Genetic line differences in survival and pathogen load in young layer chicks after Salmonella enterica serovar enteritidis exposure

Videla Rodriguez E, Smith VA, van den Brand H, Rodenburg TB, Visser B. A two-step Bayesian network approach to identify key SNPs associated to multiple phenotypic traits in four purebred laying hen lines

When purebred laying hen chicks hatch, they remain at a rearing farm until approximately 17 weeks of age, after which they are transferred to a laying farm. Chicks or pullets are removed from the flocks during these 17 weeks if they display any rearing abnormality. The aim of this study was to investigate associations between single nucleotide polymorphisms (SNPs) and rearing success of 4 purebred White Leghorns layer lines by implementing a Bayesian network approach. Phenotypic traits and SNPs of four purebred genetic White Leghorn layer lines were available for 23,000 rearing batches obtained between 2010 and 2020. Associations between incubation traits (clutch size, embryo mortality), rearing traits (genetic line, first week mortality, rearing abnormalities, natural death, rearing success, pullet flock age, and season) and SNPs were analyzed, using a two-step Bayesian Network (BN) approach. Furthermore, the SNPs were connected to their corresponding genes, which were further explored in bioinformatics databases. BN analysis revealed a total of 28 SNPs associated with some of the traits: ten SNPs were associated with clutch size, another 10 with rearing abnormalities, a single SNP with natural death, and seven SNPs with first week mortality. Exploration via bioinformatics databases showed that one of the SNPs (ENAH) had a protein predicted network composed of 11 other proteins. The major hub of this SNP was CDC42 protein, which has a role in egg production and reproduction. The results highlight the power of BNs in knowledge discovery and how their application in complex biological systems can help getting a deeper understanding of functionality underlying genetic variation of rearing success in laying hens. Improved welfare and production might result from the identified SNPs. Selecting for these SNPs through breeding could reduce stress and increase livability during rearing.

Genetics of rearing success in four pure laying hen lines during the first 17 weeks of age

This study aimed to investigate the genetics of rearing success (RS) in laying hens. Four rearing traits: clutch size (CS), first week mortality (FWM), rearing abnormalities (RA), and natural death (ND), were included as factors determining RS. Pedigree, genotypic, and phenotypic records of 4 purebred genetic lines of White Leghorn layers were available for 23,000 rearing batches obtained between 2010 and 2020. FWM and ND showed little or no variation amongst the 4 genetic lines over the years 2010-2020, whereas an increase was observed for CS and a decrease for RA. To determine whether these traits were heritable, genetic parameters for each trait were estimated, using a Linear Mixed Model. Heritabilities within lines were low (0.05-0.19 for CS, 0.01-0.04 for FWM, 0.02-0.06 for RA, 0.02-0.04 for ND, and 0.01-0.07 for RS). Additionally, genome wide association study was done to scan the genomes of the breeders to reveal single nucleotide polymorphisms (SNPs) associated with these traits. Manhattan plots indicated the existence of 12 different SNPs having a significant effect on RS. Thus, the identified SNPs will increase the understanding of the genetics of RS in laying hens.

Differential immunological response detected in mRNA expression profiles among diverse chicken lines in response to Salmonella challenge

Salmonella enterica serovar Enteritidis is a bacterial pathogen that contributes to poultry production losses and human foodborne illness. The bacterium elicits a broad immune response involving both the innate and adaptive components of the immune system. Coordination of the immune response is largely directed by cytokines. The objective of the current study was to characterize the expression of a select set of cytokines and regulatory immune genes in three genetically diverse chicken lines after infection with S. Enteritidis. Leghorn, Fayoumi and broiler day-old chicks were orally infected with pathogenic S. Enteritidis or culture medium. At 2 and 18 h postinfection, spleens and ceca were collected and mRNA expression levels for 7 genes (GM-CSF, IL2, IL15, TGF-β1, SOCS3, P20K, and MHC class IIβ) were evaluated by real-time quantitative PCR. Genetic line had a significant effect on mRNA expression levels of IL15, TGF-β1, SOCS3 and P20K in the spleen and on P20K and MHC class IIβ in the cecum. Comparing challenged vs. unchallenged birds, the expression of SOCS3 and P20K mRNA were significantly higher in the spleen and cecum, while MHC class IIβ mRNA was significantly lower in spleen. Combining the current RNA expression results with those of previously reported studies on the same samples reveals distinct RNA expression profiles among the three genetic chicken lines and the 2 tissues. This study illustrates that these diverse genetic lines have distinctively different immune response to S. Enteritidis challenge within the spleen and the cecum.

Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens

BACKGROUND

Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors that control the level of Salmonella carriage in chickens (Gallus gallus) under controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines N and 61 were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition, using a 16S rRNA gene high-throughput sequencing approach.

RESULTS

Our results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Among the 617 operational taxonomic units (OTU) observed, more than 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between the high and low Salmonella carriers, with 39 differentially abundant OTU. Using metagenome functional prediction based on 16S data, several metabolic pathways that are potentially associated to microbiota taxonomic differences (e.g. short chain fatty acids pathways) were identified between high and low carriers.

CONCLUSIONS

Overall, our findings demonstrate that the caecal microbiota composition differs between genetic lines of chickens. This could be one of the reasons why the investigated lines differed in Salmonella carriage levels under experimental infection conditions.

Polymorphic characterisation of gallinacin candidate genes and their molecular associations with growth and immunity traits in chickens

1.Four gallinacin (GAL) genes were assessed by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) to characterise these genes in Fayoumi (F) and Rhode Island Red (R) breeds and their crosses of Rhode Island Red × Fayoumi (½R½F) and Fayoumi × Rhode Island Red (½F½R).2.Genes examined were GAL2, GAL3, GAL4 and GAL5. The molecular associations between the SNPs of the gallinacin genes and body weight, caecal bacterial count and the serum antibody titres of IgA, IgG and IgM were determined. In the R breed, the frequency of TC genotype was higher than TT and CC genotypes for the GAL3 gene. The GG genotype frequency was higher than AA and AG genotypes for the GAL4 gene in the other genetic groups, and the CA genotype frequency was higher than CC and AA genotypes in crosses for the GAL5 gene.3.In all populations, the frequency of the C allele was higher than the T allele for the GAL3 gene, the G allele was higher than the A allele for the GAL4 gene and the C allele was higher than the A allele for the GAL5 gene. The observed heterozygosity in R, ½R½F and ½F½R was 0.476, 0.375 and 0.158 for the GAL3 gene, 0.458, 0.615 and 0.250 for the GAL4 gene and 0.053, 0.792 and 0.739 for the GAL5 gene, while the expected heterozygosities were 0.490, 0.430 and 0.145 for the GAL3 gene, 0.430, 0.348 and 0.219 for the GAL4 gene and 0.229, 0.478 and 0.496 for the GAL5 gene, respectively.4.On a molecular level, the genotype TT was significantly higher for body weight than TC and CC genotypes in the GAL3 gene. Birds with the GG genotype had a significantly lower Salmonella typhimurium count than birds with AA genotype in the GAL4 gene. Birds with the genotype AA had higher significant body weights than those with CC and CA genotypes in the GAL5 gene.5.The results indicated that the GAL3, GAL4 and GAL5 genes are potential candidates for selection programmes to improve S. typhimurium resistance and body weight in chickens.

Cecal CircRNAs Are Associated With the Response to Salmonella Enterica Serovar Enteritidis Inoculation in the Chicken

Circular RNAs (circRNAs) are a class of endogenous noncoding RNA, which is different from linear RNA. CircRNA is an RNA molecule with a closed loop structure formed by reverse splicing. CircRNAs have been studied in several organisms, however, the circRNAs associated with the response to Salmonella enterica serovar Enteritidis (SE) inoculation in chickens are still unclear. In the current study, Jining Bairi chickens were inoculated with SE. CircRNAs involved in the response to SE inoculation were identified through next-generation sequencing. Our results showed that there were 5,118 circRNAs identified in the control and treated groups. There were 62 circRNAs significantly differentially expressed following SE inoculation. Functional classification revealed that those significantly differentially expressed circRNAs were associated with immune system process, rhythmic process and signaling following SE inoculation. CircRNAs NC_006091.4: 65510578|65515090, NC_006099.4: 16132825|16236906, and NC_006099.4: 15993284|16006290 play important roles in the response to SE inoculation. The findings in the current study provide evidence that circRNA alterations are involved in the response to SE inoculation in the chicken.

Messenger RNA Sequencing and Pathway Analysis Provide Novel Insights Into the Susceptibility to Salmonella enteritidis Infection in Chickens

Salmonella enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Controlling poultry SE infection will have great practical significance for human public health, as poultry are considered to be important sources and carriers of the disease. In this study, the splenic transcriptomes of challenged-susceptible (S), challenged-resistant (R) and non-challenged (C) chicks (3-days old, specific-pathogen-free White Leghorn) were characterized in order to identify the immune-related gene markers and pathways. A total of 934 significant differentially expressed genes (DEGs) were identified in comparisons among the C, R and S birds. First reported here, the DEGs involved in the Forkhead box O (FoxO) signaling pathway, especially FoxO3, were identified as potential markers for host resistance to SE infection. The challenged-susceptible birds exhibited strong activation of the FoxO signaling pathway, which may be a major defect causing immune cell apoptosis as part of SE-induced pathology; these S birds also showed weak activation of mitogen-activated protein kinase (MAPK)-related genes, contrasting with strong splenic activation in the R birds. Interestingly, suppression of several pathways in the immune response against Salmonella, including cytokine-cytokine receptor interaction and Jak-STAT, was only found in S birds and there was evidence of cross-talk among these pathways, perhaps contributing to susceptibility to Salmonella infection. These findings will help facilitate understanding resistance and susceptibility to SE infection in the earliest phases of the host immune response through Salmonella-induced pathways, provide new approaches to develop strategies for SE prevention and treatment, and may enhance innate resistance by genetic selection in animals.

Allelic variation in TLR4 is linked to resistance to Salmonella Enteritidis infection in chickens

Salmonella Enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Polymorphisms of the TLR4 gene may affect recognition by Toll-like receptor 4 (TLR4) of bacterial lipopolysaccharide (LPS), leading to differences in host resistance to pathogenic infections. The present study has investigated polymorphic loci of chicken TLR4 (ChTLR4) in ten chicken breeds, electrostatic potentials of mutant structures of TLR4, and a linkage analysis between allelic variation and survival ratio to infection with SE in specific-pathogen-free (SPF) White Leghorns. A total of 19 Single Nucleotide Polymorphisms (SNPs), of which 10 were novel, were found in chicken breeds. Seven newly identified amino acid variants (C68G, G674A, G782A, A896T, T959G, T986A, and A1104C) and previously reported important mutations (G247A, G1028A, C1147T, and A1832G) were demonstrated in the extracellular domain of the ChTLR4 gene. Significant changes in surface electrostatic potential of the ectodomain of TLR4, built by homology modeling, were observed at the Glu83Lys (G247A), Arg298Ser (A896T), Ser368Arg (A1104C), and Gln611Arg (A1832G) substitutions. Linkage analysis showed that one polymorphic locus G247A of TLR4 gene, common in all breeds examined, was significantly associated with increased resistance to SE in SPF White Leghorns chicks (log-rank P-value = 0.04). The genotypes from A1832G SNPs did not show statistically significant survival differences. This study has provided the first direct evidence that G247A substitution in ChTLR4 is associated with increased resistance to Salmonella Enteritidis.

Differences in host breed and diet influence colonization by Campylobacter jejuni and induction of local immune responses in chicken

BACKGROUND

Chickens are regarded as the main reservoir for human campylobacteriosis. Little is known about the interaction between Campylobacter jejuni (C. jejuni) and chickens. This interaction may be influenced by the stage of maturation of the immune system, developing gut microbiota composition and other factors including breed and diet. Our aim was to investigate the impact of breed, and diet on C. jejuni colonization and host immune responses in chickens. Birds were inoculated with 10⁴ colony forming units (CFU) of C. jejuni or diluent at one (Exp. 1) or 22 (Exp. 2) days post hatch. We compared local immune cell subpopulations, cytokine expression levels, and gut microbiota composition between broiler-type (BT) and layer-type (LT) birds fed with either commercial broiler feed (bf) or layer feed (lf).

RESULTS

Lower colonization rates were observed in the older age group independent of breed and diet. Independent of breed, birds fed with bf showed higher CFU of C. jejuni compared to lf-fed groups. Campylobacter jejuni-inoculation had a significant effect on lymphocyte numbers and cytokine expression levels in BT birds independent of feeding strategy (p < 0.05). These effects were not detected in LT birds, only LT birds fed with bf showed a significant increase in IL-8-expression at 7 days post C. jejuni inoculation compared to LT-control birds (p < 0.05). Diet influenced gut microbiota composition in a comparable manner between BT and LT birds, but changes in microbiota composition associated with C. jejuni inoculation varied between breeds.

CONCLUSIONS

Diet and breed influenced C. jejuni colonization, immune responses and microbiota composition to a different extent comparing between LT and BT birds. The mechanisms behind these differences have to be elucidated further. Our results suggest that selection for more resistant breeds in combination with adapted feeding strategies may help to reduce Campylobacter colonization levels in commercial poultry in the future.

Differential ex vivo responses of primary leukocytes from turkey pedigree lines to Salmonella Heidelberg

Escalating product recalls as a consequence of Salmonella-contaminated poultry products have resulted in detrimental economic impacts in the poultry industry. One potential long-term alternative method to Salmonella prevention is genetic selection to improve innate resistance. This study evaluated the ex vivo effects of Salmonella Heidelberg (SH) on phagocytic and bactericidal leukocyte function in turkeys from six pedigree lines (A-F). Day-of-hatch poults (n = 48) were placed and raised in cages (2 birds/gender/genetic line/cage) to 35 d when heterophils and peripheral blood mononuclear cells (PBMCs) were extracted from males and females of each line. Cells were used in phagocytic and bactericidal assays to determine the ex vivo effects of SH on turkey leukocyte activity. Data were analyzed using the Fit Model platform in JMP Pro 10.0 (SAS Institute Inc.) with differences considered significant at P ≤ 0.05 and data reported as LS Means with SEM. Although genetic line had no significant effect on phagocytosis of SH by heterophils and PBMCs, cumulatively, female cells exhibited higher phagocytosis potential than those from males. The main effect of gender was significant on bactericidal activity of PBMCs when incubated at a 1:10 and 1:100 PBMC to SH ratio. Genetic line also had a significant effect on bactericidal activity of PBMCs with cells from line F exhibiting the best activity. These results suggest that gender had a marked cumulative effect on phagocytosis of SH by heterophils and PBMCs while both genetic line and gender had a prominent effect on bacterial killing of SH by turkey PBMCs. Once able to determine genetic markers associated with these immune responses to Salmonella, genetic selection for increased resistance may become feasible in turkeys.

Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus

Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.

The effects of polymorphisms in IL-2, IFN-γ, TGF-β2, IgL, TLR-4, MD-2, and iNOS genes on resistance to Salmonella enteritidis in indigenous chickens

Salmonella Enteritidis is a major cause of food poisoning worldwide, and poultry products are the main source of S. Enteritidis contamination for humans. Among the numerous strategies for disease control, improving genetic resistance to S. Enteritidis has been the most effective approach. We investigated the association between S. Enteritidis burden in the caecum, spleen, and liver of young indigenous chickens and seven candidate genes, selected on the basis of their critical roles in immunological functions. The genes included those encoding interleukin 2 (IL-2), interferon-γ (IFN-γ), transforming growth factor β2 (TGF-β2), immunoglobulin light chain (IgL), toll-like receptor 4 (TLR-4), myeloid differentiation protein 2 (MD-2), and inducible nitric oxide synthase (iNOS). Two Malaysian indigenous chicken breeds were used as sustainable genetic sources of alleles that are resistant to salmonellosis. The polymerase chain reaction restriction fragment-length polymorphism technique was used to genotype the candidate genes. Three different genotypes were observed in all of the candidate genes, except for MD-2. All of the candidate genes showed the Hardy-Weinberg equilibrium for the two populations. The IL-2-MnlI polymorphism was associated with S. Enteritidis burden in the caecum and spleen. The TGF-β2-RsaI, TLR-4-Sau 96I, and iNOS-AluI polymorphisms were associated with the caecum S. Enteritidis load. The other candidate genes were not associated with S. Enteritidis load in any organ. The results indicate that the IL-2, TGF-β2, TLR-4, and iNOS genes are potential candidates for use in selection programmes for increasing genetic resistance against S. Enteritidis in Malaysian indigenous chickens.

Toward integrative genomics study of genetic resistance to Salmonella and Campylobacter intestinal colonization in fowl

Salmonella enterica serotypes Enteritidis and Typhimurium and Campylobacter jejuni are responsible for most cases of food poisoning in Europe. These bacteria do not cause severe disease symptoms in chicken, but they are easily propagated by symptomless chicken carriers which cannot be easily isolated. This animal tolerance is detrimental to food safety. In this particular case, increasing animal's resistance is not sufficient, since some animals considered as resistant are able to carry bacteria during several weeks without displaying disease symptoms. We review studies aimed at evaluating the resistance of chicken to Salmonella and Campylobacter intestinal colonization, either a few days or several weeks after infection. While studies of the genetic control of Campylobacter colonization are only beginning, mostly due to technical difficulties in infection protocols, genetic studies of Salmonella colonization have been conducted for now more than 20 years. They have initially reported an estimation of the genetic parameters associated with resistance to Salmonella colonization and are now aimed at identifying the genomic regions controlling variation of this trait in experimental lines and commercial populations. With the advent of high-throughput genomics, we are closer than ever to identify the true genes controlling resistance to Enterobacteria colonization in chicken. The comparison of genes involved in early resistance to intestinal colonization with genes controlling resistance to bacteria persistence several weeks after infection (i.e., carrier-state) should soon highlight the differences between the molecular mechanisms underlying those two distinct phenotypes. It will also be highly interesting to compare the genes or genomic regions controlling Campylobacter and Salmonella, in order to evaluate the feasibility of a selection conducted on both bacteria simultaneously.

Orally administered P22 phage tailspike protein reduces salmonella colonization in chickens: prospects of a novel therapy against bacterial infections

One of the major causes of morbidity and mortality in man and economically important animals is bacterial infections of the gastrointestinal (GI) tract. The emergence of difficult-to-treat infections, primarily caused by antibiotic resistant bacteria, demands for alternatives to antibiotic therapy. Currently, one of the emerging therapeutic alternatives is the use of lytic bacteriophages. In an effort to exploit the target specificity and therapeutic potential of bacteriophages, we examined the utility of bacteriophage tailspike proteins (Tsps). Among the best-characterized Tsps is that from the Podoviridae P22 bacteriophage, which recognizes the lipopolysaccharides of Salmonella enterica serovar Typhimurium. In this study, we utilized a truncated, functionally equivalent version of the P22 tailspike protein, P22sTsp, as a prototype to demonstrate the therapeutic potential of Tsps in the GI tract of chickens. Bacterial agglutination assays showed that P22sTsp was capable of agglutinating S. Typhimurium at levels similar to antibodies and incubating the Tsp with chicken GI fluids showed no proteolytic activity against the Tsp. Testing P22sTsp against the three major GI proteases showed that P22sTsp was resistant to trypsin and partially to chymotrypsin, but sensitive to pepsin. However, in formulated form for oral administration, P22sTsp was resistant to all three proteases. When administered orally to chickens, P22sTsp significantly reduced Salmonella colonization in the gut and its further penetration into internal organs. In in vitro assays, P22sTsp effectively retarded Salmonella motility, a factor implicated in bacterial colonization and invasion, suggesting that the in vivo decolonization ability of P22sTsp may, at least in part, be due to its ability to interfere with motility… Our findings show promise in terms of opening novel Tsp-based oral therapeutic approaches against bacterial infections in production animals and potentially in humans.

Fine mapping of the chicken salmonellosis resistance locus (SAL1)

Salmonella enterica serovar Typhimurium is a Gram-negative bacterium that has a significant impact on both human and animal health. It is one of the most common food-borne pathogens responsible for a self-limiting gastroenteritis in humans and a similar disease in pigs, cattle and chickens. In contrast, intravenous challenge with S. Typhimurium provides a valuable model for systemic infection, often causing a typhoid-like infection, with bacterial replication resulting in the destruction of the spleen and liver of infected animals. Resistance to systemic salmonellosis in chickens is partly genetically determined, with bacterial numbers at systemic sites in resistant lines being up to 1000-fold fewer than in susceptible lines. Identification of genes contributing to disease resistance will enable genetic selection of resistant lines that will reduce Salmonella levels in poultry flocks. We previously identified a novel resistance locus on Chromosome 5, designated SAL1. Through the availability of high-density SNP panels in the chicken, combined with advanced back-crossing of the resistant and susceptible lines, we sought to refine the SAL1 locus and identify potential positional candidate genes. Using a 6(th) generation backcross mapping population, we have confirmed and refined the SAL1 locus as lying between 54.0 and 54.8 Mb on the long arm of Chromosome 5 (F = 8.72, P = 0.00475). This region spans 14 genes, including two very striking functional candidates; CD27-binding protein (Siva) and the RAC-alpha serine/threonine protein kinase homolog, AKT1 (protein kinase B, PKB).

MHC haplotype and susceptibility to experimental infections (Salmonella Enteritidis, Pasteurella multocida or Ascaridia galli) in a commercial and an indigenous chicken breed

In three independent experimental infection studies, the susceptibility and course of infection of three pathogens considered of importance in most poultry production systems, Ascaridia galli, Salmonella Enteritidis and Pasteurella multocida were compared in two chicken breeds, the indigenous Vietnamese Ri and the commercial Luong Phuong. Furthermore, the association of the Major Histocompatibility Complex (MHC) with disease-related parameters was evaluated, using alleles of the LEI0258 microsatellite as markers for MHC haplotypes. The Ri chickens were found to be more resistant to A. galli and S. Enteritidis than commercial Luong Phuong chickens. In contrast, the Ri chickens were more susceptible to P. multocida, although production parameters were more affected in the Luong Phuong chickens. Furthermore, it was shown that the individual variations observed in response to the infections were influenced by the MHC. Using marker alleles of the microsatellite LEI0258, which is located within the MHC region, several MHC haplotypes were identified as being associated with infection intensity of A. galli. An association of the MHC with the specific antibody response to S. Enteritidis was also found where four MHC haplotypes were shown to be associated with high specific antibody response. Finally, one MHC haplotype was identified as being associated with pathological lesions and mortality in the P. multocida experiment. Although not statistically significant, our analysis suggested that this haplotype might be associated with resistance. These results demonstrate the presence of local genetic resources in Vietnamese chickens, which could be utilized in breeding programmes aiming at improving disease resistance.

Genetic lines differ in Toll-like receptor gene expression in spleens of chicks inoculated with Salmonella enterica serovar Enteritidis

Toll-like receptors (TLR) recognize evolutionarily conserved molecular motifs (pathogen-associated molecular patterns) of infectious microbes and initiate innate immune response upon activation with relevant pathogens. This study investigated the acute effect of Salmonella Enteritidis challenge on TLR mRNA expression in cecum and spleen of birds from 3 distinct genetic lines. Chicks from broiler, Leghorn, and Fayoumi lines were inoculated or mock-inoculated with Salmonella Enteritidis. The mRNA expression levels of TLR2, TLR4, and TLR5 genes were assessed by quantitative reverse transcription-PCR of cecum and spleen tissue harvested at 2 or 18 h postinoculation (PI). There were no significant genetic line effects on TLR mRNA expression in spleen or cecum of mock-infected birds, or in the cecum of infected birds. Genetic line effect was significant (P < 0.05) on TLR mRNA expression in the spleen of Salmonella Enteritidis-infected birds. The Fayoumi line had higher TLR2 and TLR4 expression than Leghorn, higher TLR2 mRNA expression than broiler, and the broiler line had higher TLR5 expression than Leghorn and Fayoumi. In Salmonella Enteritidis-infected birds, the TLR2 expression in both cecum and spleen and TLR4 expression in spleen were significantly higher at 18 h PI than 2 h PI. The results demonstrate a significant genetic line effect on TLR expression in the spleen of Salmonella Enteritidis-infected birds, which may partly explain genetic variability in immune response to Salmonella Enteritidis.

Toll-like receptor gene expression in cecum and spleen of advanced intercross line chicks infected with Salmonella enterica serovar Enteritidis

Understanding the changes in host gene expression that occur with bacterial infection will help to elucidate the basis of molecular genetic control of disease resistance. The effect of infecting chicks with Salmonella enterica serovar Enteritidis on the RNA expression level of Toll-like receptor (TLR) genes, and the correlation between TLR RNA expression level and bacterial burden in the cecum and spleen of young birds was studied. Chicks from two advanced intercross lines were either infected or mock infected with S. enteritidis at 1 day of age. The RNA expression levels of TLR2, TLR4 and TLR5 genes were assessed by quantitative reverse transcriptase-PCR (qRT-PCR) in cecum and spleen tissues harvested at one week post-infection. Infected chicks had significant upregulation of TLR2 RNA expression in spleen, TLR4 RNA expression in both cecum and spleen, and downregulation of TLR5 RNA expression in cecum. Bacterial burden of S. enteritidis in infected birds was not correlated with TLR RNA expression level. Infecting chicks with S. enteritidis caused an increase in TLR2, TLR4 and TLR5 RNA expression level in spleen in males but not in females. The effect of sex on response to S. enteritidis infection suggests a role for TLR signaling pathways in sex-based modulation of immune response to pathogens. High correlation between TLR2 and TLR4 mRNA expression level in cecum of S. enteritidis infected birds suggests coordinated regulation or simultaneous stimulation of these genes by S. enteritidis. In conclusion, this study clearly showed that young chicks respond to S. enteritidis infection by upregulating TLR2, TLR4 RNA expression. The downregulation of TLR5 RNA expression was observed in cecum by S. enteritidis infection, which might be beneficial to protect host cells from overstimulation by bacterial flagellin.

Association of interleukin-10 cluster genes and Salmonella response in the chicken

Salmonella enteritidis lipopolysaccharide stimulates interleukin 10 (IL10) gene expression in chickens. Four genes in the IL10 cluster [polymeric immunoglobulin receptor (PIGR), interleukin 10 (IL10), map kinase-activated protein kinase 2 (MAPKAPK2), and ligatin (LGTN)] plus dual-specificity tyrosine-(Y)-phosphorylation regulated kinase1A (DYRK1A) were investigated using the F(8) generation of 2 related advanced intercross lines (AIL). The AIL were generated by crossing outbred broilers with dams of 2 highly inbred lines (Leghorn and Fayoumi). Intercrossing continued within the 2 dam lines. The F(8) chicks (n = 132) were intraesophageally inoculated at 1 d with S. enteritidis. At d 7 or 8, both spleen tissue and cecal contents were cultured to quantify S. enteritidis load. The F(8) population was genotyped for one single nucleotide polymorphism (SNP) per gene by using a multiplexed SNaPshot assay. Association of gene SNP with S. enteritidis bacterial burden was analyzed by the GLM. The MAPKAPK2 and IL10 genes were highly (P < 0.001) associated with S. enteritidis burden in spleen tissue and cecal luminal content. Suggestive associations (P < 0.05) of PIGR with spleen tissue and cecal content were found. The results suggest that SNP in MAPKAPK2 and IL10 were strongly associated with Salmonella burden and may be valuable in generating resistant birds by marker-assisted selection.

Global gene expression profile after Salmonella enterica Serovar enteritidis challenge in two F8 advanced intercross chicken lines

A chicken 13K cDNA microarray was used to profile global gene expression after Salmonella enteritidis (SE) challenge of young chickens. Two F8 advanced intercross lines (AIL), broiler by Leghorn, and broiler by Fayoumi, were studied. Day-old chicks were orally inoculated with SE, and spleens were harvested at day 7 or 8 post-inoculation. The SE bacteria burden in the spleen was quantified. The 20% high and 20% low SE burden birds within each AIL and harvest time were studied by microarray. The loop design was used for pair-comparison between high and low SE burden challenged birds and unchallenged birds, within each AIL and harvest time. The signal intensity of each gene was globally normalized and expressed on the natural log scale. A mixed model including line, treatment, time, array (random effect), dye, and all two-way interactions among treatment, time, and line was used to identify differentially expressed candidate genes at the 1% significance level. The results suggest that genetics, time, and interaction between genetics and time play important roles in gene regulation of SE infection and colonization in chickens. The differentially expressed genes identified in the current study are candidates for detailed hypothesis-driven investigation of genes determining resistance to SE in chickens.

Analyses of Five gallinacin genes and the Salmonella enterica serovar Enteritidis response in poultry

Gallinacins in poultry are functional equivalents of mammalian beta-defensins, which constitute an integral component of the innate immune system. Salmonella enterica serovar Enteritidis is a gram-negative bacterium that negatively affects both human and animal health. To analyze the association of genetic variations of the gallinacin genes with the phenotypic response to S. enterica serovar Enteritidis, an F1 population of chickens was created by crossing four outbred broiler sires to dams of two highly inbred lines. The F1 chicks were evaluated for bacterial colonization after pathogenic S. enterica serovar Enteritidis inoculation and for circulating antibody levels after inoculation with S. enterica serovar Enteritidis bacterin vaccine. Five candidate genes were studied, including gallinacins 2, 3, 4, 5, and 7. Gene fragments were sequenced from the founder individuals of the resource population, and a mean of 13.2 single-nucleotide polymorphisms (SNP) per kilobase was identified. One allele-defining SNP per gene was utilized to test for statistical associations of sire alleles with progeny response to S. enterica serovar Enteritidis. Among the five gallinacin genes evaluated, the Gal3 and Gal7 SNPs in broiler sires were found to be associated with antibody production after S. enterica serovar Enteritidis vaccination. Utilization of these SNPs as molecular markers for the response to S. enterica serovar Enteritidis may result in the enhancement of the immune response in poultry.

Toll-like receptor agonists stimulate differential functional activation and cytokine and chemokine gene expression in heterophils isolated from chickens with differential innate responses

Heterophils isolated from distinct broilers (lines A and B) differ in function and cytokine gene expression profiles. Nothing is known about Toll-like receptor (TLR) expression nor functional activation and cytokine/chemokine gene expression of line A and B heterophils when stimulated with TLR agonists. We found that line A and B heterophils express the same range of TLRs. All the bacterial TLR agonists, peptidoglycan, the synthetic lipoprotein Pam3CSK4, ultra-pure lipopolysaccharide, and flagellin all induced significantly greater functional activation of heterophils from line A compared to B. Only stimulation with the guanosine analog, loxoribine, (LOX) induced a significantly greater functional response in B over A. Additionally, all heterophils from line A stimulated with the bacterial TLR agonists had dramatic upregulation of pro-inflammatory cytokine and chemokine mRNA expression, whereas heterophils from line B had little or no upregulation of these genes. However, stimulation of all heterophils from line B with the bacterial TLR agonists and LOX induced a significant upregulation of IFN-alpha, with little transcription of this cytokine gene in line A heterophils. These findings suggest that the difference in heterophil functional efficiency between these parent lines is due to recognition of pathogens and activation of signaling pathways that induce innate cytokine and chemokine responses.

Reducing the Carriage of Foodborne Pathogens in Livestock and Poultry

Several foodborne pathogens, including Salmonella species and campylobacters, are common contaminants in poultry and livestock. Typically, these pathogens are carried in the animal's intestinal tract asymptomatically; however, they can be shed in feces in large populations and be transmitted by other vectors from feces to animals, produce, or humans. A wide array of interventions has been developed to reduce the carriage of foodborne pathogens in poultry and livestock, including genetic selection of animals resistant to colonization, treatments to prevent vertical transmission of enteric pathogens, sanitation practices to prevent contamination on the farm and during transportation, elimination of pathogens from feed and water, feed and water additives that create an adverse environment for colonization by the pathogen, and biological treatments that directly or indirectly inactivate the pathogen within the host. To successfully reduce the carriage of foodborne pathogens, it is likely that a combination of intervention strategies will be required.

Genetic resistance to Salmonella infection in domestic animals

Genetic resistance to Salmonella infection in experimental animal models is well described. However, genetic resistance in domestic animals, which has potentially great value in terms of controlling Salmonella in the food chain, has been relatively poorly described. Recent advances in genetics and immunology have identified several factors that influence resistance in chickens and pigs in particular. Resistance to systemic salmonellosis in the chicken is encoded by a number of factors including Nramp1 (now termed Slc11a1) and a novel gene, SAL1 that leads to increased macrophage activity against Salmonella. Studies in outbred, and in particular, inbred chickens have revealed considerable differences in levels of colonization of the gastrointestinal tract and responses to vaccination. Factors influencing this appear to include innate immune function, MHC and Nramp. In pigs several immune factors, including polymorphonuclear cell activity, have been shown to influence resistance.

Analysis of Chicken TLR4, CD28, MIF, MD-2, and LITAF Genes in a Salmonella enteritidis Resource Population

Salmonella enteritidis is a foodborne pathogen that negatively affects both animal and human health. Genetic variations in response to pathogenic SE colonization or to SE vaccination were measured in a chicken resource population. Outbred broiler sires and 3 diverse, highly inbred dam lines produced 508 F1 progeny that were evaluated for either bacterial colonization after pathogenic SE inoculation or circulating antibody level after SE vaccination. Five candidate genes were selected for study, based on their biological function as possibly affecting response to SE: toll-like receptor 4 (TLR4), T-cell specific surface protein (CD28), macrophage migration inhibitory factor (MIF), MD-2, and lipopolysaccharide-induced tumor necrosis factor (TNF)-alpha factor (LITAF). Gene fragments were sequenced from the founder lines of the resource population. The LITAF and MIF genes were homozygous for all sires. Single nucleotide polymorphisms (SNP) were identified in 3 genes (TLR4, CD28, and MD-2) and were used to test for associations of sire SNP with SE response. Linear mixed models were used for statistical analyses. The CD28 broiler sire SNP was associated with both bacterial load in the cecum (P < 0.003) and vaccine antibody response (P < 0.05). The MD-2 SNP was associated (P < 0.04) with the bacterial load in the spleen. The use of these SNP in these genes in marker-assisted selection may result in enhancement of disease resistance.

Antibody responses in the serum and gut of chicken lines differing in cecal carriage of Salmonella enteritidis

Salmonella frequently causes human foodborne infections. Contaminated products from poultry infected with Salmonella enteritidis are mainly involved. This serovar is able to colonize the gastrointestinal tract and generally produces a chronic asymptomatic carrier state in poultry, except in very young birds. We have developed a model of S. enteritidis carriage in chicks and found that four chicken lines, B13, L2, PA12 and Y11 differ in their cecal colonization by S. enteritidis, whereas their systemic organs are similarly infected. We have monitored the serum and gut antibody responses of these four lines to S. enteritidis for 9 weeks post inoculation (pi). We confirm that S. enteritidis infected the spleens of the four chicken lines similarly, and that it often colonized the ceca at levels significantly higher in B13 and L2 chicks than those of the PA12 and Y11 chicks. The serum IgM and IgG antibody responses were high and the serum IgA antibody responses low. In contrast, the intestinal secretions contained mostly IgA antibodies. The serum IgM antibody values of the four chicken lines were similar. However, the B13 and L2 chicks often had significantly higher serum IgG and IgA antibody responses than PA12 and Y11 chicks. Only the B13 and L2 chicks showed high, persistent levels of IgA antibody in intestinal secretions. These results suggest that most antibody responses are related to cecal colonization by S. enteritidis. They also indicate that factors other than the antibody levels are involved in the control of this colonization.

Candidate gene approach: potentional association of caspase-1, inhibitor of apoptosis protein-1, and prosaposin gene polymorphisms with response to Salmonella enteritidis challenge or vaccination in young chicks

Salmonella enteritidis (SE) contamination of poultry products is a major cause of foodborne disease worldwide. Caspase-1 and inhibitor of apoptosis protein-1 (IAP-1) were selected as candidate genes for chicken response to SE because their proteins play critical roles in the apoptotic pathway when intracellular bacteria interact with host cells. Prosaposin (PSAP) was selected as a positional candidate gene based on a previous quantitative trait loci (QTL) linkage study using the same population. The F1 offspring of outbred sires crossed with three diverse, highly inbred dam lines (two major histocompatibility complex-congenic Leghorn lines named G-B1 and G-B2, and one Fayoumi line) were used to define the phenotypes. The F1 birds were involved in either pathogenic SE challenge, in which spleen and cecum content bacterial load were quantified, or SE vaccination, in which plasma antibody level to SE vaccine was evaluated. A polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) assay was developed to identify single-nucleotide polymorphism (SNP) in the three genes. The F1 offspring of heterozygous sires for each gene were genotyped. The sire caspase-1 gene was significantly associated with cecum content bacterial load (P = 0.04) in the three combined dam line crosses, and with spleen bacterial load in the G-B1 cross (P=0.02). The sire caspase-1 gene was also significantly associated with antibody level to SE vaccine (P=0.03) in F1 males in the three combined dam line crosses. The sire IAP-1 gene was significantly associated with spleen bacterial load (P=0.04) in the three combined dam-line crosses, and interacted with dam-line genetics (P = 0.01) for cecum content bacterial load. The sire PSAP gene significantly interacted with sex for spleen bacterial load (P = 0.004). This study is the first to demonstrate the association of SNPs for caspase-1, IAP-1, and PSAP genes with SE vaccine and with pathogen challenge response in chickens.

Observations on Salmonella contamination of commercial laying farms before and after cleaning and disinfection

Little is known about the effectiveness of the cleaning and disinfection methods in use on commercial laying farms in Great Britain. Samples were taken from poultry house structures and equipment of five cage layer flocks, five barn egg production flocks and two free-range flocks. In the free-range houses there was a decrease in Salmonella after cleaning and disinfection, although the soil in the paddocks remained contaminated. In the barn and especially the cage layer houses, significant residual contamination remained on the surfaces of buildings and equipment. Wildlife pests were also found to be carrying Salmonella in the disinfected houses and free-range paddocks.

Natural resistance-associated macrophage protein 1 gene polymorphisms and response to vaccine against or challenge with Salmonella enteritidis in young chicks

Salmonella enteritidis (SE) contamination of poultry products is of global food-safety concern. The natural resistance-associated macrophage protein 1 (NRAMP1) affects host innate immunity to intracellular bacteria because of its ability to transport divalent cations in late endosome/lysosomes. Studying the association of the NRAMP1 gene and chicken innate immune response to SE can, therefore, aid understanding and enhancement of chicken genetic resistance to SE. The chicken NRAMP1 gene was investigated as a candidate gene for SE response in a unique resource population. Outbred broiler sires and three diverse, highly inbred dam lines (two major histocompatibility complex-congenic Leghorn and one Fayoumi line) produced F1 progeny that were evaluated as young chicks for either bacterial load in spleen and cecum after pathogenic SE inoculation or antibody level after SE vaccination. Thirty-seven single nucleotide polymorphisms (SNP) were identified in 3.1 kb of genomic DNA of the NRAMP1 gene. A PCR-RFLP assay was developed to identify a SNP in a conserved transport motif. The sire NRAMP1 gene SNP was associated (P < 0.02) with antibody level to SE vaccine for Sire 8170 offspring in the two Leghorn crosses. In Sire 8296 offspring, NRAMP1 was associated (P < 0.02) with spleen bacterial load in the combined dam-line crosses. This study demonstrated the association of a SNP polymorphism in a highly conserved region of NRAMP1 with SE vaccine and pathogen challenge response in young chicks, indicating that either NRAMP1 or a linked gene controls these SE-response traits.

Candidate genes for resistance to Salmonella enteritidis colonization in chickens as detected in a novel genetic cross

Salmonellosis is a zoonotic disease that is problematic for both animal production and food safety. A novel genetic cross, named the Iowa Salmonella response resource population (ISRRP), was established to elucidate the genetic control of resistance to Salmonella enteritidis (SE) colonization in young chicks, to characterize unique resistance alleles, and to estimate gene interaction effects. Outbred broiler sires were mated with dams of diverse, highly inbred, light-bodied lines to produce an F(1) generation that was informative for all heterozygous alleles of the sires. Mating F(1) sires back to dams of the corresponding inbred line produced a backcross generation. To mimic the natural route of exposure and thus afford the opportunity to investigate mucosal immunity, pathogenic SE were inoculated into the esophagus of day-old chicks. After 1 week, the SE colonizing the cecal lumen and the spleen were enumerated. Candidate genes were selected for analysis based upon one of the two criteria. Functional candidates were genes with reported activity related to the tested traits. Positional candidates were genes mapped near microsatellites that were linked, in other phases of this project, with antibody levels to SE vaccine. Broiler sire alleles of the MHC class I, NRAMP1, PSAP, and IAP1 genes showed association with SE colonization in the F(1) generation of this novel disease resistance resource population.

Microsatellites linked to Salmonella enterica Serovar Enteritidis burden in spleen and cecal content of young F1 broiler-cross chicks

Contamination of poultry and poultry products by Salmonella enterica Serovar Enteritidis (SE) continues to be problematic even though biosafety management practices have aided in reduction of the SE burden. Identification of molecular markers linked to disease resistance loci would further reduce SE burden by enabling selection for genetic resistance. The objectives of this study were therefore to evaluate specific genomic regions for resistance to SE burden in young broiler-cross chicks and to evaluate the interaction of allele with dam line and sex. Three hatches of F1 chicks were produced by crossing sires from a broiler breeder male line with hens from three highly inbred lines (Fayoumi 15.2, and MHC-congenic G-B1 and G-B2 Leghorn). At 1 d of age, the chicks were intraesophageally inoculated with SE phage type 13a. Spleen and cecal content samples were harvested at 1 wk, and the levels of SE were quantified by serial plate dilution. Each of the F1 chicks was genotyped with four microsatellites that had previously been shown to be linked to antibody response to SE vaccine. All four microsatellites had a significant (P < or = 0.05) main effect or interaction with dam line or sex on the level of SE in spleen and cecal contents.

Salmonella enterica serovar enteritidis burden in broiler breeder chicks genetically associated with vaccine antibody response

The relationship between antibody response to Salmonella enteritidis vaccine and internal organ burden of S. enteritidis is not fully understood. The genetic relationship, therefore, between postchallenge S. enteritidis burden and antibody response to S. enteritidis vaccine was determined in broiler breeder chicks. Sibling chicks from a broiler breeder male line were either inoculated with a pathogenic S. enteritidis or vaccinated with a commercial S. enteritidis vaccine. Spleen, liver, cecal wall, and cecal content samples from S. enteritidis-challenged chicks (n = 120) were cultured for enumeration of bacteria. Unchallenged chicks (n = 314) were vaccinated at 11 days of age, and serum samples were taken at 10 days postvaccination. Antibody response to vaccination and number of S. enteritidis in cecal content cultures were negatively correlated (-0.772), demonstrating that genetic potential for greater antibody response to S. enteritidis vaccine is associated with lesser S. enteritidis bacterial burden in cecal content of broiler breeder chicks. The findings suggest that genetic selection for vaccine antibody responsiveness can lower bacterial burden in the gut lumenal content and, thus, potentially reduce contamination of poultry products at processing.