points to several plausible mechanisms by which bornaviral infection may result in extreme proventricular dilatation.

The success of a systematic review depends on the availability, accessibility and quality of literature related to the review question. This paper presents the literature found in four systematic reviews conducted for a selection of zoonotic hazards in four livestock value chains in Africa, as well as setting out the challenges in conducting the reviews. The protocol was designed following international standards, and addressed four questions around prevalence, risk factors, control options and impact of various hazards and populations. Searches were conducted in four online databases. Articles were screened for relevance, and quality was assessed before data extraction. Literature on zoonotic hazards was in general scarce and access to full articles was limited. Overall, 25–40% of papers were considered poor quality. The diversity of approaches and designs in the studies compromised the ability to generate summarized estimates. We found that the emphasis of veterinary research has been on livestock problems rather than public health issues, although this seems to be shifting in the last decade; we also found there are limited studies on impact and control. While increasing literature is being published around zoonoses in Africa, this is still inadequate to appropriately inform policy and guide research efforts.

The tetracyclines (TTC) and sulfonamides are among the most common residues found in bulk raw milk samples. Detection of drug residues in bulk milk (BM) tankers demonstrates that the product is not suitable for human consumption. Discarding BM with residue-contaminated milk is a waste of a valuable commodity, and a repurposing for consumption at calf ranches is a way to recapture some value. However, if calves consuming milk with drug residues are slaughtered for veal, their meat could contain drug residues. The objective of this review is to provide a residue avoidance strategy for TTC and sulfonamide residues in veal. To determine the pharmacokinetic properties of each drug a structured review of the literature was performed and the study inclusion criteria were that the publication used dairy breed calves, with body weight <330 kg or <6 months of age. The most pertinent parameters were determined to be plasma, tissue elimination half-lives, and systemic bioavailability. The results of this review were integrated with milk and tissue testing levels of quantification and tissue tolerances to formulate a recommended withdrawal interval for calves ingesting this milk. The suggested withdrawal interval of 20 days will ensure that no veal calves will test positive for residues from being fed this milk.

The physiological role of the gastrointestinal microbiota has become an important subject of nutrition research in pigs in the past years, and the importance of intestinal microbial activity in the etiology of disease is doubtless. This review summarizes the recent knowledge related to the microbial ecology of protein fermentation and the appearance of protein-derived metabolites along the pig intestine. The amount of fermentable protein depends on factors such as dietary protein concentration, protein digestibility due to secondary or tertiary structure, the interaction with dietary compounds or anti-nutritional factors, and the secretion of endogenous proteins into the gut lumen. High protein diets increase the luminal concentrations and epithelial exposure to putatively toxic metabolites and increase the risk for post-weaning diarrhea, but the mechanisms are not yet clarified. Although the use of fermentable carbohydrates to reduce harmful protein-derived metabolites in pigs is well-established, recent studies suggest that the inclusion of fermentable carbohydrates into diets with low protein digestibility or high dietary protein level may not ameliorate all negative effects with regard to epithelial response. Based on the current knowledge, the use of diets with low levels of high-quality protein may help to reduce the risk for intestinal disease in young pigs.

Infectious bovine keratoconjunctivitis (IBK) is a common and important disease of calves. Without effective vaccines, antibiotic therapy is often implemented to minimize the impact of IBK. This review updates a previously published systematic review regarding comparative efficacy for antibiotic treatments of IBK. Available years of Centre for Biosciences and Agriculture International and MEDLINE databases were searched, including non-English results. Also searched were the American Association of Bovine Practitioners and World Buiatrics Congress conference proceedings from 1996 to 2016, reviews since 2013, reference lists from relevant trials, and U.S. Food and Drug Administration New Animal Drug Application summaries. Eligible studies assessed antibiotic treatment of naturally-occurring IBK in calves randomly allocated to group at the individual level. Outcomes of interest were clinical score, healing time, unhealed ulcer risk, and ulcer surface area. A mixed-effects model comparing active drug with placebo was employed for all outcomes. Heterogeneity was assessed visually and using Cochran's Q-test. Thirteen trials assessing nine treatments were included. Compared with placebo, most antibiotic treatments were effective. There was evidence that the treatment effect differed by day of outcome measurement. Visually, the largest differences were observed 7–14 days post-treatment. These results indicate improved IBK healing with many antibiotics and suggest the need for randomized trials comparing different antibiotic treatments.

To effectively mitigate antimicrobial resistance in the agricultural ecosystem, there is an increasing pressure to reduce and eliminate the use of in-feed antibiotics for growth promotion and disease prevention in food animals. However, limiting antibiotic use could compromise animal production efficiency and health. Thus, there is an urgent need to develop effective alternatives to antibiotic growth promoters (AGPs). Increasing evidence has shown that the growth-promoting effect of AGPs was highly correlated with the reduced activity of bile salt hydrolase (BSH), an intestinal bacterial enzyme that has a negative impact on host fat digestion and energy harvest; consistent with this finding, the population of Lactobacillus species, the major intestinal BSH-producer, was significantly reduced in response to AGP use. Thus, BSH is a key mechanistic microbiome target for developing novel alternatives to AGPs. Despite recent significant progress in the characterization of diverse BSH enzymes, research on BSH is still in its infancy. This review is focused on the function of BSH and its significant impacts on host physiology in human beings, laboratory animals and food animals. The gaps in BSH-based translational microbiome research for enhanced animal health are also identified and discussed.

Salmonella enterica is an important food borne pathogen that is frequently carried by swine. Carrier animals pose a food safety risk because they can transmit S. enterica to finished food products in the processing plant or by contamination of the environment. Environmental contamination has become increasingly important as non-animal foods (plant-based) have been implicated as sources of S. enterica. The prevalence of S. enterica in swine is high and yet carrier animals remain healthy. S. enterica has developed a highly sophisticated set of virulence factors that allow it to adapt to host environments and to cause disease. It is assumed that S. enterica also has developed unique ways to maintain itself in animals and yet not cause disease. Here we describe our research to understand persistence. Specifically, data are presented that demonstrates that detection of most carrier animals requires specific stresses that cause S. enterica to be shed from pigs. As well, we describe a phenotypic phase variation process that appears to be linked to the carrier state and a complex set of factors that control phenotypic phase variation. Finally, we describe how the composition of the gut bacterial microbiome may contribute to persistence and at the least how S. enterica might alter the composition of the gut bacterial microbiome.

Intramammary infection (IMI) treatment and prevention at drying-off is one of the leading causes for using antimicrobials on dairy farms. The objective of the current paper is to describe the protocol used for conducting a systematic review of the literature on non-antibiotic strategies that can be used on dairy cows at dry off to treat and prevent IMI. Relevant literature will be identified using a combination of database search strategies and iterative screening of references. To be included in the review, articles will have to: (1) be published after 1969; (2) be written in English, French, or Spanish; (3) use a study design such as a controlled trial, an observational study, or an experimental study conducted in vivo; (4) be conducted on commercial dairy cows; (5) investigate a non-antibiotic intervention used at dry off; and finally, (6) report on a relevant mastitis outcome. Titles and abstracts, then full articles will be reviewed for inclusion. Specific data will be extracted and risk of bias will be assessed for all included articles. The planned systematic review will be the first to colligate, in a coherent whole, studies investigating non-antibiotic strategies for treating and preventing IMI at drying-off.