Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms.

Animal husbandry is increasing yearly due to the growing demand for meat and livestock products, among other reasons. To meet these demands, prophylactic antibiotics are used in the livestock industry (i.e., poultry farming) to promote health and stimulate animal growth. However, antibiotics are not fully metabolized by animals, and they are evacuated to the environment with excreta. Animal manure is used as fertilizer to reduce the volume of waste generated in the livestock sector. However, manure often contains microorganisms harboring antibiotic resistance genes (ARGs). Then, the microbiome of manure applicate to the soil may contribute to the spread of antibiotic resistance in the environment, including autochthonous soil-dwelling microorganisms. The present study was conducted during the crops growing season in Poland (May to September 2019) to determine the influence of poultry manure as well as poultry manure supplemented with selected antibiotics on the diversity of the soil microbiome in treatments that had not been previously fertilized with manure and the ability of antibiotic-resistant bacteria to transfer ARGs to other soil bacteria. Antibiotic concentrations were elevated at the beginning of the study and decreased over time. Poultry manure induced significant changes in the structure of microbial communities in soil; the diversity of the soil microbiome decreased, and the abundance of bacterial genera Bradyrhizobium, Streptomyces, and Pseudomonas, which are characteristic of the analyzed manure, increased. Over time, soil microbial diversity was restored to the state observed before the application of manure. Genes conferring resistance to multiple drugs as well as genes encoding resistance to bacitracin and aminoglycosides were the most frequently identified ARGs in the analyzed bacteria, including on mobile genetic elements. Multidrug resistance was observed in 17 bacterial taxa, whereas ARGs were identified in 32 bacterial taxa identified in the soil microbiome. The results of the study conclude that the application of poultry manure supplemented with antibiotics initially affects soil microbiome and resistome diversity but finally, the soil shows resilience and returns to its original state after time, with most antibiotic resistance genes disappearing. This phenomenon is of great importance in sustainable soil health after manure application.

Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry.

Salmonella, one of the major infectious diseases in poultry, causes considerable economic losses in terms of mortality and morbidity, especially in countries that lack effective vaccination programs. Besides being resistant to diseases, indigenous chicken breeds are also a potential source of animal protein in developing countries. For understanding the disease resistance, an indigenous chicken line Kashmir faverolla, and commercial broiler were selected. RNA-seq was performed after challenging the chicken with Salmonella Typhimurium. Comparative differential expression results showed that following infection, a total of 3153 genes and 1787 genes were differentially expressed in the liver and spleen, respectively. The genes that were differentially expressed included interleukins, cytokines, NOS2, Avß-defensins, toll-like receptors, and other immune-related gene families. Most of the genes and signaling pathways involved in the innate and adaptive immune responses against bacterial infection were significantly enriched in the Kashmir faverolla. Pathway analysis revealed that most of the enriched pathways were MAPK signaling pathway, NOD-like receptor signaling pathway, TLR signaling pathway, PPAR signaling pathway, endocytosis, etc. Surprisingly some immune-related genes like TLRs were upregulated in the susceptible chicken breed. On postmortem examination, the resistant birds showed small lesions in the liver compared to large necrotic lesions in susceptible birds. The pathological manifestations and RNA sequencing results suggest a balancing link between resistance and infection tolerance in Kashmir faverolla. Here we also developed an online Poultry Infection Database (https://skuastk.org/pif/index.html), the first publicly available gene expression resource for disease resistance in chickens. The available database not only shows the data for gene expression in chicken tissues but also provides quick search, visualization and download capacity.

Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks.

A pandemic of Salmonella enterica serotype Enteritidis emerged in the 1980s due to contaminated poultry products. How Salmonella Enteritidis rapidly swept through continents remains a historical puzzle as the pathogen continues to cause outbreaks and poultry supply becomes globalized. We hypothesize that international trade of infected breeding stocks causes global spread of the pathogen. By integrating over 30,000 Salmonella Enteritidis genomes from 98 countries during 1949-2020 and international trade of live poultry from the 1980s to the late 2010s, we present multifaceted evidence that converges on a high likelihood, global scale, and extended protraction of Salmonella Enteritidis dissemination via centralized sourcing and international trade of breeding stocks. We discovered recent, genetically near-identical isolates from domestically raised poultry in North and South America. We obtained phylodynamic characteristics of global Salmonella Enteritidis populations that lend spatiotemporal support for its dispersal from centralized origins during the pandemic. We identified concordant patterns of international trade of breeding stocks and quantitatively established a driving role of the trade in the geographic dispersal of Salmonella Enteritidis, suggesting that the centralized origins were infected breeding stocks. Here we demonstrate the value of integrative and hypothesis-driven data mining in unravelling otherwise difficult-to-probe pathogen dissemination from hidden origins.

Parâmetros genéticos e efeitos de sexo e cruzamento recíproco sobre características de interesse econômico em aves F2 / Genetic parameters and effects of sex and reciprocal cross on economic traits in F2 broilers

Este estudo teve por objetivo estimar os parâmetros genéticos de características de interesse econômico, mensuradas em populações F2 desenvolvidas pela Embrapa Suínos e Aves utilizando cruzamento recíproco entre linhagens de corte e de postura. Ainda, foram avaliados os efeitos de sexo e de cruzamento recíproco sobre as características em estudo. Os pesos com um, 35 e 42 dias de idade; ganho de peso; consumo de ração e conversão alimentar entre 35 e 41 dias de idade; pesos dos pulmões, fígado, coração, moela, peito, pernas, carcaça, dorso, asas, cabeça, pés e gordura abdominal, além do comprimento do intestino, foram os fenótipos estudados. Foram estimados os componentes de variâncias genética aditiva e residual, além dos coeficientes de herdabilidade e das correlações genética e fenotípica. Os machos apresentaram maior peso para todas as características estudadas, nos dois cruzamentos recíprocos, exceto para gordura abdominal na população oriunda do cruzamento de machos de postura com fêmeas de corte. Os animais oriundos do cruzamento de machos de postura com fêmeas de corte foram mais pesados que os recíprocos, para todas as idades, além de apresentarem maior comprimento de intestino e maiores pesos de moela, carcaça, dorso, peito e cabeça. Os coeficientes de herdabilidade foram altos para consumo de ração e para os pesos ao nascimento, da moela e da gordura abdominal. As correlações fenotípicas estimadas foram, em sua maioria, baixas ou moderadas, contudo muitas correlações genéticas altas foram observadas. Ressalta-se que houve expressiva diferença nos coeficientes de herdabilidade de algumas características em função do cruzamento recíproco estudado, o que pode ser devido a efeitos materno, citoplasmático, ligados ao sexo ou imprinting.(AU)

This study aimed to estimate genetic parameters for several economic traits in F2 populations developed by Embrapa Swine and Poultry National Research Center, through reciprocal crosses of broilers and layer lines. Furthermore, sex and reciprocal cross effects were evaluated. Weights at 1, 35 and 42 days of age; weight gain, feed intake and feed conversion between 35 and 41 days of age; weights of the lungs, heart, liver, gizzard, breast, thighs, carcass, back, wings, head, legs and abdominal fat; and intestine length were studied. Residual and genetic additive variance components, heritability coefficients, and genetic and phenotypic correlations were estimated. Males were heavier than females for all studied traits in both reciprocal crosses, except for abdominal fat weight in chickens from the male layer x female broiler cross. Chickens from male layer x female broiler cross were heavier than those from its reciprocal cross, also having larger intestine length and gizzard, carcass, back, breast and head weights. The heritability coefficients were high for feed intake and body weight at birth, gizzard, and abdominal fat. The estimated phenotypic correlations were mostly lower or moderate, however, most high genetic correlations were observed. We found significant differences in heritability coefficients for some traits due to the reciprocal cross, which may be due maternal, cytoplasmic, sex-linked or imprinting effects.(AU)

Applying complex models to poultry production in the future--economics and biology.

The ability to determine the optimal broiler feed nutrient density that maximizes margin over feeding cost (MOFC) has obvious economic value. To determine optimal feed nutrient density, one must consider ingredient prices, meat values, the product mix being marketed, and the projected biological performance. A series of 8 feeding trials was conducted to estimate biological responses to changes in ME and amino acid (AA) density. Eight different genotypes of sex-separate reared broilers were fed diets varying in ME (2,723-3,386 kcal of ME/kg) and AA (0.89-1.65% digestible lysine with all essential AA acids being indexed to lysine) levels. Broilers were processed to determine carcass component yield at many different BW (1.09-4.70 kg). Trial data generated were used in model constructed to discover the dietary levels of ME and AA that maximize MOFC on a per broiler or per broiler annualized basis (bird × number of cycles/year). The model was designed to estimate the effects of dietary nutrient concentration on broiler live weight, feed conversion, mortality, and carcass component yield. Estimated coefficients from the step-wise regression process are subsequently used to predict the optimal ME and AA concentrations that maximize MOFC. The effects of changing feed or meat prices across a wide spectrum on optimal ME and AA levels can be evaluated via parametric analysis. The model can rapidly compare both biological and economic implications of changing from current practice to the simulated optimal solution. The model can be exploited to enhance decision making under volatile market conditions.

[Assessment of animal welfare aspects in extreme breeds of rabbits, poultry and pigeons]. / Zur Beurteilung von Tierschutzaspekten bei Extremzuchten von Rassekaninchen, Rassegeflügel und Rassetauben.

In a review based on literature searches animal welfare related characteristics in extreme breed types of rabbits, poultry and pigeons are summarized. Animal welfare aspects are assessed and measures for improvement are described.

The National Animal Germplasm Program: challenges and opportunities for poultry genetic resources.

In the United States, poultry genetic resources have consolidated because of economic pressures. Such consolidations can potentially jeopardize the poultry industry and the ability of research communities to respond to future challenges. To address the loss of genetic resources for all livestock and aquatic species, USDA established the National Animal Germplasm Program (NAGP) in 1999. Since the initiation of NAGP, population surveys have been conducted on nonindustrial chicken and turkey breeds. These surveys not only provide insight into breed status, but also serve as a benchmark for future comparisons. The survey results revealed that 20 chicken breeds and 9 turkey breeds were in various stages of being lost. The NAGP has initiated an ex situ repository for cryopreserved germplasm and tissue that already contains 59 chicken lines and 2,915 tissue samples. As the NAGP, along with its industry and university partners, continues developing the ex situ collection, there are research opportunities in cryopreserved tissue utilization and studies of genetic diversity. For cryopreserved tissues, several key research areas include improving the cryopreservation protocols for rooster and tom semen by using cryoprotectants other than glycerol and utilizing embryonic cells. Although surveys have been conducted on public research lines and rare breeds, there is a void in understanding the level of genetic diversity present in U.S. poultry populations. Therefore, an opportunity exists to perform a series of genetic diversity studies using molecular- based approaches. Such an evaluation can help clarify population differences between research lines and rare breeds and, thereby, facilitate conservation strategies. There appears to be growing consumer interest in poultry products derived from heritage breeds and/or poultry raised in nonindustrial production systems. Although the depth of such market trends is unknown, such an interest may provide an important niche for rare poultry breeds and, thereby, strengthen the genetic base.

Breeding and genetics--historical perspective.

This paper is a review of selection methods that have been used in commercial breeding of table egg stocks, broilers, and turkeys, based on the author's experience. In addition, a number of historic developments that have shaped or influenced the selection process are listed and the significance of each is discussed. The merits of mass selection are noted and compared with the multiple forms of family selection, e.g., full or half sibs, progeny testing, and recurrent methods. Each of these methods is believed to have nearly universal application in applied breeding programs being practiced today. This review concludes that a combination of individual and family selection practices aimed at improving multiple traits simultaneously is required to remain a successful supplier of breeding stock to the current commercial industry.

Genetic selection strategies--population genetics.

This paper provides an overview of the association between population genetics and selection strategies in poultry. Relationships between artificial and natural selection and among causes contributing to limits to artificial selection are discussed. Homeostasis and resource allocations at the individual and at the population level are reviewed. Examples from poultry demonstrate where human intervention has circumvented biological limits. Lastly, this paper considers the role of population genetics in future breeding strategies for poultry.

Commercial approaches to genetic selection for growth and feed conversion in domestic poultry.

Tremendous genetic progress has been observed historically for growth and feed conversion through the efforts of the primary breeding companies. However, significant between-strain variation still exists due to differences in selection emphasis and selection techniques practiced by these organizations. This paper provides an overview of methods currently employed in commercial poultry breeding with reference to factors complicating program design and future challenges facing the industry. Mass selection for body weight has resulted in a significant reduction in the number of days required to grow bird to market weight with indirect improvements in feed conversion. Direct selection for feed conversion is accomplished through part record testing of males that have been preselected for body weight, conformation, and defect traits. Data are commonly subjected to complex statistical analysis both to correct feed conversion for variation in body weight and to improve the accuracy of breeding value estimates. Feed conversion breeding values of male sibs are sometimes used for the selection of female candidates as well. Selection for growth rate and efficiency has resulted in negative complications, such as ascites, reduced reproductive performance, skeletal abnormalities, and increased carcass fatness. Some of these factors may be partially ameliorated through modified selection practices. If not addressed by the breeding industry, the disruption of physiological homeostasis might ultimately represent economic and genetic barriers to further progress in improving growth and efficiency. Modern techniques in molecular genetics, utilized in conjunction with traditional quantitative genetic approaches, will provide additional opportunities to circumvent these physiological complications associated with genetic selection for growth and feed efficiency.

The selection index--then, now, and for the future.

When improvement is desired for several traits that may differ in variability, heritability, economic importance, and in the correlation among their phenotypes and genotypes, simultaneous multiple-trait index selection was more effective than independent culling levels or sequential selection. Such comparisons required definition of aggregate breeding value determined jointly by breeding values and economic importance of the component traits. The economic weight should approximate the partial regression of cost per unit of enterprise output value on breeding value for each trait. These can vary with production and marketing system, with performance of traits, and with breed role (i.e., paternal, maternal, or general) in crossbreeding systems. Genetic gains desired to maintain competitive ranking also may define the relative importance of traits. Because information available to estimate breeding values varies among the ages and categories of individuals under selection and because means are unknown, regressed (BLUP) predictions of trait breeding values are useful. They allow appropriate economic weights to be applied as the last step for predicting aggregate breeding values for individuals of different age classes, and they simplify choosing the proportions of selected breeders from each age class that maximize rate of change in aggregate breeding values. Inappropriate economic weights or errors in the parameters used to predict trait breeding values overestimate realized response in true aggregate breeding value.