Aquaculture is the fastest growing food-producing sector, providing an acceptable supplement to and substitute for wild fish and plants. Increased production intensification, particularly in high-value species, involves substantial stress, which, as in other captive livestock species, has resulted in outbreaks of major diseases and related mortalities. Widespread use of antibiotics has led to the development of antibiotic-resistant bacteria and the accumulation of antibiotics in the environment and the flesh of fish. Thus, recently effort has been dedicated to vaccine development. Vaccination in fish is complicated by their aquatic environment. Individual injections are labor-intensive and stressful, since fish have to be removed from the water and anaesthetized. Some vaccines offer a limited duration of protection, and thus booster applications are required. In salmonid species, many commercial vaccines use oil-based adjuvants, resulting in a greatly improved duration of protection. However, oil-based adjuvants have been related to significant growth depression, internal adhesions and injection site melanization, resulting in carcass downgrading. Oral administration to aquatic species is by far the most appealing method of vaccine delivery: there is no handling of the fish, which reduces stress; and administration is easy and suitable for mass immunization. However, few oral vaccines have been commercialized, due in part to the increased quantity of antigen required to provoke an immune response, and the lack of an adequate duration of protection. For effective oral delivery, protective antigens must avoid digestive hydrolysis and be taken up in the hindgut in order to induce an effective protective immune response. Antigen encapsulation technologies have been used to protect antigen; however, such strategies can be expensive and are not always effective. Alternative approaches, currently under development, are discussed.

Disease is a major source of economic loss to the livestock industry. Understanding the role of genetic factors in immune responsiveness and disease resistance should provide new approaches to the control of disease through development of safe synthetic subunit vaccines and breeding for disease resistance. The major histocompatibility complex (MHC) has been an important candidate locus for immune responsiveness studies. However, it is clear that other loci play an important role. Identifying these and quantifying the relative importance of MHC and non-MHC genes should result in new insights into host–pathogen interactions, and information that can be exploited by vaccine designers. The rapidly increasing information available about the bovine genome and the identification of polymorphisms in immune-related genes will offer potential candidates that control immune responses to vaccines. The bovine MHC, BoLA, encodes two distinct isotypes of class II molecules, DR and DQ, and in about half the common haplotypes the DQ genes are duplicated and expressed. DQ molecules are composed of two polymorphic chains whereas DR consists of one polymorphic and one non-polymorphic chain. Although, it is clear that MHC polymorphism is related to immune responsiveness, it is less clear how different allelic and locus products influence the outcome of an immune response in terms of generating protective immunity in outbred animals. A peptide derived from foot-and-mouth disease virus (FMDV) was used as a probe for BoLA class II function. Both DR and DQ are involved in antigen presentation. In an analysis of T-cell clones specific for the peptide, distinct biases to particular restriction elements were observed. In addition inter-haplotype pairings of DQA and DQB molecules produced functional molecules, which greatly increases the numbers of possible restriction elements, compared with the number of genes, particularly in cattle with duplicated DQ genes. In a vaccine trial with several peptides derived from FMDV, BoLA class II DRB3 polymorphisms were correlated with both protection and non-protection. Although variation in immune responsiveness to the FMDV peptide between different individuals is partly explainable by BoLA class II alleles, other genetic factors play an important role. In a quantitative trait locus project, employing a second-generation cross between Charolais and Holstein cattle, significant sire and breed effects were also observed in T-cell, cytokine and antibody responses to the FMDV peptide. These results suggest that both MHC and non-MHC genes play a role in regulating bovine immune traits of relevance to vaccine design. Identifying these genes and quantifying their relative contributions is the subject of further studies.

Mastitis is not only a major cause of economic losses to the dairy industry but also a major problem in ensuring the quality and safety of the milk, associated with high somatic cell counts and residues of antibiotics used for treatment. One innovative approach to protection against mastitis is to stimulate the animal's natural defense mechanisms. Technological advances in immunological research have increased our ability to exploit the immunity of the bovine mammary gland during periods of high susceptibility to disease. The trace element selenium affects the innate and the adaptive immune responses of the mammary gland through cellular and humoral activities. Substantial research has been carried out on the effect of selenium (Se) on the immune function of the mammary gland and subsequent improvement in bovine udder health and mastitis control. Levels higher than current recommendations and Se-yeast can potentially be used to enhance our capacity to modulate the physiological mechanisms of the bovine mammary gland to respond to infection. This article provides an overview of the most recent research in this field.

Today, a few differing sources of selenium (Se), i.e. inorganic, organic, and nano forms of Se, are used as feed supplements for poultry. Published research indicates that nano-Se and organic Se possess comparable efficiency to inorganic Se in increasing GSH-Px activity of plasma and various tissues, but they deposit at higher rates in various tissues. However, there are principal differences in absorption mechanisms, metabolism, and efficiency of these three forms of Se. The aim of this review was to analyze the available literature on the effects of different Se sources and levels in the diet on glutathione peroxidase (GSH-Px) activity, tissue Se distribution and growth performance in poultry. Higher levels of Se increase GSH-Px activity in the body, but this reaches a plateau even if Se concentrations in diet increase further, while the deposition of Se in tissues increases as Se content in diet increases. In addition, many studies have shown the positive effects of adding Se to diet on growth performance in poultry. Optimal Se supplementation is necessary not only for good poultry health but also to ensure and preserve meat quality during storage and to provide human beings with this microelement.

Livestock welfare assessment helps monitor animal health status to maintain productivity, identify injuries and stress, and avoid deterioration. It has also become an important marketing strategy since it increases consumer pressure for a more humane transformation in animal treatment. Common visual welfare practices by professionals and veterinarians may be subjective and cost-prohibitive, requiring trained personnel. Recent advances in remote sensing, computer vision, and artificial intelligence (AI) have helped developing new and emerging technologies for livestock biometrics to extract key physiological parameters associated with animal welfare. This review discusses the livestock farming digital transformation by describing (i) biometric techniques for health and welfare assessment, (ii) livestock identification for traceability and (iii) machine and deep learning application in livestock to address complex problems. This review also includes a critical assessment of these topics and research done so far, proposing future steps for the deployment of AI models in commercial farms. Most studies focused on model development without applications or deployment for the industry. Furthermore, reported biometric methods, accuracy, and machine learning approaches presented some inconsistencies that hinder validation. Therefore, it is required to develop more efficient, non-contact and reliable methods based on AI to assess livestock health, welfare, and productivity.

Avian influenza (AI) virus is one of the most important diseases of the poultry industry around the world. The virus has a broad host range in birds and mammals, although the natural reservoir is wild birds where it typically causes an asymptomatic to mild infection. The virus in poultry can cause a range of clinical diseases and is defined either as low pathogenic AI (LPAI) or highly pathogenic AI (HPAI) depending on the type of disease it causes in chickens. Viruses that replicate primarily on mucosal surfaces and cause mild disease with low mortality are termed LPAI. Viruses that replicate on mucosal surfaces and systemically and cause severe disease with a mortality rate of 75% or greater in experimentally infected chickens are referred to as HPAI. A virus that is highly pathogenic in chickens may infect but result in a completely different disease and replication pattern in other host species. Outbreaks of HPAI have been relatively uncommon around the world in the last 50 years and have had limited spread within a country or region with one major exception, Asian lineage H5N1 that was first identified in 1996. This lineage of virus has spread to over 60 countries and has become endemic in poultry in at least four countries. AI virus also represents a public health threat, with some infected humans having severe disease and with a high case fatality rate. AI remains a difficult disease to control because of the highly infectious nature of the virus and the interface of domestic and wild animals. A better understanding of the disease and its transmission is important for control.

Progress in producing improved vaccines against bacterial diseases of cattle is limited by an incomplete understanding of the pathogenesis of these agents. Our group has been involved in investigations of two members of the family Pasteurellaceae, Mannheimia haemolytica and Haemophilus somnus, which illustrate some of the complexities that must be confronted. Susceptibility to M. haemolytica is greatly increased during active viral respiratory infection, resulting in rapid onset of a severe and even lethal pleuropneumonia. Despite years of investigation, understanding of the mechanisms underlying this viral–bacterial synergism is incomplete. We have investigated the hypothesis that active viral infection increases the susceptibility of bovine leukocytes to the M. haemolytica leukotoxin by increasing the expression of or activating the β2 integrin CD11a/CD18 (LFA-1) on the leukocyte surface. In vitro exposure to proinflammatory cytokines (i.e. interleukin-1β, tumor necrosis factor-α and interferon-γ) increases LFA-1 expression on bovine leukocytes, which in turn correlates with increased binding and responsiveness to the leukotoxin. Alveolar macrophages and peripheral blood leukocytes from cattle with active bovine herpesvirus-1 (BVH-1) infection are more susceptible to the lethal effects of the leukotoxin ex vivo than leukocytes from uninfected cattle. Likewise, in vitro incubation of bovine leukocytes with bovine herpesvirus 1 (BHV-1) potentiates LFA-1 expression and makes the cells more responsive to leukotoxin. A striking characteristic of H. somnus infection is its propensity to cause vasculitis. We have shown that H. somnus and its lipo-oligosaccharide (LOS) trigger caspase activation and apoptosis in bovine endothelial cells in vitro. This effect is associated with the production of reactive oxygen and nitrogen intermediates, and is amplified in the presence of platelets. The adverse effects of H. somnus LOS are mediated in part by activation of endothelial cell purinergic receptors such as P2X7. Further dissection of the pathways that lead to endothelial cell damage in response to H. somnus might help in the development of new preventive or therapeutic regimens. A more thorough understanding of M. haemolytica and H. somnus virulence factors and their interactions with the host might identify new targets for prevention of bovine respiratory disease.

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.

The close relationship between gastrointestinal (GI) microbiota and its host has an impact on the health status of an animal that reaches beyond the GI tract. A balanced microbiome stimulates the immune system, aids in the competitive exclusion of transient pathogens and provides nutritional benefits to the host. With recent rapid advances in high-throughput sequencing technology, molecular approaches have become the routinely used tools for ecological studies of the feline microbiome, and have revealed a highly diverse and complex intestinal ecosystem in the feline GI tract. The major bacterial groups are similar to those found in other mammals, with Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria constituting more than 99% of intestinal microbiota. Several nutritional studies have demonstrated that the feline microbiota can be modulated by the amount of soluble fibers (i.e., prebiotics) and macronutrients (i.e., protein content) in the diet. Initial clinical studies have suggested the presence of a dysbiosis in feline inflammatory bowel disease (IBD). Recently, metagenomic approaches have attempted to characterize the microbial gene pool. However, more studies are needed to describe the phylogenetic and functional changes in the intestinal microbiome in disease states and in response to environmental and dietary modulations. This paper reviews recent studies cataloging the microbial phylotypes in the GI tract of cats.

Ethnomedicine is an integral part of traditional medical practices in many countries of the developing world. A large proportion of the population uses this form of treatment for primary health care and for the treatment of ailments in their livestock. Livestock is a major asset for resource-poor smallholder farmers and pastoralists throughout the world and internal parasites are recognized by these communities as having an impact on livestock health. Parasitic infections are among those infections that traditional healers confidently treat and against which an enormous variety of remedies exist. Many of these are based on the use of plant preparations. Although various methods have been used for the validation of traditional phytomedical preparations, there is a lack of standardization of these procedures. The present study is aimed at providing an overview of ethnoveterinary deworming preparations, the various methods that have been used in their validation and the future prospects for their use against helminth parasites of ruminant livestock in developing countries, with an emphasis on nematode parasites. Recommendations are made on the procedures that should be followed to conduct in vivo and in vitro assays. Fostering better interaction between traditional healers and scientists is advocated to prevent harmful overexploitation, both of local knowledge and of plant species that may have effects against nematode parasites.

Enterohemorrhagic Escherichia coli, particularly the O157(:H7) serogroup, has become a worldwide public health concern. Since cattle feces are often implicated as the source of E. coli O157 in human infections, considerable resources have been devoted to defining the epidemiology and ecology of E. coli O157 in cattle environments so that control might begin at the farm level. Diagnostic limitations and the complexity of often interrelated microbial, animal, herd, environmental and production factors have hindered the determination of the epidemiology, ecology and subsequent farm-level control of E. coli O157. The widespread distribution of E. coli O157, the transitory nature of fecal shedding, multiple potential environmental sources, lack of species specificity, and age-, feed- and time-related differences in cattle prevalence are documented. However, the significance and/or role of these factors in the epidemiology and ecology of E. coli O157 is still unclear. Cattle are a major source of E. coli O157, but it may be simplistic to believe that most herds are relatively closed systems with small percentages of cattle serving as true reservoirs. Practical on-farm control may require explicit definitions of the seemingly complex system(s) and the microbial, animal, herd, environmental and production factors involved in the multiplication, maintenance and transmission of E. coli O157.

The pleuromutilins are the only antimicrobial agents with sufficient minimum inhibitory concentration (MIC) values left to treat swine dysentery in Sweden. Other antimicrobials are either not approved for use against swine dysentery or only partly active against Brachyspira hyodysenteriae. To date, in Sweden two pleuromutilins, tiamulin and valnemulin, are authorized for use in pigs. This study includes a comparison between MICs of tiamulin and valnemulin for Swedish field isolates of B. hyodysenteriae, as determined by broth dilution. For different isolates the MIC of tiamulin was between 0 and 8 times higher than that of valnemulin. No resistance to pleuromutilins was recorded (tiamulin MIC range 0.031–2 μg/ml, valnemulin MIC range ≤0.016–1 μg/ml). In vitro development of tiamulin resistance was also studied. Two B. hyodysenteriae and two B. pilosicoli strains became resistant to tiamulin following reiterated passages on agar containing tiamulin in increasing concentrations. The resistance emerged slowly and three of the strains that went through more than 60 passages increased their tiamulin MICs from 0.031–0.25 to more than 128 μg/ml. The tiamulin MIC for one B. hyodysenteriaestrain that went through 29 passages increased from 0.0125 to 4 μg/ml. One B. pilosicoli strain developed cross-resistance to valnemulin; the MIC increased from 0.25 to more than 64 μg/ml. The valnemulin MIC for one B. hyodysenteriae strain increased from 0.031 μg/ml to 32 μg/ml. Valnemulin MIC was not determined for the B. hyodysenteriae strain that only went through 29 passages. The valnemulin MIC of the other B. pilosicoli strain increased from 0.031 to 4 μg/ml.

Mannheimia haemolytica is the major cause of severe pneumonia in bovine respiratory disease (BRD). Early M. haemolytica bacterins were either ineffective or even enhanced disease in vaccinated cattle, which led to studies of the bacterium's virulence factors and potential immunogens to determine ways to improve vaccines. Studies have focused on the capsule, lipopolysaccharide, various adhesins, extracellular enzymes, outer membrane proteins, and leukotoxin (LKT) resulting in a strong database for understanding immune responses to the bacterium and production of more efficacious vaccines. The importance of immunity to LKT and to surface antigens in stimulating immunity led to studies of individual native or recombinant antigens, bacterial extracts, live-attenuated or mutant organisms, culture supernatants, combined bacterin-toxoids, outer membrane vesicles, and bacterial ghosts. Efficacy of several of these potential vaccines can be shown following experimental M. haemolytica challenge; however, efficacy in field trials is harder to determine due to the complexity of factors and etiologic agents involved in naturally occurring BRD. Studies of potential vaccines have led current commercial vaccines, which are composed primarily of culture supernatant, bacterin-toxoid, or live mutant bacteria. Several of those can be augmented experimentally by addition of recombinant LKT or outer membrane proteins.

Loop-mediated isothermal amplification (LAMP) is a simple, powerful state-of-the-art gene amplification technique used for the rapid diagnosis and early detection of microbial diseases. Many LAMP assays have been developed and validated for important epizootic diseases of livestock. We review the LAMP assays that have been developed for the detection of 18 viruses deemed notifiable of ruminants, swine and poultry by the World Organization for Animal Health (OIE). LAMP provides a fast (the assay often takes less than an hour), low cost, highly sensitive, highly specific and less laborious alternative to detect infectious disease agents. The LAMP procedure can be completed under isothermal conditions so thermocyclers are not needed. The ease of use of the LAMP assay allows adaptability to field conditions and works well in developing countries with resource-limited laboratories. However, this technology is still underutilized in the field of veterinary diagnostics despite its huge capabilities.

Persistent or difficult-to-treat Staphylococcus aureus infections in animals and humans may be related to small colony variants (SCVs) that can hide inside host cells and modulate host defenses. S. aureus SCVs have gained much attention in human medicine but have been underestimated and overlooked in veterinary medicine. Recently, an SCV isolated from a dairy cow with a history of chronic mastitis was shown to possess similar phenotypic and transcriptomic properties to those of human SCVs. SCVs form small, colorless, non-hemolytic colonies after 48 h, are only slowly coagulase positive, fail to ferment mannitol, and can revert to the parental phenotype. The phenotype of SCVs is mostly related to alterations in hemin and/or menadione biosynthesis or to thymidine deficiency. Transcriptomic analysis of SCVs shows up-regulation of genes involved in glycolytic and arginine–deiminase pathways, capsular biosynthesis; increased sigma B activity; and down-regulation of genes for α-hemolysin, coagulase and effector molecule RNA III of the global virulence regulator Agr. Similar results are reported at the protein level. SCVs are less virulent but successful persisters in infection models. SCVs persist longer and at higher numbers within non-phagocytes than do their parents. SCVs survive within spacious vacuoles up to 24 h within cultured bovine mammary epithelial cells, likely due to up-regulation of protective mechanisms that counteract the lethal acidic environment of the phagolysosome. Persistence of SCVs within host cells may explain failures in antimicrobial therapy and vaccinations.

In the past decade, the pandemics of highly pathogenic avian influenza H5N1 and the novel H1N1 influenza have both illustrated the potential of influenza viruses to rapidly emerge and spread widely in animals and people. Since both of these viruses are zoonotic, these pandemics have been the driving force behind a renewed commitment by the medical and veterinary professions to practice One World, One Health for the control of infectious diseases. The discovery in 2004 that an equine origin H3N8 influenza virus was the cause of an extensive epidemic of respiratory disease in dogs in the USA came as a surprise; at that time dogs were thought to be refractory to infection with influenza viruses. In 2007, a second emerging canine influenza was confirmed in Korea, but this time the causal virus was an H3N2 avian influenza virus. This review focuses on recent events associated with equine and canine influenza viruses. While these viruses do not appear to be zoonotic, the close association between humans and dogs, and to a lesser extent horses, demands that we develop better surveillance and control strategies for emerging diseases in companion animals within the context of One World, One Health.

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.

Innate immunity provides frontline antiviral protection and bridges adaptive immunity against virus infections. However, viruses can evade innate immune surveillance potentially causing chronic infections that may lead to pandemic diseases. Porcine reproductive and respiratory syndrome virus (PRRSV) is an example of an animal virus that has developed diverse mechanisms to evade porcine antiviral immune responses. Two decades after its discovery, PRRSV is still one of the most globally devastating viruses threatening the swine industry. In this review, we discuss the molecular and cellular composition of the mammalian innate antiviral immune system with emphasis on the porcine system. In particular, we focus on the interaction between PRRSV and porcine innate immunity at cellular and molecular levels. Strategies for targeting innate immune components and other host metabolic factors to induce ideal anti-PRRSV protection are also discussed.

Necrotic enteritis (NE), caused by Clostridium perfringens (CP), is one of the most common of poultry diseases, causing huge economic losses to the poultry industry. This review provides an overview of the pathogenesis of NE in chickens and of the interaction of CP with the host immune system. The roles of management, nutrition, probiotics, and vaccination in reducing the incidence and severity of NE in poultry flocks are also discussed.

The worldwide poultry industry provides a substantial proportion of the nutritional requirement of the human population. To keep pace with the increasing demand for the high-quality, low-cost protein source that poultry provides, intensive rearing practices have been developed within the past few decades. For example, chickens are housed routinely in crowded environments under adverse conditions, and genetic strains have been selected for rapid growth, high protein-to-fat content and superior egg-laying characteristics. A major negative consequence of these practices has been an increase in the incidence of diseases. Enteric diseases in particular have emerged as a major problem threatening the future viability of the poultry industry. A variety of methods have been used to combat avian diseases in the commercial setting, including improved farm management practices, the use of antibiotic drugs, the selection of disease-resistant strains of chickens, and the manipulation of the chicken’s immune system. In the latter category, the development of vaccines against the major avian diseases has become a priority in the poultry industry. This review will highlight recent progress in vaccine development against three major avian enteric pathogens: Eimeria, Cryptosporidium and Salmonella.