Selection of broilers with improved innate immune responsiveness to reduce on-farm infection by foodborne pathogens

RNA-Seq Profiling between Commercial and Indigenous Iranian Chickens Highlights Differences in Innate Immune Gene Expression

The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5). Overall, 1327 genes were significantly differentially expressed, of which 1013 genes were upregulated in the commercial versus the indigenous breed, while 314 were more highly expressed in the indigenous birds. Furthermore, our results demonstrated that the SPARC, ATP6V0D2, IL4I1, SMPDL3A, ADAM7, TMCC3, ULK2, MYO6, THG1L and IRG1 genes were the most significantly expressed genes in the commercial birds and the PAPPA, DUSP1, PSMD12, LHX8, IL8, TRPM2, GDAP1L1, FAM161A, ABCC2 and ASAH2 genes were the most significant in the indigenous chickens. Of notable finding in this study was that the high-level gene expressions of heat-shock proteins (HSPs) in the indigenous breeds could serve as a guideline for future genetic improvement. This study identified genes with breed-specific expression, and comparative transcriptome analysis helped understanding of the differences in underlying genetic mechanisms between commercial and local breeds. Therefore, the current results can be used to identify candidate genes for further breed improvement.

Genetic variation in chicken interferon signalling pathway genes in research lines showing differential viral resistance

Avian viruses of economic interest are a significant burden on the poultry industry, affecting production traits and resulting in mortality. Furthermore, the zoonosis of avian viruses risks pandemics developing in humans. Vaccination is the most common method of controlling viruses; however current vaccines often lack cross-protection against multiple strains of each virus. The mutagenicity of these viruses has also led to virulent strains emerging that can overcome the protection offered by vaccines. Breeding chickens with a more robust innate immune response may help in tackling current and emerging viruses. Understanding the genetic evolution of different lines will thus provide a useful tool in helping the host in the fight against pathogens. This study focuses on the interferon genes and their receptors in different chicken lines that are known to be more resistant or susceptible to particular avian viruses. Comparing genotypic differences in these core immune genes between the chicken lines may explain the phenotypic differences observed and aid the identification of causative variations. The relative resistance/susceptibility of each line to viruses of interest (Marek's disease virus, infectious bursal disease, infectious bronchitis virus and avian influenza virus) has previously been determined. Here we identify single nucleotide polymorphisms in interferons and downstream genes. Functional prediction tools were used to identify variants that may be affecting protein structure, mRNA secondary structure or transcription factor and micro-RNA binding sites. These variants were then considered in the context of the research lines and their distribution between phenotypes. We highlight 60 variants of interest in the interferon pathway genes that may account for susceptibility/resistance to viral pathogens.

Age and sex related changes in fattening performance, dermatitis, intestinal histomorphology, and serum IgG level of slow- and fast-growing broilers under the intensive system

Due to consumers' concerns about broiler welfare, slow-growing broilers (SGB) have also been used in production. Fast-growing broilers (FGB) reach slaughter weight earlier the slow growing. This study was aimed to determine the sex-related changes in fattening performance, dermatitis, intestinal histomorphology, and serum IgG level of SGB and FGB under the intensive system during the 10 weeks. A total of 336 one-day-old broilers were distributed into four equal groups (FGB-female, FGB-male, SGB-female, and SGB-male) consisting of a 2 × 2 factorial design. The main factors were genotype (FGB and SGB) and sex (female and male). Each treatment had 6 duplicates consisting of 14 broilers. They were placed on the litter pens. The experiment lasted 10 weeks. The body weight, body weight gain, feed consumption, and feed-to-gain ratio were determined weekly during the experiment. One broiler close to the average body weight from each pen (6 broilers in the group) has been slaughtered each week and intestinal histomorphology was determined. Additionally, IgG levels in the blood and dermatitis were determined. While the period in which the body weight gain was the highest in the FGB was up to 6 week of age, this period lasted until the 7 week of age in the SGB (P < 0.001). It has been determined that FGB have the best feed efficiency ability during both 6 weeks of fattening period and 10 weeks of fattening period (P < 0.001). The difference between the sex in terms of the feed efficiency appeared after the age of 4 weeks and this difference continued until the age of 9 weeks (P < 0.01). It was determined that villus height, crypt depth, and the ratio of villus height to crypt depth in the jejunum region were higher in FGB from the age of 1 week than in SGB (P < 0.05). It was observed that the incidence of dermatitis increased in the FGB (P < 0.001). It has been determined that the genotype (P < 0.01) and period (P < 0.001) were effective according to the IgG level. These results indicate that 7 and 8 weeks can be considered important periods in terms of economic efficiency in SGB and FGB reared for 10 weeks under the same management systems and it was observed that both genotypes would be more susceptible to diseases at the age of 6 weeks.

Advances in genetic selection and breeder practice improve commercial layer hen welfare

Modern commercial layer breeds represent the culmination of ~7000 years of natural genetic selection. This selection was driven in former times by a combination of genetic-shift and -drift events, that led to chickens being favoured as domesticated species for meat and egg production. More recently, in the early 20th century, the concept of hybrid vigour was discovered and accelerated the natural breeding progress that delivered new genetic lines and more favourable production traits. In the mid-20th century, the broiler-type and egg layer-type lines diverged and, in the 21st century, genetic analysis has further accelerated the progress made towards extended primary breeding characteristics such as egg quality, production and feed-intake traits, together with secondary breeding characteristics such as behavioural traits that have improved robustness in different housing systems, climates and feed types, which together have significantly improved welfare traits. Most recently, there has been the adoption of higher-powered computational analytics together with quantitative trait loci and single-nucleotide polymorphism assessment, which have further improved the uniformity of production traits within breeds. Most importantly, this has provided the primary breeding companies with improved and broader basis of selection of the modern commercial layer breeds, which also improved the alignment of layer strains with market requirements, and diverse variations in housing, nutritional and environmental conditions. This is also testament to the speed with which the commercial layer geneticists can respond to changing welfare policy on factors such as stocking density and beak treatment. The present paper reviews the modern approaches to genetic selection, including considerations of and benefits to the welfare state of commercial layers.

Profiles of expression pattern and tissue distribution of host defense peptides genes in different chicken (Gallus gallus) breeds related to body weight

Host defense peptides (HDPs) are an important first line of defense with antimicrobial and immunomodulatory properties. Selection for increased body weight is hypothesized to be related to reduced immune response. We studied the relationships among body weight, age, and the HDP expression patterns in intestine and immune organs. We used chickens with marked differences of body sizes. The non-selected Daweishan mini chickens showed the highest indexes of immune organs and the lowest concentrations of the plasma immune parameters C3, C4, IgA, and IgY, while the commercial Avian broiler showed the opposite results. The Daweishan mini chickens showed the highest mRNA expressions of HDP genes in small intestine followed by the semi-selected Wuding chickens. Compared with local breeds, broiler chickens showed higher mRNA expression of HDP genes in spleen, thymus, and bursa. Body weight and HDP expression levels were negatively correlated in the intestine and positively in the immune organs. Our results indicated that the HDP immune regulatory roles in small intestine acted as first line of defense in innate immunity in local breeds, and as an adaptive immunity in broiler chickens. Selection was associated with different expression expressions of HDP genes in breed-, age-, and organ-specific manners.

An integrated transcriptomics and metabolomics study of the immune response of newly hatched chicks to the cytosine-phosphate-guanine oligonucleotide stimulation

The immunological immaturity of the innate immune system during the first-week post-hatch enables pathogens to infect chickens, leading to the death of the animals. Current preventive solutions to improve the resistance of chicks to infections include vaccination, breeding, and sanitation. Other prophylactic solutions have been investigated, such as the stimulation of animal health with immunostimulants. Recent studies showed that administration of immune-modulators to one-day-old chicks, or in ovo, significantly reduces mortality in experimental bacterial or viral infection challenge models. Owing to a lack of molecular biomarkers required to evaluate chicken immune responses and assess the efficacy of vaccines or immune-modulators, challenge models are still used. One way to reduce challenge experiments is to define molecular signatures through omics approaches, resulting in new methodologies to rapidly screen candidate molecules or vaccines. This study aims at identifying a dual transcriptomics and metabolomics blood signature after administration of CpG-ODN (cytosine-phosphate-guanine oligodeoxynucleotides), a reference immune-stimulatory molecule. A clinical study was conducted with chicks and transcriptomics and metabolomics analyses were performed on whole-blood and plasma samples, respectively. Differentially expressed genes and metabolites with different abundance were identified in chicks treated with CpG-ODN. The results showed that CpG-ODN activated the innate immune system, within hours after administration, and its effect lasted over time, as metabolomics and transcriptomics profiles still varied 6 D after administration. In conclusion, through an integrated clinical omics approach, we deciphered in part the mode of action of CpG-ODN in post-hatch chicks.

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses

To address the need for sensitive high-throughput assays to analyse avian innate and adaptive immune responses, we developed and validated a highly multiplexed qPCR 96.96 Fluidigm Dynamic Array to analyse the transcription of chicken immune-related genes. This microfluidic system permits the simultaneous analysis of expression of 96 transcripts in 96 samples in 6 nanolitre reactions and the 9,216 reactions are ready for interpretation immediately. A panel of 89 genes was selected from an RNA-seq analysis of the transcriptional response of chicken macrophages, dendritic cells and heterophils to agonists of innate immunity and from published transcriptome data. Assays were confirmed to be highly specific by amplicon sequencing and melting curve analysis and the reverse transcription and preamplification steps were optimised. The array was applied to RNA of various tissues from a commercial line of broiler chickens housed at two different levels of biosecurity. Gut-associated lymphoid tissues, bursa, spleen and peripheral blood leukocytes were isolated and transcript levels for immune-related genes were defined. The results identified blood cells as a potentially reliable indicator of immune responses among all the tissues tested with the highest number of genes significantly differentially transcribed between birds housed under varying biosecurity levels. Conventional qPCR analysis of three differentially transcribed genes confirmed the results from the multiplex qPCR array. A highly multiplexed qPCR-based platform for evaluation of chicken immune responses has been optimised and validated using samples from commercial chickens. Apart from applications in selective breeding programmes, the array could be used to analyse the complex interplay between the avian immune system and pathogens by including pathogen-specific probes, to screen vaccine responses, and as a predictive tool for immune robustness.

In Ovo Administration of Innate Immune Stimulants and Protection from Early Chick Mortalities due to Yolk Sac Infection

Omphalitis or yolk sac infection (YSI) and colibacillosis are the most common infectious diseases that lead to high rates of early chick mortalities (ECMs) in young chicks. Out of numerous microbial causes, avian pathogenic Escherichia coli (APEC) or extraintestinal pathogenic E. coli infections are considered the most common cause of these conditions. YSI causes deterioration and decomposition of yolk, leading to deficiency of necessary nutrients and maternal antibodies, retarded growth, poor carcass quality, and increased susceptibility to other infections, including omphalitis, colibacillosis, and respiratory tract infection. Presently, in ovo injection of antibiotics, heavy culling, or after hatch use of antibiotics is practiced to manage ECM. However, increased antibiotic resistance and emergence of "super bugs" associated with use or misuse of antibiotics in the animal industry have raised serious concerns. These concerns urgently require a focus on host-driven nonantibiotic approaches for stimulation of protective antimicrobial immunity. Using an experimental YSI model in newborn chicks, we evaluated the prophylactic potential of three in ovo-administered innate immune stimulants and immune adjuvants for protection from ECM due to YSI. Our data have shown >80%, 65%, and 60% survival with in ovo use of cytosine-phosphodiester-guanine (CpG) oligodeoxynucleotides (ODN), polyinosinic:polycytidylic acid, and polyphosphazene, respectively. In conclusion, data from these studies suggest that in ovo administration of CpG ODN may serve as a potential candidate for replacement of antibiotics for the prevention and control of ECM due to YSI in young chicks.

Testing plasma subtilisin inhibitory activity as a selective marker for dermo resistance in eastern oysters

Recent findings have suggested that eastern oyster plasma possesses inhibitors of the protease subtilisin, which play a role in the host defense against Perkinsus marinus, a protist parasite causing dermo. A study was conducted to determine whether plasma subtilisin inhibitory activity (PSIA) could be used as a selective marker in breeding programs for dermo resistance. Eastern oysters Crassostrea virginica from 2 wild Louisiana populations shown to differ in dermo resistance were collected and their PSIA was measured. Three groups of oysters were established to spawn from each population. One group was composed of randomly sampled oysters (i.e. unselected) and the other 2 groups were composed of oysters with the highest or lowest PSIA. After spawning, progenies were deployed in October 2014 in a dermo endemic area and sampled quarterly for 2 yr to measure their mortality, growth, P. marinus infection intensity, condition index, PSIA, and the gene expression of 3 subtilisin inhibitors (cvSI-1, cvSI-2, and cvSI-3). Oyster cumulative mortalities of the progenies of all groups increased both years from April to October, concomitant with increasing P. marinus infection intensities. Mortalities and P. marinus infection intensities differed markedly between the 2 populations, but differences between the unselected and selected groups of each population were limited. Measurements of PSIA and cvSI-1, cvSI-2, and cvSI-3 gene expressions between the progenies of all groups showed few differences. CvSI-1 gene expression in surviving oysters of the most susceptible population was increased at the end of the study, adding additional support to the potential role of cvSI-1 defense against P. marinus.

A comparative study of acute-phase protein concentrations in historical and modern broiler breeding lines

Acute-phase proteins (APP) are secreted from the liver as a result of inflammation or infection and are measurable in serum and plasma. To determine whether the constitutive APP serum amyloid A (SAA), alpha-1-acid glycoprotein (AGP), ceruloplasmin (Cp), and ovotransferrin (Ovt) have changed as a result of selection for improved production and growth characteristics over the last 40 yr two historical broilers lines were compared to a modern line of the same lineage. Serum was harvested from blood samples taken from the 3 broiler lines on days 10, 17, and 20, and the APP concentrations were determined using immunoassay methods. Most of the significant changes observed were age related, with SAA and Cp having significantly lower concentrations at day 20 than days 10 and 17 in all lines. The only significant difference between lines was observed at day 20 on which both Cp (P = 0.01) and AGP (P = 0.03) were significantly higher in the modern line than the 90s line, though no significant differences were noted between the modern and 70s line. When evaluating the difference in APP concentrations between males (Cx) and females (Px) across all 3 lines, females had a higher SAA at day 17 and lower SAA at day 20, P = 0.0078 and 0.0327 respectively, and males had a significantly higher Ovt on days 17 and 20 (P = 0.0002 and P = 0.003 respectively). These results reveal that APP concentrations fluctuate over this early period of growth and that the changes in APP serum concentration appear uniform between 3 lines with very contrasting selection history, suggesting the improvements made in meat production efficiency since the 1970s have not affected the circulating concentrations of these constitutively expressed APP.

Overexpressing ovotransferrin and avian β-defensin-3 improves antimicrobial capacity of chickens and poultry products

Zoonotic and foodborne diseases pose a significant burden, decreasing both human and animal health. Modifying chickens to overexpress antimicrobials has the potential to decrease bacterial growth on poultry products and boost chicken innate immunity. Chickens overexpressing either ovotransferrin or avian β-defensin-3 (AvβD3) were generated using Tol-2 transposons. Transgene expression at the RNA and protein level was seen in egg white, breast muscle, and serum. There were significant differences in the immune cell populations in the blood, bursa, and spleen associated with transgene expression including an increased proportion of CD8+ cells in the blood of ovotransferrin and AvβD3 transgenic birds. Expression of the antimicrobials inhibited the in vitro growth of human and chicken bacterial pathogens and spoilage bacteria. For example, transgene expression significantly reduced growth of aerobic and coliform bacteria in breast muscle and decreased the growth of Salmonella enterica in egg white. Overall these results indicate that overexpression of antimicrobials in the chicken can impact the immune system and increase the antimicrobial capacity of poultry products.

Food-Associated Stress Primes Foodborne Pathogens for the Gastrointestinal Phase of Infection

The incidence of foodborne outbreaks and product recalls is on the rise. The ability of the pathogen to adapt and survive under stressful environments of food processing and the host gastrointestinal tract may contribute to increasing foodborne illnesses. In the host, multiple factors such as bacteriolytic enzymes, acidic pH, bile, resident microflora, antimicrobial peptides, and innate and adaptive immune responses are essential in eliminating pathogens. Likewise, food processing and preservation techniques are employed to eliminate or reduce human pathogens load in food. However, sub-lethal processing or preservation treatments may evoke bacterial coping mechanisms that alter gene expression, specifically and broadly, resulting in resistance to the bactericidal insults. Furthermore, environmentally cued changes in gene expression can lead to changes in bacterial adhesion, colonization, invasion, and toxin production that contribute to pathogen virulence. The shared microenvironment between the food preservation techniques and the host gastrointestinal tract drives microbes to adapt to the stressful environment, resulting in enhanced virulence and infectivity during a foodborne illness episode.

Evaluation of genetic resistance to Salmonella Pullorum in three chicken lines

Resistance to diseases varies considerably among populations of the same species and can be ascribed to both genetic and environmental factors. Salmonella Pullorum (SP) is responsible for significant losses in the poultry industry, especially in developing countries. To better understand SP resistance in chicken populations with different genetic backgrounds, we orally challenged 3 chicken lines with SP-a highly selected commercial breed (Rhode Island Red, RIR), a local Chinese chicken (Beijing You, BY), and a synthetic layer line (dwarf, DW)-at 4 d of age. Two traits related to SP resistance, survival, and bacterial carriage in the spleen were evaluated after infection. Survival rates were recorded up to 40 d of age when all chickens still alive were killed to verify the presence of SP in the spleen to determine carrier state. Mortalities for RIR, BY, and DW chicks were 25.1%, 8.3%, and 22.7%, respectively, and the corresponding carrier-states in the spleens were 17.9%, 0.6%, and 15.8%. Survival and carrier-state heritabilities were estimated using an animal threshold model. Survival heritability was 0.197, 0.091, and 0.167 in RIR, BY, and DW populations, respectively, and the heritabilities of carrier state for DW and RIR were 0.32 and 0.16, respectively. This is the first time that the heritability of the SP carrier state has been evaluated in chickens. Our study provides experimental evidence that chickens with various genetic background exhibited significantly different SP-resistant activities and heritabilities. These results may be useful for selecting lines with better disease resistance.

Does selection for growth rate in broilers affect their resistance and tolerance to Eimeria maxima?

Chickens exhibit varied responses to infection with Eimeria parasites. We hypothesise that broilers selected for increased growth rate will show lower resistance and tolerance to a coccidian challenge. 288 chickens of fast (F) or slow (S) growing lines were inoculated with 0 (control), 2500 (low-dose), or 7000 (high-dose) sporulated E. maxima oocysts at 13 days of age in two consecutive rounds. Gain and Intake were measured daily and their values relative to BW at the point of infection were calculated over the pre-patent (days 1-4 post-infection), acute (d5-8 pi), and recovery (d9-12 pi) phases of infection to assess the impact of infection. Levels of plasma carotenoids, vitamins E and A, long bone mineralisation, caecal microbiota diversity indices, and histological measurements were assessed at the acute (d6 pi) and recovery stage (d13 pi). In addition, we measured the levels of nitric oxide metabolites and the number of parasite genome copies in the jejunumat d6pi. In absolute terms F birds grew 1.42 times faster than S birds when not infected. Infection significantly reduced relative daily gain and intake (P < 0.001), with the effects being most pronounced during the acute phase (P < 0.001). Levels of all metabolites were significantly decreased, apart from NO which increased (P < 0.001) in response to infection on d6pi, and were accompanied by changes in histomorphometric features and the presence of E. maxima genome copies in infected birds, which persisted to d13pi. Furthermore, infection reduced tibia and femur mineralisation, which also persisted to d13pi. Reductions in measured variables were mostly independent of dose size, as was the level of parasite replication. The impact of infection was similar for S and F-line birds for all measured parameters, and there were no significant interactions between line x dose size on any of these parameters. In conclusion, our results suggest that line differences in productive performance do not influence host responses to coccidiosis when offered nutrient adequate diets.

Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities

Preharvest strategies to reduce zoonotic pathogens in food animals are important components of the farm-to-table food safety continuum. The problem is complex; there are multiple pathogens of concern, multiple animal species under different production and management systems, and a variety of sources of pathogens, including other livestock and domestic animals, wild animals and birds, insects, water, and feed. Preharvest food safety research has identified a number of intervention strategies, including probiotics, direct-fed microbials, competitive exclusion cultures, vaccines, and bacteriophages, in addition to factors that can impact pathogens on-farm, such as seasonality, production systems, diet, and dietary additives. Moreover, this work has revealed both challenges and opportunities for reducing pathogens in food animals. Animals that shed high levels of pathogens and predominant pathogen strains that exhibit long-term persistence appear to play significant roles in maintaining the prevalence of pathogens in animals and their production environment. Continued investigation and advancements in sequencing and other technologies are expected to reveal the mechanisms that result in super-shedding and persistence, in addition to increasing the prospects for selection of pathogen-resistant food animals and understanding of the microbial ecology of the gastrointestinal tract with regard to zoonotic pathogen colonization. It is likely that this continued research will reveal other challenges, which may further indicate potential targets or critical control points for pathogen reduction in livestock. Additional benefits of the preharvest reduction of pathogens in food animals are the reduction of produce, water, and environmental contamination, and thereby lower risk for human illnesses linked to these sources.

MyD88 Polymorphisms and Association with Susceptibility to Salmonella Pullorum

Myeloid differentiation primary response gene 88 (MYD88), a universal adapter protein, plays an important role in activating the nuclear factor-κB (NF-κB) and regulating the expression of proinflammatory genes like tumor necrosis factor (TNF) and interleukin-1 (IL-1), which were highly involved in Salmonella Pullorum infection. To detect the relationship between polymorphisms of the MyD88 gene and Salmonella Pullorum disease, we screened the coding region (CDS) of the MYD88 gene by DNA pool construction and sequencing based on case-control study. Eight single nucleotide polymorphisms (SNPs) in the sequenced fragment (5 exons), 7 known loci and one novel mutation named G4810372T (SNP8), were found in the fifth exon. In addition, we found 7 nonsynonymous substitutions. The allele frequency of only one SNP, g.4810191C > T (SNP1), was significantly different (P < 0.05) between case and control groups. The genotype frequencies of SNP1 (g.4810191C > T) and SNP3 (g.4810257G > T) were of significant difference between the case and the control groups (P < 0.05). Collectively, SNPs of the MyD88 gene were significantly associated with susceptibility to Salmonella Pullorum infection, which can be used as a disease-resistant marker in chicken. These results provided a theoretical basis for future research on chicken breeding by marker-assisted selection.

The identification of loci for immune traits in chickens using a genome-wide association study

The genetic improvement of disease resistance in poultry continues to be a challenge. To identify candidate genes and loci responsible for these traits, genome-wide association studies using the chicken 60k high density single nucleotide polymorphism (SNP) array for six immune traits, total serum immunoglobulin Y (IgY) level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against Avian Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed. RT-qPCR was used to quantify the relative expression of the identified candidate genes. Nine significantly associated SNPs (P < 2.81E-06) and 30 SNPs reaching the suggestively significant level (P < 5.62E-05) were identified. Five of the 10 SNPs that were suggestively associated with the antibody response to SRBC were located within or close to previously reported QTL regions. Fifteen SNPs reached a suggestive significance level for AIV antibody titer and seven were found on the sex chromosome Z. Seven suggestive markers involving five different SNPs were identified for the numbers of heterophils and lymphocytes, and the heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16, were significantly associated with serum total IgY concentration, and the five most significant were located within a narrow region spanning 6.4kb to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this region, changes in IL4I1, CD1b transcripts were consistent with the concentrations of IgY, while abundances of TRIM27 and ZNF692 showed reciprocal changes to those of IgY concentrations. This study has revealed 39 SNPs associated with six immune traits (total serum IgY level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against AIV and SRBC) in Beijing-You chickens. The narrow region spanning 247kb on chromosome 16 is an important QTL for serum total IgY concentration. Five candidate genes related to IgY level validated here are novel and may play critical roles in the modulation of immune responses. Potentially useful candidate SNPs for marker-assisted selection for disease resistance are identified. It is highly likely that these candidate genes play roles in various aspects of the immune response in chickens.

Intestinal colonization of broiler chickens by Campylobacter spp. in an experimental infection study

Consumption of poultry meat is considered as one of the main sources of human campylobacteriosis, and there is clearly a need for new surveillance and control measures based on quantitative data on Campylobacter spp. colonization dynamics in broiler chickens. We conducted four experimental infection trials, using four isolators during each infection trial to evaluate colonization of individual broiler chickens by Campylobacter jejuni over time. Individual and pooled faecal samples were obtained at days 4, 7 and 12 post-inoculation (p.i.) and caecal samples at day 12 p.i. There were large differences between broiler chickens in the number of C. jejuni in caecal and faecal material. Faecal samples of C. jejuni ranged from 4·0 to 9·4 log c.f.u./g and from 4·8 to 9·3 log c.f.u./g in the caeca. Faecal c.f.u./g decreased with time p.i. Most variation in c.f.u. for faecal and caecal samples was attributed to broiler chickens and a minor part to isolators, whereas infection trials did not affect the total variance. The results showed that pooled samples within isolators had lower c.f.u./g compared to the arithmetic mean of the individual samples. There was a significant correlation between faecal c.f.u./g at days 4 and 7 p.i., days 7 and 12 p.i. and for caecal and faecal c.f.u./g at day 12 p.i.

The peripheral blood transcriptome reflects variations in immunity traits in swine: towards the identification of biomarkers

BACKGROUND

Immune traits (ITs) are potentially relevant criteria to characterize an individual's immune response. Our aim was to investigate whether the peripheral blood transcriptome can provide a significant and comprehensive view of IT variations in pig.

RESULTS

Sixty-day-old Large White pigs classified as extreme for in vitro production of IL2, IL10, IFNγ and TNFα, phagocytosis activity, in vivo CD4⁻/CD8⁺ or TCRγδ + cell counts, and anti-Mycoplasma antibody levels were chosen to perform a blood transcriptome analysis with a porcine generic array enriched with immunity-related genes. Differentially expressed (DE) genes for in vitro production of IL2 and IL10, phagocytosis activity and CD4⁻/CD8⁺ cell counts were identified. Gene set enrichment analysis revealed a significant over-representation of immune response functions. To validate the microarray-based results, a subset of DE genes was confirmed by RT-qPCR. An independent set of 74 animals was used to validate the covariation between gene expression levels and ITs. Five potential gene biomarkers were found for prediction of IL2 (RALGDS), phagocytosis (ALOX12) or CD4⁻/CD8⁺ cell count (GNLY, KLRG1 and CX3CR1). On average, these biomarkers performed with a sensitivity of 79% and a specificity of 86%.

CONCLUSIONS

Our results confirmed that gene expression profiling in blood represents a relevant molecular phenotype to refine ITs in pig and to identify potential biomarkers that can provide new insights into immune response analysis.

Transgenerational epigenetic effects on innate immunity in broilers: an underestimated field to be explored?

Transgenerational epigenetics is becoming more and more important for understanding the variation of physiological responses of individuals to the environment and the inheritance of these responses based on all mechanisms other than the actual DNA nucleotide sequence. Transgenerational epigenetics is the phenomenon that the information of the environment of (usually) a female animal is translated into memory-like responses preparing the offspring. As a consequence, individuals of the next generation may show different phenotypic traits depending whether their mothers were kept under different environmental conditions. This may result in either positive or negative effects on the next-generation individuals, which is different from individuals from mothers that have been kept in a different environment. Transgenerational epigenetic effects have been proposed and indicated for specific immune (T cell and antibody) responses (especially in mammals, but also in birds) and innate immunity (nonvertebrates), but surprisingly very little is known of transgenerational effects on innate immunity in chickens. Given the short lifespan of the chicken and therefore the likely dependence of chicken on innate immune mechanisms, more attention should be given to this arm of immunity and mechanisms of inheritance including transgenerational effects that can be initiated in the breeder generation. In addition, it is becoming evident that innate immunity also underlies metabolic disorders in broilers. In the current paper, we will argue that although very little is known of transgenerational effects of innate immunity in poultry, more attention should be given to this type of study. We will illustrate examples of transgenerational epigenetics, and finally propose strategies that should reveal the presence of transgenerational epigenetic effects on innate immunity in chickens and strategies to modulate breeder birds such that these effects positively affect innate immunity of broilers. It is suggested that a mismatch between breeder environment and broiler environment may account for unwanted effects of innate immunity in the broiler.

Regulation of macrophage and dendritic cell function by pathogens and through immunomodulation in the avian mucosa

Macrophages (MPh) and dendritic cells (DC) are members of the mononuclear phagocyte system. In chickens, markers to distinguish MPh from DC are lacking, but whether MPh and DC can be distinguished in humans and mice is under debate, despite the availability of numerous markers. Mucosal MPh and DC are strategically located to ingest foreign antigens, suggesting they can rapidly respond to invading pathogens. This review addresses our current understanding of DC and MPh function, the receptors expressed by MPh and DC involved in pathogen recognition, and the responses of DC and MPh against respiratory and intestinal pathogens in the chicken. Furthermore, potential opportunities are described to modulate MPh and DC responses to enhance disease resistance, highlighting modulation through nutraceuticals and vaccination.

Modulation of chicken intestinal immune gene expression by small cationic peptides as feed additives during the first week posthatch

We have been investigating modulation strategies tailored around the selective stimulation of the host's immune system as an alternative to direct targeting of microbial pathogens by antibiotics. One such approach is the use of a group of small cationic peptides (BT) produced by a Gram-positive soil bacterium, Brevibacillus texasporus. These peptides have immune modulatory properties that enhance both leukocyte functional efficiency and leukocyte proinflammatory cytokine and chemokine mRNA transcription activities in vitro. In addition, when provided as a feed additive for just 4 days posthatch, BT peptides significantly induce a concentration-dependent protection against cecal and extraintestinal colonization by Salmonella enterica serovar Enteritidis. In the present studies, we assessed the effects of feeding BT peptides on transcriptional changes on proinflammatory cytokines, inflammatory chemokines, and Toll-like receptors (TLR) in the ceca of broiler chickens with and without S. Enteritidis infection. After feeding a BT peptide-supplemented diet for the first 4 days posthatch, chickens were then challenged with S. Enteritidis, and intestinal gene expression was measured at 1 or 7 days postinfection (p.i.) (5 or 11 days of age). Intestinal expression of innate immune mRNA transcripts was analyzed by quantitative real-time PCR (qRT-PCR). Analysis of relative mRNA expression showed that a BT peptide-supplemented diet did not directly induce the transcription of proinflammatory cytokine, inflammatory chemokine, type I/II interferon (IFN), or TLR mRNA in chicken cecum. However, feeding the BT peptide-supplemented diet primed cecal tissue for increased (P ≤ 0.05) transcription of TLR4, TLR15, and TLR21 upon infection with S. Enteritidis on days 1 and 7 p.i. Likewise, feeding the BT peptides primed the cecal tissue for increased transcription of proinflammatory cytokines (interleukin 1β [IL-1β], IL-6, IL-18, type I and II IFNs) and inflammatory chemokine (CxCLi2) in response to S. Enteritidis infection 1 and 7 days p.i. compared to the chickens fed the basal diet. These small cationic peptides may prove useful as alternatives to antibiotics as local immune modulators in neonatal poultry by providing prophylactic protection against Salmonella infections.

Transcriptomic response of porcine PBMCs to vaccination with tetanus toxoid as a model antigen

The aim of the present study was to characterize in vivo genome-wide transcriptional responses to immune stimulation in order to get insight into the resulting changes of allocation of resources. Vaccination with tetanus toxoid was used as a model for a mixed Th1 and Th2 immune response in pig. Expression profiles of PBMCs (peripheral blood mononuclear cells) before and at 12 time points over a period of four weeks after initial and booster vaccination at day 14 were studied by use of Affymetrix GeneChip microarrays and Ingenuity Pathway Analysis (IPA). The transcriptome data in total comprised more than 5000 genes with different transcript abundances (DE-genes). Within the single time stages the numbers of DE-genes were between several hundred and more than 1000. Ingenuity Pathway Analysis mainly revealed canonical pathways of cellular immune response and cytokine signaling as well as a broad range of processes in cellular and organismal growth, proliferation and development, cell signaling, biosynthesis and metabolism. Significant changes in the expression profiles of PBMCs already occurred very early after immune stimulation. At two hours after the first vaccination 679 DE-genes corresponding to 110 canonical pathways of cytokine signaling, cellular immune response and other multiple cellular functions were found. Immune competence and global disease resistance are heritable but difficult to measure and to address by breeding. Besides QTL mapping of immune traits gene expression profiling facilitates the detection of functional gene networks and thus functional candidate genes.

Early immune dynamics following infection with Salmonella enterica serovars Enteritidis, Infantis, Pullorum and Gallinarum: cytokine and chemokine gene expression profile and cellular changes of chicken cecal tonsils

Salmonella enterica subspecies enterica infection remains a serious problem in a wide range of animals and in man. Poultry-derived food is the main source of human infection with the non-host-adapted serovars while fowl typhoid and pullorum disease are important diseases of poultry. We have assessed cecal colonization and immune responses of newly hatched and older chickens to Salmonella serotypes Enteritidis, Infantis, Gallinarum and Pullorum. S. Enteritidis and S. Infantis colonized the ceca more efficiently than S. Gallinarum and S. Pullorum. Salmonella infection was also associated with increased staining for B-lymphocytes and macrophages in the cecal tonsils of infected birds. S. Enteritidis infection in newly hatched birds stimulated the expression of CXCLi1 and CXCLi2 chemokines in the cecal tonsils, while S. Gallinarum up-regulated the expression of LITAF. In older chickens, S. Enteritidis infection resulted in a significantly higher expression of CXCLi2, iNOS, LITAF and IL-10 while S. Pullorum appeared to down-regulate CXCLi1 expression in the cecal tonsils. Data from spleens showed either no expression or down-regulation of the tested genes.

Transcript profiling of pattern recognition receptors in a semi domesticated breed of buffalo, Toda, of India

The primary objective of this study was to assess the expression profile and levels of toll-like receptor (TLR) mRNAs in the spleen, lung, mediastinal lymph node (MLN), jejunum, rectum, skin and peripheral blood mononuclear cells (PBMC) of Toda and Murrah buffalos. Spleen and PBMC had increased expression of TLR mRNAs 2, 4, 5, 6, 8, 9 and 10; lung had increased expression of TLR mRNAs 2, 4, 5, 6 and 8, MLN TLR mRNA 6, 9, 10 and decrease in TLR 3 and 7 mRNAs in skin. No significant differences were observed in the expression levels of any of the TLR mRNA in jejunum and rectum. Toda buffaloes showed significantly higher expression levels of TLR 9 mRNA in MLN, TLR mRNAs 1, 5, 6, 9 and 10 in skin and TLR mRNAs 2, 4, 7 and 9 in PBMC than Murrah buffaloes living in the vicinity. Toda and Murrah buffaloes were inoculated with TLR5 (flagellin) and TLR9 (CpG ODN) ligands in vivo and expression levels of the respective TLRs analyzed 12h later. Following CpG inoculation, Toda buffaloes had significantly higher levels of TLR 9 mRNA expression but not in Murrah. However, flagellin induction did not increase TLR 5 mRNA expression in both these breeds. Histological sections of the skin were made and infiltrating cell clusters were graded and quantified. Following CpG inoculation, Toda buffaloes showed higher numbers of infiltrating grade 1 and grade 3 cell clusters while Murrah showed lower numbers of infiltrating grade 1 cells as compared to mock-inoculated skin sections. Flagellin treatment revealed no significant differences in infiltrating cell clusters in both the breeds. The results have shown differential expression of TLR mRNAs in various tissues between two divergent buffalo breeds with the highest difference in TLR expression profile seen in the skin, the largest portal of entry of pathogens, of Toda.

Crosstalk between innate and adaptive immune responses to infectious bronchitis virus after vaccination and challenge of chickens varying in serum mannose-binding lectin concentrations

Mannose-binding lectin (MBL), a C-type collectin with structural similarities to C1q, is an innate pattern-recognition molecule that is sequestered to sites of inflammation and infections. MBL selectively binds distinct chemical patterns, including carbohydrates expressed on all kinds of pathogens. The present study shows that serum MBL levels influence the ability of chickens to clear the respiratory tract of virus genomes after an infectious bronchitis virus (IBV) infection. The primary IBV infection induced changes in circulating T-cell populations and in the specific antibody responses. Serum MBL levels also influenced IBV vaccine-induced changes in circulating T-cell populations. Moreover, addition of mannose to an IBV vaccine altered both vaccine-induced changes in circulating T-cell populations and IBV specific vaccine and infection-induced antibody responses in chickens with high serum MBL levels. These data demonstrate that MBL is involved in the regulation of the adaptive immune response to IBV.

Effects of lactobacilli on cytokine expression by chicken spleen and cecal tonsil cells

Lactobacillus acidophilus, Lactobacillus reuteri, and Lactobacillus salivarius are all normal residents of the chicken gastrointestinal tract. Given the interest in using probiotic bacteria in chicken production and the important role of the microbiota in the development and regulation of the host immune system, the objective of the current study was to examine the differential effects of these bacteria on cytokine gene expression profiles of lymphoid tissue cells. Mononuclear cells isolated from cecal tonsils and spleens of chickens were cocultured with one of the three live bacteria, and gene expression was analyzed via real-time quantitative PCR. All three lactobacilli induced significantly more interleukin 1beta (IL-1beta) expression in spleen cells than in cecal tonsil cells, indicating a more inflammatory response in the spleen than in cecal tonsils. In cecal tonsil cells, substantial differences were found among strains in the capacity to induce IL-12p40, IL-10, IL-18, transforming growth factor beta4 (TGF-beta4), and gamma interferon (IFN-gamma). In conclusion, we demonstrated that L. acidophilus is more effective at inducing T-helper-1 cytokines while L. salivarius induces a more anti-inflammatory response.

Associations between vaccinations against protozoal and viral infections and Salmonella in broiler flocks

Reducing the burden of Salmonella in broiler flocks presents a challenge for public health. Worldwide, grow-out broilers are routinely vaccinated to prevent or lessen clinical manifestation of other infections. In this exploratory analysis we tested if details of a routine vaccination programme delivered to conventional grow-out broilers were associated with the burden of Salmonella in the flock as it progressed through its production cycle. None of the flocks studied were vaccinated against Salmonella or received a competitive exclusion product. The flocks were reared on conventional grow-out farms in southeastern USA, and sampled in a prospective field observational study. We observed significant associations between the content and design of a grow-out vaccination programme targeting other infections and the probability of detecting Salmonella in the broiler flock at different time points throughout the production cycle. To the best of the authors' knowledge, this is the first field report of such associations.

Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review

Salmonellosis is a frequent disease in poultry stocks, caused by several serotypes of the bacterial species Salmonella enterica and sometimes transmitted to humans through the consumption of contaminated meat or eggs. Symptom-free carriers of the bacteria contribute greatly to the propagation of the disease in poultry stocks. So far, several candidate genes and quantitative trait loci (QTL) for resistance to carrier state or to acute disease have been identified using artificial infection of S. enterica serovar Enteritidis or S. enterica serovar Typhimurium strains in diverse genetic backgrounds, with several different infection procedures and phenotypic assessment protocols. This diversity in experimental conditions has led to a complex sum of results, but allows a more complete description of the disease. Comparisons among studies show that genes controlling resistance to Salmonella differ according to the chicken line studied, the trait assessed and the chicken's age. The loci identified are located on 25 of the 38 chicken autosomal chromosomes. Some of these loci are clustered in several genomic regions, indicating the possibility of a common genetic control for different models. In particular, the genomic regions carrying the candidate genes TLR4 and SLC11A1, the Major Histocompatibility Complex (MHC) and the QTL SAL1 are interesting for more in-depth studies. This article reviews the main Salmonella infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far.