Since the discovery of the polymerase chain reaction (PCR) 20 years ago, an avalanche of scientific publications have reported major developments and changes in specialized equipment, reagents, sample preparation, computer programs and techniques, generated through business, government and university research. The requirement for genetic sequences for primer selection and validation has been greatly facilitated by the development of new sequencing techniques, machines and computer programs. Genetic libraries, such as GenBank, EMBL and DDBJ continue to accumulate a wealth of genetic sequence information for the development and validation of molecular-based diagnostic procedures concerning human and veterinary disease agents. The mechanization of various aspects of the PCR assay, such as robotics, microfluidics and nanotechnology, has made it possible for the rapid advancement of new procedures. Real-time PCR, DNA microarray and DNA chips utilize these newer techniques in conjunction with computer and computer programs. Instruments for hand-held PCR assays are being developed. The PCR and reverse transcription–PCR (RT–PCR) assays have greatly accelerated the speed and accuracy of diagnoses of human and animal disease, especially of the infectious agents that are difficult to isolate or demonstrate. The PCR has made it possible to genetically characterize a microbial isolate inexpensively and rapidly for identification, typing and epidemiological comparison.

Bovine respiratory disease (BRD) is a frequent disease concern in dairy cattle and is most commonly diagnosed in young dairy heifers. The impact of BRD is highly variable, depending on the accuracy and completeness of detection, effectiveness of treatment, and on-farm culling practices. Consequences include decreased rate of weight gain, a higher culling risk either as heifers or as cows, delayed age at first service, delayed age at first calving, and in some cases, lower future milk production. In this data set of 104,100 dairy replacement heifers from across the USA, 36.6% had one or more cases diagnosed within the first 120 days of age with the highest risk of new cases occurring prior to weaning. Comparison of the raising cost for heifers with BRD and those without a recorded history of BRD resulted in an estimated cost per incident case occurring in the first 120 days of age of $252 or $282, depending upon whether anticipated future milk production differences were considered or not. Current market conditions contributed to a cost estimate that is significantly higher than previously published estimates, driven in part by the losses associated with selective culling of a subset of heifers that experienced BRD.

Swine dysentery (SD) caused by the intestinal spirochete Brachyspira hyodysenteriae is an economically important disease in pig-producing countries throughout the world. To date, no specific serologic assay is commercially available for the diagnosis of pigs with SD. Several serologic techniques have been identified in the past; however, these tests have all used either whole-cell proteins or lipopolysaccharide (LPS) as the antigen. Whole-cell antigens are plagued with false-positive reactions due to cross-reactivity with common proteins shared with other spirochetes. LPS antigens produce fewer false-positives; however, false-negatives may result due to LPS components being serogroup-specific. Generally, these techniques are useful for detecting infected herds, but are unreliable for the detection of individual infected pigs. In order to develop improved serologic tests it will be necessary to identify suitable diagnostic antigens, in particular immunogenic cell-surface structures which are specific to B. hyodysenteriae but common amongst different strains of the species. Recently, we identified and cloned a 30-kDa outer membrane lipoprotein (BmpB) which is specific to B. hyodysenteriae and is recognized by experimentally and naturally infected pigs. In this review we summarize the available serologic tests for SD, and speculate on the use of recombinant BmpB as an antigen for future development of an improved serologic test for SD diagnosis.

Until the early 1990s there were just three recognized species in the pestivirus genus, bovine viral diarrhea virus (BVDV), border disease virus (BDV) and classical swine fever virus (CSFV). Subsequently BVDV were divided into two different species, BVDV1 and BVDV2 and four additional putative pestivirus species have been identified, based on phylogenetic analysis. The four putative pestivirus specices, listed in chronological order of published reports, are Giraffe (isolated from one of several giraffes in the Nanyuki District of Kenya suffering from mucosal disease-like symptoms), HoBi (first isolated from fetal bovine serum originating in Brazil and later from samples originating in Southeast Asia), Pronghorn (isolated from an emaciated blind pronghorn antelope in the USA), and Bungowannah (isolated following an outbreak in pigs, resulting in still birth and neonatal death, in Australia). In addition to the emergence of putative new species of pestivirus, changes in host and virulence of recognized or ‘classic’ pestiviruses have led to reevaluation of disease control programs and management of domestic and wildlife populations.

Addition of sub-therapeutic antibiotics to the feed of food-producing animals for growth promotion and disease prevention has become a common agricultural practice in many countries. The emergence of antibiotic-resistant pathogens is a looming concern associated with the use of antibiotic growth promoters (AGPs) around the world. In addition, some studies have shown that AGPs may not only affect antibiotic resistance but may also stimulate the dissemination of virulence factors via bacteriophages. Although only a few studies are currently available in the literature regarding this topic, in this article we endeavor to provide a perspective about how AGPs would impact the transmission of virulence factors by horizontal gene transfer via phages in a few pathogenic bacterial species significant to livestock production.

Transition cow diseases can negatively impact animal welfare and reduce dairy herd profitability. Transition cow disease incidence has remained relatively stable over time despite monitoring and management efforts aimed to reduce the risk of developing diseases. Dairy cattle disease risk is monitored by assessing multiple factors, including certain biomarker test results, health records, feed intake, body condition score, and milk production. However, these factors, which are used to make herd management decisions, are often reviewed separately without considering the correlation between them. In addition, the biomarkers that are currently used for monitoring may not be representative of the complex physiological changes that occur during the transition period. Predictive modeling, which uses data to predict future or current outcomes, is a method that can be used to combine the most predictive variables and their interactions efficiently. The use of an effective predictive model with relevant predictors for transition cow diseases will result in better targeted interventions, and therefore lower disease incidence. This review will discuss predictive modeling methods and candidate variables in the context of transition cow diseases. The next step is to investigate novel biomarkers and statistical methods that are best suited for the prediction of transition cow diseases.

Systematic reviews and meta-analyses are used to summarize and interpret evidence for clinical decision-making in human health. The extent of the application of these methods in veterinary medicine and animal agriculture is unknown. The goal of this scoping study was to ascertain trends in the publication of systematic reviews and meta-analyses examining animal health, animal performance, and on-farm food safety. Online databases were searched for reviews published between 1993 and 2018 that focused on relevant outcomes in domestic livestock, companion animals, or wildlife species. In total 1787 titles and abstracts underwent data characterization. Dairy cattle, fish, and pigs were the most common target commodity groups. Few articles investigated both health and performance outcomes (only health: n = 418; only performance: n = 701; both health and performance: n = 103). Most of the reviews (67.6%, n = 1208/1787) described a meta-analysis but did not state in the title or abstract that a systematic review was also conducted, which is potentially problematic. Adherence to reporting guidelines is recommended for all systematic reviews and meta-analyses. For research areas with many reviews, an evidence repository is recommended. For less well-reviewed areas, additional investigation may be necessary to identify the reasons for the lack of synthesis research.

Foot-and-mouth disease (FMD) is one of the most serious transboundary, contagious viral diseases of cloven-hoofed livestock, because it can spread rapidly with high morbidity rates when introduced into disease-free herds or areas. Epidemiological simulation modeling can be developed to study the hypothetical spread of FMD and to evaluate potential disease control strategies that can be implemented to decrease the impact of an outbreak or to eradicate the virus from an area. Spatial analysis, a study of the distributions of events in space, can be applied to an area to investigate the spread of animal disease. Hypothetical FMD outbreaks can be spatially analyzed to evaluate the effect of the event under different control strategies. The main objective of this paper is to review FMD-related articles on FMD epidemiology, epidemiological simulation modeling and spatial analysis with the focus on disease control. This review will contribute to the development of models used to simulate FMD outbreaks under various control strategies, and to the application of spatial analysis to assess the outcome of FMD spread and its control.

Avian pneumovirus (APV; officially known as turkey rhinotracheitis virus) is an emergent pathogen of birds in the USA that results in upper respiratory tract disease in turkeys. Six years after the first outbreak in the USA, the disease continues to ravage turkey flocks, primarily in the state of Minnesota. From 1997 to 2000, the industry recorded losses estimated at US$15 million per annum. Researchers have developed sensitive diagnostic techniques, including the enzyme-linked immunosorbent assay and the reverse transcriptase–polymerase chain reaction, which, when used together, are highly sensitive in detecting APV outbreaks in commercial turkey flocks. Phylogenetic analysis of the nucleotide and predicted amino acid sequence of 15 US viruses isolated between 1996 and 2000 demonstrated that the US viruses are relatively homogenous but different from the European APV subgroups A and B, resulting in the classification of US isolates into subgroup C. Infectious APV was isolated from sentinel waterfowls placed close to an infected commercial turkey farm and from wild Canada geese captured in Minnesota, suggesting that free-ranging birds may be involved in the spread of APV. Current efforts to prevent and control the infection include improving management and biosecurity practices and developing attenuated live and deletion mutant vaccines capable of conferring protection.

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.

Randomized controlled trials of veterinary vaccines are essential if we are to have a reasonable understanding of how those vaccines can be expected to perform when used in the field. This manuscript reviews a few (but certainly not all) of the key elements that need to be considered in the design of veterinary vaccine trials. The first step in the design of such a trial is to have a clear statement of the objective of the trial that reflects what is expected of the vaccine (e.g. should it minimize clinical disease or does it need to prevent infection?). Because domestic animals are often managed in groups, the ‘unit of concern’ used in a vaccine trial becomes of great importance. Whether the trial should be carried out at the individual or group level will depend on the objectives of the trial and the extent of concern about ‘group effects’ affecting the trial. Sample sizes will also be influenced heavily by the choice of unit of concern and the nature of the primary outcome being assessed. Finally, while there is no easy solution (except to conduct group-level trials, which may be logistically impossible), the potential for group effects to influence the trial outcome must be considered.

Pathogens that enter the body via mucosal surfaces face unique defense mechanisms that combine the innate barrier provided by the mucus layer with an adaptive response typified by the production and transepithelial secretion of pathogen-specific IgA. Both the measurement and induction of mucosal responses pose significant challenges for experimental and practical application and may need to be adapted to the species under study. In particular, for livestock, immunization procedures developed in small rodent models are not always effective in large animals or compatible with management practices. This paper reviews the latest advances in our understanding of the processes that lead to secretory IgA responses and how this relates to the development of mucosal immunization procedures and adjuvants for veterinary vaccines. In addition, it highlights the complex interactions that can take place between the pathogen and the host's immune response, with specific reference to Chlamydia/Chlamydophila infections in sheep.

One area where the feedlot industry has been historically weak is the area of BRD “case definition” or diagnosis. Numerous studies demonstrate a weak correlation between lung lesions at harvest and treatment history. This poor track record is due in part to lack of specific chute side diagnostic tools. To analyze the effectiveness of current diagnostic tools (temperature, manual lung scores, and Whisper® lung scores), two data sets were collected. The first evaluated the correlation between rectal temperature, manual lung scores, and case fatality rate in feedlot cattle pulled for BRD. The second evaluated the relative accuracy of Whisper® scores and rectal temperature. Fever was defined as a rectal temperature of 104.5° F or greater. Manual lung scores better correlated with case fatality rate than fever. When fever and Whisper® scores were compared, a Whisper® score of 1 or less better predicted survival than a temperature of less than 104.5° F. The combination of no fever and Whisper® score of 1 or less best predicted survival. The determination of Whisper® score along with rectal temperature in cattle identified with signs of acute BRD can improve case definition, improve risk assessment, and allow more targeted use of antibiotics.

The aim of this systematic review was to investigate the prevalence of leptospirosis among stray and sheltered dogs worldwide. Six databases were searched, which resulted in the retrieval of 476 articles. Sixty articles were selected for analysis according to 10 quality criteria. Among the selected papers, 26 papers [43.4% (26/60)] met five of the 10 quality criteria established, 10 papers [16.7% (10/60)] met three criteria, nine papers [15.0% (9/60)] met four criteria, six papers [10.0% (6/60)] met six criteria, four papers [6.7% (4/60)] met eight criteria, and three papers [5.0% (3/60)] met nine of the 10 criteria, whereas two papers [1.7% (1/60)] met two and seven [1.7% (1/60)] criteria. Publications originated mainly from the Americas [45.0% (27/60)] and in the last 16 years (2003–2019) [81.7% (49/60)], and most of the sampled dogs were stray dogs [65.0% (39/60)]. The most commonly used diagnostic test for leptospirosis was the microscopic agglutination test [78.4% (47/60)] followed by polymerase chain reaction [21.7% (13/60)], and the most common serovars were Canicola [71.4% (35/49)], Icterohaemorrhagiae [65.3% (32/49)], Grippotyphosa [40.8% (20/49)], and Pomona [40.8% (20/49)]. In conclusion, our results showed that Leptospira spp. are present in unowned dogs worldwide; however, the low-methodological quality of the recovered cross-sectional studies precluded a meta-analysis.

Conceptualizing climate as a distinct variable limits our understanding of the synergies and interactions between climate change and the range of abiotic and biotic factors, which influence animal health. Frameworks such as eco-epidemiology and the epi-systems approach, while more holistic, view climate and climate change as one of many discreet drivers of disease. Here, I argue for a new paradigmatic framework: climate-change syndemics. Climate-change syndemics begins from the assumption that climate change is one of many potential influences on infectious disease processes, but crucially is unlikely to act independently or in isolation; and as such, it is the inter-relationship between factors that take primacy in explorations of infectious disease and climate change. Equally importantly, as climate change will impact a wide range of diseases, the frame of analysis is at the collective rather than individual level (for both human and animal infectious disease) across populations.

Research in big data, informatics, and bioinformatics has grown dramatically (Andreu-Perez J, et al., 2015, IEEE Journal of Biomedical and Health Informatics 19, 1193–1208). Advances in gene sequencing technologies, surveillance systems, and electronic medical records have increased the amount of health data available. Unconventional data sources such as social media, wearable sensors, and internet search engine activity have also contributed to the influx of health data. The purpose of this study was to describe how ‘big data’, ‘informatics’, and ‘bioinformatics’ have been used in the animal health and veterinary medical literature and to map and chart publications using these terms through time. A scoping review methodology was used. A literature search of the terms ‘big data’, ‘informatics’, and ‘bioinformatics’ was conducted in the context of animal health and veterinary medicine. Relevance screening on abstract and full-text was conducted sequentially. In order for articles to be relevant, they must have used the words ‘big data’, ‘informatics’, or ‘bioinformatics’ in the title or abstract and full-text and have dealt with one of the major animal species encountered in veterinary medicine. Data items collected for all relevant articles included species, geographic region, first author affiliation, and journal of publication. The study level, study type, and data sources were collected for primary studies. After relevance screening, 1093 were classified. While there was a steady increase in ‘bioinformatics’ articles between 1995 and the end of the study period, ‘informatics’ articles reached their peak in 2012, then declined. The first ‘big data’ publication in animal health and veterinary medicine was in 2012. While few articles used the term ‘big data’ (n = 14), recent growth in ‘big data’ articles was observed. All geographic regions produced publications in ‘informatics’ and ‘bioinformatics’ while only North America, Europe, Asia, and Australia/Oceania produced publications about ‘big data’. ‘Bioinformatics’ primary studies tended to use genetic data and tended to be conducted at the genetic level. In contrast, ‘informatics’ primary studies tended to use non-genetic data sources and conducted at an organismal level. The rapidly evolving definition of ‘big data’ may lead to avoidance of the term.

The ability of the fish industry to provide a continuous supply of fish protein depends on both proper biosecurity and strategies to significantly reduce the risk of infectious diseases. Vaccination is a safe and effective means to prevent disease and to increase the productivity and profitability of farmed fish. Vaccines are likely to be the prime prophylactic measure of the future because of rapidly developing advances in fish vaccine technology and producer acceptance. The efficacy of a vaccine is influenced by a variety of factors that must be considered in the development of vaccination strategies for fish. This review highlights some of these factors. The response to a modified live vaccine against Edwardsiella ictaluri is used for illustration.

Paratuberculosis is a worldwide infectious disease caused by Mycobacterium avium ssp. paratuberculosis (MAP). Various ruminant species can be affected by the disease, and the diagnosis of the disease is challenging in the absence of a gold standard test. The aim of this systematic review protocol is to determine the accuracy of the direct and indirect diagnostic tests for MAP infection with a special focus on sheep and goats.

Bovine respiratory disease (BRD) is the most common cause of morbidity and mortality in North American beef cattle. In recent years, isolation of strains of Mannheimia haemolytica that are resistant to multiple different classes of antimicrobials has become commonplace. New research would suggest that the routine use of antimicrobials by some cattle operations might be driving emerging resistance patterns, with the majority of the spread observed due to propagation of strains of M. haemolytica that have acquired integrative conjugative elements. To date, there is little information evaluating the impact of antimicrobial resistance on clinical outcome in cattle with BRD.

The USDA:APHIS National Animal Health Monitoring System collects data on health and health management in livestock and poultry populations throughout the USA in order to provide stakeholders with population estimates to use as benchmarks for comparison, to guide policy development, and to identify research needs and prioritize education efforts. Recent studies of both the beef cattle feedlot industry and dairy heifer rearing operations provided information about BRD occurrence as well as information about prevention and treatment practices used on these operations. While a great deal of effort is dedicated to BRD prevention, there are still opportunities to improve the strategies used. Despite efforts to prevent the disease, BRD continues to be widespread on both of these types of operations.