Sheep and goats occupy a premier place in the livestock industry and contribute significantly to the world economy. Their populations are threatened by a number of health hazards, among the most notable of which are goat pox and sheep pox. These diseases inflict substantial losses in terms of reduced productivity and lower quality of wool and leather. They pose a major obstacle to the intensive rearing of sheep and goats and considerably hamper international trade. A comprehensive knowledge of goat pox and sheep pox would help in the diagnosis, prevention and control as well as the management of these diseases in a proper and effective manner. Although the two diseases are easily identified from the clinical signs and host species affected, laboratory tests are needed for confirmation. A battery of simple but highly efficient diagnostic methods and reagents is available for goat pox and sheep pox. However, the best way to control these diseases is the prophylactic immunization of all susceptible animals with a potent and efficacious vaccine, especially in areas where these diseases are endemic.

Mastitis is among the most common and challenging diseases of dairy animals. It is an inflammation of udder tissues due to physical damage, chemical irritation, or infection caused by certain pathogens. Bovine mastitis has been known for ages, but its complex etiology and multi-factorial nature make it difficult to control. Mastitis may have a negative impact on human health by inducing antibiotic-resistant pathogens that may spread, which is threatening. Researchers are continuously struggling to devise suitable methods for mastitis control. Management strategies are mainly focused on disease prevention by farm management which includes proper hygiene, trained staff to monitor minor changes in the udder or milk, and better diagnostic and treatment methods. New technologies which have the potential to unravel this complicated disease include improved diagnostic tools, based on advanced genomics or proteomics, prevention, based on vaccines and immune modulators, and metabolic products of probiotics such as bacteriocins and gene therapy.

The equine intestinal tract contains a complex microbial population (microbiota) that plays an important role in health and disease. Despite the undeniable importance of a ‘normal’ microbiota, understanding of the composition and function of this population is currently limited. As methods to characterize the microbiota and its genetic makeup (the microbiome) have evolved, the composition and complexity of this population are starting to be revealed. As is befitting a hindgut fermenter, members of the Firmicutes phylum appear to predominate, yet there are significant populations of numerous other phyla. The microbiome appears to be profoundly altered in certain disease states, and better understanding of these alterations may offer hope for novel preventive and therapeutic measures. The development and increasing availability of next generation sequencing and bioinformatics methods offer a revolution in microbiome evaluation and it is likely that significant advances will be made in the near future. Yet, proper use of these methods requires further study of basic aspects such as optimal testing protocols, the relationship of the fecal microbiome to more proximal locations where disease occurs, normal intra- and inter-horse variation, seasonal variation, and similar factors.

Porcine circovirus type 2 (PCV2) is a small, non-enveloped, circular, single-stranded DNA virus of economic importance in the swine industry worldwide. Based on the sequence analyses of PCV2 strains, isolates can be divided into five subtypes (PCV2a–e). PCV2 is an ubiquitous virus based on serological and viremia data from countries worldwide. In addition, PCV2 DNA was discovered in archived samples prior to the first recognition of clinical disease. Recently, a worldwide shift in PCV2 subtype from PCV2a to PCV2b occurred. PCV2 DNA can be detected in fecal, nasal, oral and tonsillar swabs as well as in urine and feces from both naturally and experimentally infected pigs. PCV2 DNA can be detected early in the infectious process and persists for extended periods of time. The effectiveness of disinfectants for reducing PCV2 in vitro is variable and PCV2 is very stable in the pig environment. Limited data exist on the horizontal transmission of PCV2. Direct transmission of PCV2 between experimentally or naturally infected animals and naïve animals has been documented and the incorporation of clinical or subclinically infected animals into a population represents a risk to the herd. Indirect transmission through the oral, aerosol or vaccine routes is likely a lesser risk for the transmission of PCV2 in most swine populations but may be worth evaluating in high heath herds. The objective of this review was to discuss data on the epidemiology and horizontal transmission of PCV2.

Pork production began to flourish in the USA after the practice of finishing pigs on corn was popularized in the late 1600s. By the 1840s, there were 35 million pigs and 20 million people in the USA and Cincinnati was the world's largest pork market. Between 1890 and the present, the total number of pigs in the USA has remained at 50–60 million, but dramatic changes in swine husbandry over the course of the 20th century have metamorphosed pig production from small, extensive (outdoor), labor-dependent enterprises into large, intensive (indoor), capital-dependent, production systems. This development has led to debate concerning the impact of swine production on animal/human health, the environment, and the welfare of the animals under our care. In a very tangible way, the future of pork production depends on effectively addressing the public's concerns regarding animal welfare and health. Here, we review basic sensory and behavioral aspects of swine with the objective of reaching a better understanding of pig behavior and pig welfare. The premise of this discussion is that safeguarding animal welfare and health is good for pigs, pork producers and the animal-conscious public.

Lipopolysaccharide on the surface of Escherichia coli constitutes the O antigens which are important virulence factors that are targets of both the innate and adaptive immune systems and play a major role in host–pathogen interactions. O antigens are responsible for antigenic specificity of the strain and determine the O serogroup. The designation of O serogroups is important for classifying E. coli strains, for epidemiological studies, in tracing the source of outbreaks of gastrointestinal or other illness, and for linking the source to the infection. For conventional serogroup identification, serotyping by agglutination reactions against antisera developed for each of the O serogroups has been used. In the last decade, many O-antigen gene clusters that encode for the enzymes responsible for the synthesis of the variable oligosaccharide region on the surface of the bacteria have been sequenced and characterized. Unique gene sequences within the O-antigen gene clusters have been targeted for identification and detection of many O groups using the polymerase chain reaction and microarrays. This review summarizes current knowledge on the DNA sequences of the O-antigen gene clusters, genetic-based methods for O-group determination and detection of pathogenic E. coli based on O-antigen and virulence gene detection, and provides perspectives on future developments in the field.

Many bursate nematodes are of major importance to animal health. Animals are often parasitized by multiple species that differ in their prevalence, relative abundance and/or pathogenicity. Implementation of effective management strategies for these parasites requires reliable methods for their detection in hosts, identification to the species level and measurement of intensity of infection. One major problem is the difficulty of accurately identifying and distinguishing many species of bursate nematode because of the remarkable morphological similarity of their eggs and larvae. The inability to identify, with confidence, individual nematodes (irrespective of their life-cycle stage) to the species level by morphological methods has often led to a search for species-specific genetic markers. Studies over the past 15 years have shown that sequences of the internal transcribed spacers of ribosomal DNA provide useful genetic markers, providing the basis for the development of PCR-based diagnostic tools. Such molecular methods represent powerful tools for studying the systematics, epidemiology and ecology of bursate nematodes and, importantly, for the specific diagnosis of infections in animals and humans, thus contributing to improved control and prevention strategies for these parasites.

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.

This paper presents an overview of intestinal spirochete infections of chickens. It focuses particularly on studies in Australia, where recent surveys of 136 layer and broiler breeder flocks have revealed a high rate of infection (>40%) with intestinal spirochetes. Infection was not detected in broiler flocks. Approximately 50% of isolates from infected flocks were Brachyspira (Serpulina) intermedia or B. pilosicoli, with the other isolates being B. innocens, B. murdochii or the proposed species ‘B. pulli’. No isolates of B. alvinipulli were found. Intestinal spirochetes were significantly associated with wet litter problems and/or reduced egg production. Experimental infection of point-of-lay birds with either B. intermedia or B. pilosicoli caused reduced egg production, and, with B. intermedia, a significant increase in fecal moisture content. Infection with B. innocens caused no significant changes. In-water treatment of a flock with a mixed spirochete infection using lincospectin resulted in a slimy diarrhea lasting for 2–3 weeks, followed by absence of spirochetes for 3 months. Birds treated with tiamulin remained healthy, and had a reduced level of infection with intestinal spirochetes (30%) for 3 months. Trials are under way to test the efficacy of antimicrobials in point-of-lay chickens experimentally infected with either B. intermedia or B. pilosicoli.

Classical swine fever (CSF) is endemic in large parts of the world and it is a major threat to the pig industry in general. Vaccination and stamping out have been the most successful tools for the control and elimination of the disease. The systematic use of modified live vaccines (MLV), which are very efficacious and safe, has often preceded the elimination of CSF from regions or countries. Oral vaccination using MLV is a powerful tool for the elimination of CSF from wild boar populations. Bovine virus diarrhea (BVD) is endemic in bovine populations worldwide and programs for its control are only slowly gaining ground. With two genotypes BVD virus (BVDV) is genetically more diverse than CSF virus (CSFV). BVDV crosses the placenta of pregnant cattle resulting in the birth of persistently infected (PI) calves. PI animals shed enormous amounts of virus for the rest of their lives and they are the reservoir for the spread of BVDV in cattle populations. They are the main reason for the failure of conventional control strategies based on vaccination only. In Europe two different approaches for the successful control of BVD are being used: Elimination of PI animals without or with the optional use of vaccines, respectively.

Many articles have summarized the changing epidemiology of Clostridium difficile infections (CDI) in humans, but the emerging presence of C. difficile in foods and animals and possible measures to reduce human exposure to this important pathogen have been infrequently addressed. CDIs have traditionally been assumed to be restricted to health-care settings. However, recent molecular studies indicate that this is no longer the case; animals and foods might be involved in the changing epidemiology of CDIs in humans; and genome sequencing is disproving person-to-person transmission in hospitals. Although zoonotic and foodborne transmission have not been confirmed, it is evident that susceptible people can be inadvertently exposed to C. difficile from foods, animals, or their environment. Strains of epidemic clones present in humans are common in companion and food animals, raw meats, poultry products, vegetables, and ready-to-eat foods, including salads. In order to develop science-based prevention strategies, it is critical to understand how C. difficile reaches foods and humans. This review contextualizes the current understanding of CDIs in humans, animals, and foods. Based on available information, we propose a list of educational measures that could reduce the exposure of susceptible people to C. difficile. Enhanced educational efforts and behavior change targeting medical and non-medical personnel are needed.

Bovine respiratory disease (BRD) is a worldwide health concern and is the number one disease of stocker, backgrounder, and feedlot cattle in North America. In feedlots in the USA, BRD accounts for 70–80% of all feedlot morbidity and 40–50% of all mortality. In 2011, the US Department of Agriculture's National Animal Health Monitoring System conducted a feedlot study that showed 16.2% of all feedlot cattle were treated for BRD. It is universally accepted that this number is distressingly high and that our industry has the tools available to reduce the incidence of BRD.

The major surface protein (MSP) 1a of the ehrlichial cattle pathogen Anaplasma marginale, encoded by the single-copy gene msp1α, has been shown to have a neutralization-sensitive epitope and to be an adhesin for bovine erythrocytes and tick cells. msp1α has been found to be a stable genetic marker for the identification of geographic isolates of A. marginale throughout development in acutely and persistently infected cattle and in ticks. The molecular weight of MSP1a varies among geographic isolates of A. marginale because of a varying number of tandemly repeated peptides of 28–29 amino acids. Variation in the sequence of the tandem repeats occurs within and among isolates, and may have resulted from evolutionary pressures exerted by ligand–receptor and host–parasite interactions. These repeated sequences include markers for tick transmissibility that may be important in the identification of ehrlichial pathogens because they may influence control strategies and the design of subunit vaccines.

Porcine circovirus type 2 (PCV2) causes great economic losses in growing pigs and there are several reviews on disease manifestations and lesions associated with PCV2 in growing pigs. Reproductive failure in breeding herds, predominately associated with increased numbers of mummies and non-viable piglets at parturition, is one of the disease manifestations of PCV2 infection. Boars shed low amounts of infectious PCV2 in semen for extended time periods, and vertical transmission of PCV2 to fetuses during PCV2 viremia of the dam has been experimentally confirmed. However, intrauterine-infected piglets often are clinically normal. Nevertheless, pigs infected with PCV2 by the intrauterine route can be born viremic, possibly contributing to horizontal spread of PCV2 within the breeding herd and into the nursery. Shedding of PCV2 in semen and prevalence of intrauterine-infected piglets can both be greatly reduced by PCV2 vaccination well ahead of expected PCV2 exposure. This review is a discussion on current knowledge on the effects of PCV2 infection in the dam and in in utero fetuses, including clinical signs, lesions, diagnosis and prevention through vaccination. Infection of boars with PCV2, the potential for PCV2 transmission via semen and prevention of PCV2 shedding are also discussed.

Campylobacter is a major foodborne pathogen and is commonly present in food producing animals. This pathogenic organism is highly adaptable and has become increasingly resistant to various antibiotics. Recently, both the Centers for Disease Control and Prevention and the World Health Organization have designated antibiotic-resistant Campylobacter as a serious threat to public health. For the past decade, multiple mechanisms conferring resistance to clinically important antibiotics have been described in Campylobacter, and new resistance mechanisms constantly emerge in the pathogen. Some of the recent examples include the erm(B) gene conferring macrolide resistance, the cfr(C) genes mediating resistance to florfenicol and other antimicrobials, and a functionally enhanced variant of the multidrug resistance efflux pump, CmeABC. The continued emergence of new resistance mechanisms illustrates the extraordinary adaptability of Campylobacter to antibiotic selection pressure and demonstrate the need for innovative strategies to control antibiotic-resistant Campylobacter. In this review, we will briefly summarize the trends of antibiotic resistance in Campylobacter and discuss the mechanisms of resistance to antibiotics used for animal production and important for clinical therapy in humans. A special emphasis will be given to the newly discovered antibiotic resistance.

Gastrointestinal (GI) microbes have important roles in the nutritional, immunological, and physiologic processes of the host. Traditional cultivation techniques have revealed bacterial density ranges from 104 to 105 colony forming units (CFU)/g in the stomach, from 105 to 107 CFU/g in the small intestine, and from 109 to 1011 CFU/g in the colon of healthy dogs. As a small number of bacterial species can be grown and studied in culture, however, progress was limited until the recent emergence of DNA-based techniques. In recent years, DNA sequencing technology and bioinformatics have allowed for better phylogenetic and functional/metabolic characterization of the canine gut microbiome. Predominant phyla include Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. Studies using 16S ribosomal RNA (rRNA) gene pyrosequencing have demonstrated spatial differences along the GI tract and among microbes adhered to the GI mucosa compared to those in intestinal contents or feces. Similar to humans, GI microbiome dysbiosis is common in canine GI diseases such as chronic diarrhea and inflammatory bowel diseases. DNA-based assays have also identified key pathogens contributing to such conditions, including various Clostridium, Campylobacter, Salmonella, and Escherichia spp. Moreover, nutritionists have applied DNA-based techniques to study the effects of dietary interventions such as dietary fiber, prebiotics, and probiotics on the canine GI microbiome and associated health indices. Despite recent advances in the field, the canine GI microbiome is far from being fully characterized and a deeper characterization of the phylogenetic and functional/metabolic capacity of the GI microbiome in health and disease is needed. This paper provides an overview of recent studies performed to characterize the canine GI microbiome.

Although frequentist approaches to prevalence estimation are simple to apply, there are circumstances where it is difficult to satisfy assumptions of asymptotic normality and nonsensical point estimates (greater than 1 or less than 0) may result. This is particularly true when sample sizes are small, test prevalences are low and imperfect sensitivity and specificity of diagnostic tests need to be incorporated into calculations of true prevalence. Bayesian approaches offer several advantages including direct computation of range-respecting interval estimates (e.g. intervals between 0 and 1 for prevalence) without the requirement of transformations or large-sample approximations. They also allow direct probabilistic interpretation, and the flexibility to model in a straightforward manner the probability of zero prevalence. In this review, we present frequentist and Bayesian methods for animal- and herd-level true prevalence estimation based on individual and pooled samples. We provide statistical methods for detecting differences between population prevalence and frequentist methods for sample size and power calculations. All examples are motivated using Mycobacterium avium subspecies paratuberculosis infection and we provide WinBUGS code for all examples of Bayesian estimation.

Infections with Bovine viral diarrhea virus (BVDV) are not limited to cattle, but may be detected in various species in the mammalian order Artiodactyla. Despite epidemiological evidence of BVDV infections in species other than cattle, current knowledge regarding the impact of BVDV on heterologous species is incomplete. In heterologous hosts, BVDV infections with clinical signs analogous to those in cattle have been described and include disease of multiple organ systems, most notably the reproductive tract and immune system. Clinical infections may negatively impact the health and well-being of heterologous species, including camelids and captive and free-ranging wildlife. Of additional importance are BVDV infections in small ruminants and swine where difficulties arise in laboratory testing for Border disease virus (BDV) and Classical swine fever virus (CSFV), respectively. Pestiviruses are antigenically closely related and their cross-reactivity requires additional efforts in virological testing. In cattle populations, persistently infected animals are considered the main source of BVDV transmission. This phenomenon has also been detected in heterologous species, which could facilitate reservoirs for BVDV that may be of great importance where control programs are in progress. This review summarizes the current epidemiological and clinical knowledge on heterologous BVDV infections and discusses their implications.

Commensal microflora play many roles within the mammalian gastrointestinal tract (GIT) that benefit host physiology by way of direct or indirect interactions with mucosal surfaces. Commensal flora comprises members across all microbial phyla, although predominantly bacterial, with population dynamics varying with host species, genotype, and environmental factors. Little is known, however, about the complex mechanisms regulating host–commensal interactions that underlie this mutually beneficial relationship and how alterations in the microbiome may influence host development and susceptibility to infection. Research into the gut microbiome has intensified as it becomes increasingly evident that symbiont–host interactions have a significant impact on mucosal immunity and health. Furthermore, evidence that microbial populations vary significantly throughout the GIT suggest that regional differences in the microbiome may also influence immune function within distinct compartments of the GIT. Postpartum colonization of the GIT has been shown to have a direct effect on mucosal immune system development, but information is limited regarding regional effects of the microbiome on the development, activation, and maturation of the mucosal immune system. This review discusses factors influencing the colonization and establishment of the microbiome throughout the GIT of newborn calves and the evidence that regional differences in the microbiome influence mucosal immune system development and maturation. The implications of this complex interaction are also discussed in terms of possible effects on responses to enteric pathogens and vaccines.

The pathogenesis of bovine respiratory disease (BRD) is determined by a complex interaction of environmental, infectious, and host factors. Environment trends could impact feedlot cattle by increasing their level of stress. The polymicrobial nature of BRD produces synergies between infectious agents that can alter pathogenesis. However, the nature of the host response to these environmental and infectious challenges largely determines the characteristics of the progression and outcome of BRD.