Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the ‘rare biosphere’ in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.

Use of antimicrobial approaches at drying-off for preventing new intramammary infections (IMI) during the dry period in dairy cows could be replaced by non-antimicrobial approaches. Such approaches would be of interest not only for organic but also for conventional dairy producers. The objective of the current review was to quantify the effect of non-antimicrobial internal teat sealant (ITS)-based approaches at drying-off for treating and preventing IMI, when compared with no treatment or with an antimicrobial-based approach. The protocol for this review was published before initiating the review. A total of 18 trials from 16 articles could be used to investigate the effect of an ITS-based approach. With the available results, we conclude with a high level of confidence that non-antimicrobial ITS-based dry-off approaches are efficient for preventing new IMI during the dry period when compared with no treatment, and would reduce risk of new IMI by 52%. Moreover, we are relatively confident that a bismuth subnitrate-based ITS performed better than an antimicrobial for preventing new IMI during the dry period (a risk reduction of 23%). Similarly, we are relatively confident that an ITS-based approach would only slightly or not at all reduce the prevalence of IMI at calving compared with untreated quarters.

Infection of pregnant cows with noncytopathic (ncp) bovine viral diarrhea virus (BVDV) induces rapid innate and adaptive immune responses, resulting in clearance of the virus in less than 3 weeks. Seven to 14 days after inoculation of the cow, ncpBVDV crosses the placenta and induces a fetal viremia. Establishment of persistent infection with ncpBVDV in the fetus has been attributed to the inability to mount an immune response before 90–150 days of gestational age. The result is ‘immune tolerance’, persistent viral replication and shedding of ncpBVDV. In contrast, we describe the chronic upregulation of fetal Type I interferon (IFN) pathway genes and the induction of IFN-γ pathways in fetuses of cows infected on day 75 of gestation. Persistently infected (PI) fetal IFN-γ concentrations also increased at day 97 at the peak of fetal viremia and IFN-γ mRNA was significantly elevated in fetal thymus, liver and spleen 14–22 days post maternal inoculation. PI fetuses respond to ncpBVDV infection through induction of Type I IFN and IFN-γ activated genes leading to a reduction in ncpBVDV titer. We hypothesize that fetal infection with BVDV persists because of impaired induction of IFN-γ in the face of activated Type I IFN responses. Clarification of the mechanisms involved in the IFN-associated pathways during BVDV fetal infection may lead to better detection methods, antiviral compounds and selection of genetically resistant breeding animals.

East and Southeast Asia are important pig- and poultry-producing areas, where the majority of production takes place on small-scale farms with low biosecurity levels. This systematic review synthesizes data on swine influenza virology, serology and epidemiology in East and Southeast Asia. A total of 77 research articles, literature reviews and conference papers were selected and analyzed from 510 references retrieved from PubMed and ISI Web of KnowledgeSM. The number of published articles increased in the last 3 years, which may be attributed to improvement in monitoring and/or a better promotion of surveillance data. Nevertheless, large inequalities in surveillance and research among countries are underlined. Virological results represent the largest part of published data, while the serological and epidemiological features of swine influenza in East and Southeast Asia remain poorly described. The literature shows that there have been several emergences of swine influenza in the region, and also considerable evidence of multiple introductions of North American and avian-like European strains. Furthermore, several avian-origin strains are isolated from pigs, including H5 and H9 subtypes. However, their low seroprevalence in swine also shows that pigs remain poorly infected by these subtypes. We conclude that sero-epidemioligical investigations have been neglected, and that they may help to improve virological surveillance. Inter- and intra-continental surveillance of gene flows will benefit the region. Greater investment is needed in swine influenza surveillance, to improve our knowledge of circulating strains as well as the epidemiology and disease burden in the region.

During the first half of the twentieth century, widespread regulatory efforts to control cattle brucellosis due to Brucella abortus in the Union of Soviet Socialist Republics were essentially non-existent, and control was limited to selective test and slaughter of serologic agglutination reactors. By the 1950s, 2–3 million cattle were being vaccinated annually with the strain 19 vaccine, but because this vaccine induced strong, long-term titers on agglutination tests that interfered with identification of cattle infected with field strains of B. abortus, its use in cattle was discontinued in 1970. Soviet scientists then began a comprehensive program of research to identify vaccines with high immunogenicity, weak responses on agglutination tests and low pathogenicity in humans, as a foundation for widespread control of cattle brucellosis. While several new vaccines that induced weak or no responses on serologic agglutination tests were identified by experiments in guinea pigs and cattle, a large body of experimental and field studies suggested that the smooth–rough strain SR82 vaccine combined the desired weak agglutination test responses with comparatively higher efficacy against brucellosis. In 1974, prior to widespread use of strain SR82 vaccine, over 5300 cattle farms across the Russian Federation were known to be infected with B. abortus. By January 2008, only 68 cattle farms in 18 regions were known to be infected with B. abortus, and strain SR82 continues to be the most widely and successfully used vaccine in many regions of the Russian Federation.

Fel-O-Vax FIV is an inactivated virus vaccine designed as an aid in the prevention of infection of cats, 8 weeks or older, by feline immunodeficiency virus (FIV). It contains two genetically distinct FIV strains. The efficacy of this vaccine was demonstrated in a vaccination–challenge study designed to meet various regulatory requirements for registering the vaccine. Eight-week-old kittens were vaccinated with an immunogenicity vaccine which contained minimal release levels of FIV antigens formulated with a proprietary adjuvant system. Twelve months later, all vaccinates and controls were challenged with a heterologous FIV strain. Following the vigorous challenge exposure, cats were monitored for FIV viremia. It was found that 16% of the vaccinated cats developed viremia while 90% of the controls became persistently infected with FIV, which demonstrated that the vaccine was efficacious and the protective immunity lasted for at least 12 months. The safety of the vaccine was demonstrated by a field safety trial in which only 22 mild reactions of short duration were observed following administering 2051 doses of two pre-licensing serials of Fel-O-Vax FIV to cats of various breeds, ages and vaccination histories. Thus, Fel-O-Vax FIV is safe and efficacious for the prevention of FIV infection in cats.

Brachyspira spp. were isolated from 21 of 32 sampled dogs (66%) in a colony of Swedish beagle dogs with a history of diarrhea and from 3 of 17 Swedish pet dogs (17%) with diarrhea. All Swedish isolates were weakly β-hemolytic and gave a negative indole reaction. Eighty-eight percent showed negative α-galactosidase and hippurate reactions, but a positive β-glucosidase reaction. Two isolates were hippurate positive with a negative β-glucosidase reaction. One additional German isolate diverged by showing a positive indole reaction in combination with a positive hippurate reaction. Sequencing of 16S rDNA indicated that the hippurate-positive isolates belonged to the species Brachyspira pilosicoli. Four representative isolates were examined using pulsed-field gel electrophoresis (PFGE) and compared with six reference strains and five porcine isolates of Brachyspira spp. The canine isolates clustered together in the PFGE analysis. Necropsy examination of a culture-positive B. pilosicoli colony-raised beagle dog revealed macro- and microscopical lesions of colitis with numerous spiral-shaped bacteria in the lumens of the crypts, in goblet cells and within the colonic epithelium.

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.

Porcine reproductive and respiratory syndrome (PRRS) is an economically important infectious disease of swine. Constant emergence of variant strains of PRRS virus (PPRSV) and virus-mediated immune evasion followed by viral persistence result in increased incidence and recurrence of PRRS in swine herds. Current live and killed PRRSV vaccines administered by a parenteral route are ineffective in inducing complete protection. Thus, new approaches in design and delivery of PRRSV vaccines are needed to reduce the disease burden of the swine industry. Induction of an effective mucosal immunity to several respiratory pathogens by direct delivery of a vaccine to mucosal sites has proven to be effective in a mouse model. However, there are challenges in eliciting mucosal immunity to PRRS due to our limited understanding of safe and potent mucosal adjuvants, which could potentiate the mucosal immune response to PRRSV. The purpose of this review is to discuss methods for induction of protective mucosal immune responses in the respiratory tract of pigs. The manuscript also discusses how PRRSV modulates innate, adaptive and immunoregulatory responses at both mucosal and systemic sites of infected and/or vaccinated pigs. This information may help in the design of innovative mucosal vaccines to elicit superior cross-protective immunity against divergent field strains of PRRSV.

Bungowannah virus was discovered following an outbreak of stillbirths and sudden death in young pigs. Affected animals consistently showed a myocardopathy with signs of cardiac failure. After virus isolation and PCR investigations were unsuccessful, direct fetal inoculation was undertaken. Nucleic acid purified from serum from infected fetuses was subjected to sequence-independent single-primer amplification and nucleic acid sequencing. Sequences consistent with a pestivirus were obtained. The entire genome was identified but was genetically remote from the recognized pestivirus species. This virus was not recognized by pan-pestivirus reactive monoclonal antibodies but was subsequently detected in cell cultures by immunoperoxidase staining using convalescent sow serum. Experimental infections of sows at different stages of gestation reproduced the myocarditis syndrome. Pre-weaning losses of 70 and 29% were observed following infection at days 35 and 90, respectively. Piglets infected at day 35 were shown to be persistently infected, while chronic infections were observed after fetal infection at day 55. Chronically infected piglets showed growth retardation and were viremic for up to 7 months. Myocarditis was associated with infection in late gestation (day 90). Non-pregnant sheep and cattle have been experimentally infected but with no evidence of disease. Infection of pregnant cattle in early gestation resulted in both maternal and fetal infection, but all infected fetuses mounted an antibody response to the virus. Analysis of the nucleic acid sequence confirmed that Bungowannah has a number of changes not observed in other pestiviruses. Genes encoding some of the structural proteins remain fully functional when inserted into a bovine viral diarrhea virus (BVDV) backbone. Cell culture-based studies have shown that Bungowannah virus will grow in cells extending from humans to bats as well as farm animals.

The risk of bovine respiratory disease (BRD) has a significant effect on the value of cattle in the marketplace. Calves sold in larger groups have $6.37/45.45 kg more value than those sold as singles or in small groups. Morbidity is higher in unweaned commingled calves than those marketed in groups more than 45 days following weaning. Calves with an aggressive disposition have significantly less value than docile calves, due largely to depressed performance and less carcass value. The value of cattle in the marketplace can be improved by offering larger, uniform lots of cattle that have been weaned at least 45 days. Cattle that suffer BRD in the feedlot have from $23.23 to $151.18 less value than those remaining healthy.

Clinical scoring systems have been proposed for respiratory disease diagnosis in calves, including the Wisconsin (WI) system (McGuirk in 2008) which uses five clinical signs, each partitioned into four levels of severity. Recently, we developed the California (CA) bovine respiratory disease (BRD) scoring system requiring less calf handling and consisting of six clinical signs, each classified as normal or abnormal. The objective of this study was to estimate the on-farm agreement between the WI and the CA scoring systems. A total of 100 calves were enrolled on a CA dairy and assessed for BRD case status using the two scoring systems simultaneously. The Kappa coefficient of agreement between these two systems was estimated to be 0.85, which indicated excellent agreement beyond chance. The simpler design and reduced calf handling required by the CA BRD scoring system may make it advantageous for on-farm use.

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.

Gastrointestinal illnesses are common afflictions. However, knowledge of their etiology is often lacking. Moreover, most cases of infections with reportable enteric pathogens (Campylobacter jejuni, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, Cryptosporidia and Giardia) have sporadic modes of acquisition, yet control measures are often biased towards mitigation of risks discerned by outbreak analysis. To determine the etiology of unexplained diarrhea it is important to study populations that can be matched to appropriate controls and to couple thorough classic microbiologic evaluation on receipt of specimens with archiving and outgrowth capabilities. Research evaluations should address the potential roles of a broad panel of candidate bacterial pathogens including diarrheagenic E. coli, Listeria monocytogenes, Helicobacters and jejuni Campylobacters, and also apply novel massively parallel sequencing and nucleic acid detection technologies that allow the detection of viral pathogens. To fill voids in our knowledge regarding sources of known enteric pathogens it will be critical to extend case-control studies to assess risk factors and exposures to patients with non-epidemic illnesses and to appropriate controls. By filling these gaps in our knowledge it should be possible to formulate rational prevention mechanisms for human gastrointestinal illnesses.

Bovine immunodeficiency virus (BIV) was first isolated in 1969 from a cow, R-29, with a wasting syndrome. The virus isolated induced the formation of syncytia in cell cultures and was structurally similar to maedi-visna virus. Twenty years later, it was demonstrated that the bovine R-29 isolate was indeed a lentivirus with striking similarity to the human immunodeficiency virus. Like other lentiviruses, BIV has a complex genomic structure characterized by the presence of several regulatory/accessory genes that encode proteins, some of which are involved in the regulation of virus gene expression. This manuscript aims to review biological and, more particularly, molecular aspects of BIV, with emphasis on regulatory/accessory viral genes/proteins, in comparison with those of other lentiviruses.

The control and prevention of bovine viral diarrhea virus (BVDV) infections has provided substantial challenges. Viral genetic variation, persistent infections, and viral tropism for immune cells have complicated disease control strategies. Vaccination has, however, provided an effective tool to prevent acute systemic infections and increase reproductive efficiency through fetal protection. There has been substantial controversy about the safety and efficacy of BVDV vaccines, especially when comparing killed versus modified-live viral (MLV) vaccines. Furthermore, numerous vaccination protocols have been proposed to protect the fetus and ensure maternal antibody transfer to the calf. These issues have been further complicated by reports of immune suppression during natural infections and following vaccination. While killed BVDV vaccines provide the greatest safety, their limited immunogenicity makes multiple vaccinations necessary. In contrast, MLV BVDV vaccines induce a broader range of immune responses with a longer duration of immunity, but require strategic vaccination to minimize potential risks. Vaccination strategies for breeding females and young calves, in the face of maternal antibody, are discussed. With intranasal vaccination of young calves it is possible to avoid maternal antibody interference and induce immune memory that persists for 6–8 months. Thus, with an integrated vaccination protocol for both breeding cows and calves it is possible to maximize disease protection while minimizing vaccine risks.

Neutrophilic bronchiolitis is the primary lesion in asthma-affected horses. Neutrophils are key actors in host defense, migrating toward sites of inflammation and infection, where they act as early responder cells toward external insults. However, neutrophils can also mediate tissue damage in various non-infectious inflammatory processes. Within the airways, these cells likely contribute to bronchoconstriction, mucus hypersecretion, and pulmonary remodeling by releasing pro-inflammatory mediators, including the cytokines interleukin (IL)-8 and IL-17, neutrophil elastase, reactive oxygen species (ROS), and neutrophil extracellular traps (NETs). The mechanisms that regulate neutrophil functions in the tissues are complex and incompletely understood. Therefore, the inflammatory activity of neutrophils must be regulated with exquisite precision and timing, a task achieved through a complex network of mechanisms that regulates neutrophil survival. The discovery and development of compounds that can help regulate ROS, NET formation, cytokine release, and clearance would be highly beneficial in the design of therapies for this disease in horses. In this review, neutrophil functions during inflammation will be discussed followed by a discussion of their contribution to airway tissue injury in equine asthma.

Brucellosis is a zoonotic disease caused by a number of Brucella species and is characterized by chronic macrophage infection. However, genes that may contribute to intracellular survival of the Brucella species are not well studied. This review presents, first, genomic islands that are present or absent in various Brucella species that may help establish Brucella infection and survival strategies. Second, the alteration in macrophage transcription by Brucella to permit its long-term survival within this hostile intracellular environment. A large number of macrophage gene transcripts are altered following Brucella infection indicating that Brucella is not a silent invader of host cells. Macrophage transcript levels associated with inflammation, apoptosis, signal transduction and vesicular intracellular trafficking are altered during Brucella infection, and likely contribute to intracellular survival of Brucella. Lastly, the host–pathogen interaction events associated with Brucella infection in living mice visualized in real-time using biophotonic imaging. Mice are often used to evaluate Brucella infections; however, Brucella dissemination and pathogenesis is poorly understood in mice. Biophotonic imaging of Brucella infections revealed sites of bacterial localization similar to human infections and different patterns of infection by attenuated or virulent Brucella.

Infectious bursal disease virus (IBDV) causes an immunosuppressive disease in young chickens. Two serotypes of this double-stranded RNA virus exist but only serotype 1 viruses cause disease in chickens. Detection and strain identification of IBDV is important because antigenic subtypes found within serotype 1 make it necessary to tailor vaccination programs to the antigenic type found in the bird's environment. Because conventional virus isolation and characterization are not practical for routine diagnosis of IBDV, antigen-capture enzyme-linked immunosorbent assay (ELISA) and molecular assays based on reverse transcription–polymerase chain reaction (RT-PCR) technology were developed. Compared with antigen-capture ELISA, RT-PCR assays have greater versatility and are more sensitive and specific. Strain identification has been accomplished using a variety of post-RT-PCR assays, including restriction enzyme digestion of the RT-PCR products. The resulting restriction fragment length polymorphisms (RFLP) are used to differentiate viruses into molecular groups that correlate with antigenic and pathogenic types. Recently, two types of real-time RT-PCR have been used to identify and differentiate strains of IBDV. Both methods use distance-dependent interaction between two dye molecules, known as fluorescence resonance energy transfer (FRET). The dye molecules are attached to one or more nucleotide probes that detect specific nucleotide sequences of the virus. Our laboratory has used a two-probe assay to identify single-nucleotide mutations among IBDV strains. A mutation probe is used in this assay to detect substitution mutations in a region of the viral genome that encodes a neutralizing epitope of the virus. These assays are accurate, reliable and inexpensive compared with conventional RT-PCR because they do not require RFLP or other labor-intensive post-RT-PCR assays to distinguish viral strains.

O-antigens present on the surface of Escherichia coli provide antigenic specificity for the strain and are the main components for O-serogroup designation. Serotyping using O-group-specific antisera for the identification of E. coli O-serogroups has been traditionally the gold-standard for distinguishing E. coli strains. Knowledge of the O-group is important for determining pathogenic lineage, classifying E. coli for epidemiological studies, for determining virulence, and for tracing outbreaks of diseases and sources of infection. However, serotyping has limitations, as the antisera generated against each specific O-group may cross-react, many strains are non-typeable, and others can autoagglutinate or be rough (lacking an O-antigen). Currently, the nucleotide sequences are available for most of the 187 designated E. coli O-groups. Public health and other laboratories are considering whole genome sequencing to develop genotypic methods to determine O-groups. These procedures require instrumentation and analysis that may not be accessible and may be cost-prohibitive at this time. In this review, we have identified unique gene sequences within the O-antigen gene clusters and have targeted these genes for identification of O-groups using the polymerase chain reaction. This information can be used to distinguish O-groups by developing other platforms for E. coli diagnostics in the future.