Farm Animal Populations Research Articles

A methodological framework for attributing the burden of animal disease to specific causes.

The Global Burden of Animal Diseases provides an analytical framework to measure the overall health of various farmed animal populations, to estimate the farm-level burden of different diseases, incorporating production losses due to morbidity and mortality as well as health expenditure, and to identify the wider economic and human health impacts of animal disease. Attributing the burden of animal diseases to specific causes or groups of causes requires methodological choices, including the classification of diseases and the resulting health states that manifest in loss of production. The aim of this article is to address the key challenges in the process of estimating farm-level disease burden, including ambiguity in terminology, data availability and collation, and adjustments for comorbidity. Using infection with zoonotic Brucella spp. in small ruminants as an aetiological cause of disease and abortion as a sequela of multiple diseases, practical examples of the framework are provided. Cause-specific attribution of the burden of animal disease captures temporal and spatial trends, an understanding of which is essential for planning, monitoring and evaluating animal health programmes and disease interventions.

The European livestock resistome.

Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors.

Reproductive and productive traits of cows of Holstein breed depending on the level of inbreeding

Inbreeding is one of the main criteria in programs for the conservation and use of genetic resources, and it can be used to control genetic processes in populations of farm animals. The use of inbreeding involves the production and consolidation of rare genotypes, which determine the outstanding quality of animals. The purpose of the work was to determine the reproductive and productive traits of cows of Holstein breed depending on the level of inbreeding. The research was carried out in the pedigree farm in the Kaluga region. The research of the reproductive ability of first-calf heifers obtained through inbreeding and outbreeding were shown significant differences in the duration of the calving interval. So, cows obtained through the remote inbreeding had the lowest duration calving interval (385.4 days) and their herdmates from outbreding had the longest calving interval (404,5 days), the difference was 19.1 days (p<0.05) or 5.0%. Cows from remote inbreeding had the shorter calving interval than their herdmates from moderate inbreeding by 15.9 days (p<0.05) or 4.1%. It was found that higher milk yields for 305 days of the first lactation had cows obtained through remote inbreeding (6413.1 kg), and low milk yields of milk were obtained from first-calf heifers from moderate inbreeding (5634.8 kg), the difference was 778.3 kg (p<0.05) or 9.0%. They also surpassed the milk yield of their herdmates obtained from outbreeding by 266.6 kg (p<0.05) or 4.3%. First-calf heifers obtained through moderate inbreeding were inferior in milk yield to herdmates from outbreeding by 511.7 kg or 9.1% (p<0.05).

Discriminant analysis reveals differences in breed structure in river buffaloes of Maharashtra (India).

Buffaloes are a major milch species of India, and owning a true-to-breed buffalo herd is a reverie for livestock keepers, as it substantiates their incomes. Multivariate discriminate analysis is an efficient methodology to classify different farm animal populations based on canonical discriminant function. The present study was conducted on 392 adult buffaloes using 18 body biometric traits. Except for body height and body length, all the body characters revealed significant differences amongst the four buffalo populations. Unlike cattle, distance between horns and rump width were more discriminating factors, compared to body height, leg length, chest girth, and body length. We report the most suitable discriminate function which can discriminate with maximum between-group variation in four studied populations. Mahalanobis distances were calculated between populations and they ranged from 0.786 to 1.227. Purnathadi has revealed a distinct phenotypic structure, and these buffaloes have a distinct native breeding region comprising Akola, Amravati, and Buldhana districts of Maharashtra state. On the other hand, Elachpuri animals failed to depict physical and biometric discriminations from Nagpuri, Marathwadi, and Purnathadi buffalo populations, and Elachpuri can be considered as a strain of Nagpuri buffalo.

The effectiveness of scientifically based monitoring programs and therapeutic and preventive measures for controlled infectious diseases of animals

The aim of the work was to assess the effectiveness of an improved monitoring program for controlled infectious animal diseases and individual vaccination programs for acute respiratory viral infection in cattle. To fulfill the tasks set, serological studies, PCR diagnostics, bacteriological and coprological methods of examining biological samples from animals were carried out. As a result of the work, the main factors influencing the effectiveness of vaccine prophylaxis of acute respiratory viral infection in cattle populations have been identified. It was found that in three administrative and administrative districts of the Sverdlovsk region, the main factors in 35.1% of cases are violations of the rules of vaccination of acute respiratory viral infection of cattle, in 13.5% of cases - violations of zoo-hygienic and veterinary–sanitary conditions of keeping farm animals. A comprehensive assessment of the effectiveness of individual vaccination programs for cattle against acute respiratory viral infection has been carried out, taking into account the epizootological situation in agricultural organizations. It was shown that vaccination of cattle against acute respiratory viral infection according to individual programs ensured the formation of specific immunity in 92.5-95.0% of animals. The number of immunotolerant individuals and animals with a low level of immunoreactivity in the physiological group of young cattle did not exceed 3.5%, in the physiological group of adult animals – 1.25%. The high efficiency of improved scientifically based programs for monitoring, diagnosis, therapeutic, preventive and health measures to protect animals from epizootically significant infectious diseases of cattle among the populations of farm animals of the Ural Federal District has been confirmed.

Leveraging microbiome information for animal genetic improvement

There is growing evidence that the microbiome influences host phenotypic variation. Incorporating information about the holobiont - the host and its microbiome - into genomic prediction models may accelerate genetic improvements in farmed animal populations. Importantly, these models must account for the indirect effects of the host genome on microbiome-mediated phenotypes.

Farm size distribution in the Canadian livestock sector

This study quantified the distribution of animals by farm size for portions of the dairy, beef, swine, and poultry sectors using the 2016 Census of Agriculture. Results showed that the distribution of farm sizes and animal populations were skewed or bimodal and varied by livestock type and by province. Thus, the average farm size has little meaning. Recognizing farm size diversity is important for developing effective policies and programs, conducting appropriate research, and developing practices and technologies to support farms of all sizes.

Etiological structure of leptospirosis circulated in populations of farm animals in Yakutia

It is necessary to know the etiological structure of diseases in each region of the country that affects a particular animal species for successful prevention and diagnosis of natural focal diseases, in particular leptospirosis. In this paper, the authors presented research materials on the distribution and etiological structure of pathogenic leptospirosis circulating in the populations of farm animals in Yakutia. Currently, 8 unfavorable points for animal leptospirosis have been registered in Yakutia: two cattle and six horses. A comparative analysis of the etiological structure of leptospirosis in agricultural animals (cattle, horses) testifies to the diversity of leptospira serological groups circulating in the republic. Thus 7 serogroups are registered in cattle, among which the leptospira serogroups Icterohaemorrahagiae (36.0%) and Grippotyphosa (27.1%) dominate. Infection of animals averages 3.2%, in the central zone, where about 63% of the total livestock in the region is concentrated, the level of infection of livestock in the districts of the zone ranges from 0.14 to 8.58%. The highest infection rate of animals is observed in Gorny (8.58%), Namsky (2.26%), and Yakutsk (1.35%) regions. In this zone, circulation of 6 leptospira serogroups is recorded: Grippotyphosa (30.8%), Icterohaemorrahagiae (29.0%) and Tarassovi (27.1%), to a lesser extent Canicola (7.5%), Pomona (3.7%) and Sejroe (1.9%). It should be noted that no Leptospira Hebdomadis were found in cattle in the Central Zone. In Yakut horses, 6 serogroups were identified, among which the leptospira serogroups Hebdomadis (31.5%) and Tarassovi (28.7%) dominate. In the Central zone, where the main number of horses in the region (61.1%) is concentrated the infection rate of animals is an average of 3.2%. The level of infection of horses in the districts of the zone ranges from 0.15 to 8.62%. The highest infection rate of horses is recorded in the horse breeding farms of Gorny (8.62%), Kobyaisky (8.59%), Tattinsky (6.17%), and Churapchinsky (5.74%) districts. It should be noted that L. Pomona does not occur in horses.

Genomics applied to livestock and aquaculture breeding.

The increasing global demand for food, due to the continuous growth of human population, requires improvements in the efficiency and sustainability of animal production systems. In addition, several challenges facing farming of aquatic and terrestrial organisms need to be overcome to ensure food security in the upcoming decades, e.g. adaptation to climate change, reduced availability of conventional animal feed ingredients, emerging infectious and parasitic diseases, among others. Genomic technologies such as massive parallel sequencing, high‐throughput genotyping, genome selection and gene editing, combined with highly efficient computational methods can accelerate the rate of genetic progress in animal breeding. Thus, such technologies can help us meet the needs for protein sources for human consumption in the upcoming years. This Special Issue aims at presenting current advancements in the field of genomic tools applied to aquatic and terrestrial farmed animal populations.

Особенности разработки схем оздоровительных противолейкозных мероприятий с учетом влияния эпизоотического процесса на примере Республики Башкортостан

Abstract. The study of the features of the leukemic epizootic process in agricultural organizations of the Republic of Bashkortostan was carried out. The object of the study was cattle of different groups, including calves before drinking colostrum, heifers, springer heifers, pregnant and dairy cows. The purpose was to develop general schemes of anti-leukemic measures that guarantee a reduction in the recovery period for disadvantaged areas and a decrease in the level of infection of cattle with the leukemia virus. The work was carried out in the leukemia laboratory of the department for monitoring and predicting infectious animal diseases of the Ural Federal Agrarian Scientific Research Center of the Ural Branch of the Russian Academy of Sciences. Methods. A retrospective and operational analysis of data on the laboratory methods used for the diagnosis of bovine leukemia virus was carried out. Scientific novelty consists in obtaining new knowledge about the problems of diagnostics of the bovine leukemia virus among the populations of farm animals in the Republic of Bashkortostan. The features of the leukemic epizootic process have been studied: sources, transmission routes of the leukemia virus, level of infection and incidence of bovine leukemia virus in the surveyed farms in the regions of the Republic of Bashkortostan. Results. On the basis of the data obtained, general schemes of anti-leukemic measures have been developed, which guarantee a reduction in the recovery time of disadvantaged areas and a decrease in the level of infection of livestock with the leukemia virus.

Algorithm for complex diagnostics of cattle emerging diseases

Problems of detailed studies into the epizootic process of infectious diseases of farm animals, mechanisms of interaction of pathogenic microorganisms with macroorganisms, as well as issues of health improvement and protection of animal populations from epizootically significant diseases are acute for veterinary science and practice. As a result of the studies the spectrum of pathogens in parasite cenosis on the territory of the entity of the Russian Federation was identified. The species composition of pathogens in cases of non-infectious pathology and infectious diseases in young cattle is specified. The pathogens are represented byStaphylococcus spp., Streptococcus spp., E. coli. K-99, pathogenic fungi Aspergillus spp.and yeast fungi Candida albicans, BHV-1 and BVDV. A database was compiled to upgrade the methodology of analyzing epizootological studies. The development and implementation of health and health-related programs has decreased the occurence of acute intestinal infections and respiratory tract infections in young cattle by more than 1.3 times. Multi-level epizootic surveillance of farm animal populations can prevent the occurrence and spread of particularly dangerous infections, eliminate managed infections, downgrade the risk of post-infectious complications and improve the economic efficiency of the livestock industry as a whole.

The impact of liver fluke infection on steers in Ireland: A meta-analytic approach

Post-mortem liver inspection results together with production parameters are often used to estimate the impact of liver fluke infection on farm animal populations. However, post mortem liver inspection is an imperfect method of determining the liver fluke infection status of cattle. This work estimates the difference in mean lifetime weight gain at 819 days (ΔLWG819) between steers assigned liver fluke negative (LFN) and liver fluke positive (LFP) status at post-mortem meat inspection, quantifies the potential impact of imperfect sensitivity and specificity on these results and estimates the economic impact of these differences.The study population is 32,007 steers that never moved from their birth herd in the Republic of Ireland and were slaughtered in one of two Irish meat processors in 2014. Individual animal-level data are used to generate 46 county - processor level estimates of ΔLWG819. Standard errors and confidence intervals for these estimates are derived using bootstrapping. A meta-analytic approach is then used to obtain 3 overall estimates of the effect of liver fluke status on the ΔLWG819 in all the county - processor combinations, assuming post - mortem liver inspection Se = Sp = 1, 0.99 and 0.95. A random effects model is used and 95% prediction intervals (95% PI) are calculated.Assuming Se = Sp = 1 for post - mortem liver inspection, the random effects summary estimate of ΔLWG819 (ΔLWG819(RE)) is 36 kg (95% PI: -1, 73). There is a minor change in ΔLWG819(RE) (38 kg, 95% PI: -1, 77) when Se = Sp = 0.99 is assumed but this increases to 46 kg (95% PI: -2, 94) assuming Se = Sp = 0.95. The corresponding cost in euros of these differences between the LFN and LFP steers, assuming a price per kg of €3.90, are €77.01 (95% PI: -2.57, 156.37), €80.65 (95% PI: -3.43, 164.74) and €98.67 (95% PI: -5.15, 202.27) respectively.Our results demonstrate an association between liver fluke infection and reduced weight gain. We show that the effect of liver fluke infection on weight gain in cattle is underestimated due to misclassification resulting from imperfection in post mortem meat inspection. These findings will aid researchers, farmers and veterinary practitioners to make informed decisions on the control of liver fluke on farms.

MODERN MOLECULAR-GENETIC APPROACH TO INCREASE EFFICIENCY OF SELECTION PROCESS IN ANIMAL BREEDING OF UKRAINE

MODERN MOLECULAR-GENETIC APPROACH TO INCREASE EFFICIENCY OF SELECTION PROCESS IN ANIMAL BREEDING OF UKRAINE

Genetic diversity of Barbary lion based on genealogic analysis

Genetic diversity of Barbary lion based on genealogic analysis

Animal cloning applications and issues

Significant progress in the field of biotechnology has allowed for the use of cloning in animals which is being used: to improve genetic makeup, to rescue endangered species, in tissue engineering and to increase farm animal population. Unfortunately, cloning has been met with failure due to a variety of reasons namely early and late abortions, compromised immune systems, circulatory and respiratory problems and a high rate of fetal death. The reasons of these problems are unknown, but may research groups are attempting to understand the underlying molecular and cellular mechanisms involved in cloning efficiency. Atypical epigenetic re-programming appears to be the primary cause of ineffective cloning. Understanding molecular mechanisms involving key regulatory proteins is pivotal in the success of animal cloning. This review shows the current paradigm involving animal cloning efficiency, and also further elucidates applications to improve animal cloning efficiency.

Predicting farm-level animal populations using environmental and socioeconomic variables

Accurate information on the geographic distribution of domestic animal populations helps biosecurity authorities to efficiently prepare for and rapidly eradicate exotic diseases, such as Foot and Mouth Disease (FMD). Developing and maintaining sufficiently high-quality data resources is expensive and time consuming. Statistical modelling of population density and distribution has only begun to be applied to farm animal populations, although it is commonly used in wildlife ecology. We developed zero-inflated Poisson regression models in a Bayesian framework using environmental and socioeconomic variables to predict the counts of livestock units (LSUs) and of cattle on spatially referenced farm polygons in a commercially available New Zealand farm database, Agribase. Farm-level counts of cattle and of LSUs varied considerably by region, because of the heterogeneous farming landscape in New Zealand. The amount of high quality pasture per farm was significantly associated with the presence of both cattle and LSUs. Internal model validation (predictive performance) showed that the models were able to predict the count of the animal population on groups of farms that were located in randomly selected 3km zones with a high level of accuracy. Predicting cattle or LSU counts on individual farms was less accurate. Predicted counts were statistically significantly more variable for farms that were contract grazing dry stock, such as replacement dairy heifers and dairy cattle not currently producing milk, compared with other farm types. This analysis presents a way to predict numbers of LSUs and cattle for farms using environmental and socio-economic data. The technique has the potential to be extrapolated to predicting other pastoral based livestock species.

A protocol to identify and minimise selection and information bias in abattoir surveys estimating prevalence, using Fasciola hepatica as an example

Abattoir surveys and findings from post-mortem meat inspection are commonly used to estimate infection or disease prevalence in farm animal populations. However, the function of an abattoir is to slaughter animals for human consumption, and the collection of information on animal health for research purposes is a secondary objective. This can result in methodological shortcomings leading to biased prevalence estimates. Selection bias can occur when the study population as obtained from the abattoir is not an accurate representation of the target population. Virtually all of the tests used in abattoir surveys to detect infections or diseases that impact animal health are imperfect, leading to errors in identifying the outcome of interest and consequently, information bias. Examination of abattoir surveys estimating prevalence in the literature reveals shortcomings in the methods used in these studies. While the STROBE-Vet statement provides clear guidance on the reporting of observational research, we have not found any guidelines in the literature advising researchers on how to conduct abattoir surveys. This paper presents a protocol in two flowcharts to help researchers (regardless of their background in epidemiology) to first identify, and, where possible, minimise biases in abattoir surveys estimating prevalence. Flowchart 1 examines the identification of the target population and the appropriate study population while Flowchart 2 guides the researcher in identifying, and, where possible, correcting potential sources of outcome misclassification. Examples of simple sensitivity analyses are also presented which approximate the likely uncertainty in prevalence estimates due to systematic errors. Finally, the researcher is directed to outline any limitations of the study in the discussion section of the paper. This protocol makes it easier to conduct an abattoir survey using sound methods, identifying and, where possible, minimizing biases.

Biofortification of Carrot (Daucus carota L.) with Iodine and Selenium in a Field Experiment.

The low content of iodine (I) and selenium (Se) forms available to plants in soil is one of the main causes of their insufficient transfer in the soil-plant-consumer system. Their deficiency occurs in food in the majority of human and farm animal populations around the world. Both elements are classified as beneficial elements. However, plant response to simultaneous fertilization with I and Se has not been investigated in depth. The study (conducted in 2012–2014) included soil fertilization of carrot cv. “Kazan F1” in the following combinations: (1) Control; (2) KI; (3) KIO3; (4) Na2SeO4; (5) Na2SeO3; (6) KI+Na2SeO4; (7) KIO3+Na2SeO4; (8) KI+Na2SeO3; (9) KIO3+Na2SeO3. I and Se were applied twice: before sowing and as top-dressing in a total dose of 5 kg I⋅ha-1 and 1 kg Se⋅ha-1. No negative effects of I and Se fertilization were noted with respect to carrot yield. Higher accumulation and the uptake by leaves and storage roots of I and Se were obtained after the application of KI than KIO3, as well as of Na2SeO4 than Na2SeO3, respectively. Transfer factor values for leaves and roots were about a dozen times higher for Se than for I. Selenomethionine content in carrot was higher after fertilization with Na2SeO4 than with Na2SeO3. However, it was the application of Na2SeO3, KI+Na2SeO3 and KIO3+Na2SeO3 that resulted in greater evenness within the years and a higher share of Se from selenomethionine in total Se in carrot plants. Consumption of 100 g f.w. of carrots fertilized with KI+Na2SeO3 and KIO3+Na2SeO3 can supply approximately or slightly exceed 100% of the Recommended Daily Allowance for I and Se. Moreover, the molar ratio of I and Se content in carrot fertilized with KI+Na2SeO3 and KIO3+Na2SeO3 was the best among the research plots.

Agriculture census based dynamics of changes in livestock farming of Bangladesh-A review

The present work was undertaken to determine the dynamics of changes taken place in farm animal production system of Bangladesh transmuting gradually on a cusp of increasing feed and food competition and gaining competitive advantages in domestic production of milk, meat and eggs. The data available from livestock population of the Agricultural Census of 1960 and of 1977, Agricultural and Livestock Census of 1983-84, the census of agriculture 2008 and the livestock and poultry survey of 2009 were used to figure out quantitative changes and extrapolate inherent causes of them. During the period of 1960 to 2009 human population increased at a faster pace (55.2 million to 144.0 million) than livestock population (10.5 to 17.0 livestock units). The later may be explained by a reduction of per capita availability of bovine animals (0.38 in 1960 to 0.18 in 2009) while the same for small ruminants remained similar (0.12 to 0.12, respectively), and that of poultry increased from 0.65 to 1.07, respectively. However, over the decade dairy farming, cattle fattening and commercial poultry supported increased production of livestock products. The ratio of total cows to adult male cattle of 0.56 in 1960 increased to 0.88 in 1977 reflecting farmers` interest on dairying, and the trend was being continued till 2009. Farm animal population at medium and large farms decreased over the period significantly (P<0.01) but, it increased at Non-farm and small farm levels and the difference was significant (P<0.01) in different areas of the country. Compared to the livestock unit of 1984 the extent of its increase at Non-farm and small farm level was 228.0% and 82.0%, respectively, and the extent of decrease at medium and large farm level was 24.9% and 49.9%, respectively. Fragmentation of land reduced medium and large farm numbers resulting in an increase of non-farm and small farm households over the time, and keeping farm animals by the latter gradually increased the share of livestock by land poor peoples. The trends being continued over the decades may impact livestock productions further. This requires data generation through regular agricultural census emphasizing socioeconomic and geographical changes in livestock productions more for identification and quantification of factors dictate ongoing transformation process and driving strategic policy implications to achieve sustainable livestock production integrating measures for climate changes.Bang. J. Anim. Sci. 2016. 45 (1): 1-6

The use of genomic information can enhance the efficiency of conservation programs

The development of genomic tools allows for more accurate estimates of genetic relationships between animals (genomic coancestry coefficients) than those obtained with pedigree data (pedigree-based coancestry coefficients) and thus permit better management of genetic diversity. There are different issues relevant to conservation programs that could benefit from the use of genomic data. These include establishing synthetic ex situ populations, maintaining genetic diversity, preserving original genetic structures, and eliminating exogenous genetic information. The use of dense panels of single-nucleotide polymorphism (SNPs) in strategies proposed to deal with all these issues improves the general performance of conservation programs in both farm and wild animal populations.