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

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

BACKGROUND

Domestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.

RESULTS

To comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the "hair follicle maturation" Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with "regulation of heart contraction" in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.

CONCLUSION

This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

Colonization of the Gastrointestinal Tract of Chicks with Different Bacterial Microbiota Profiles

This study aimed to investigate the consequences of early-life microbiota transplantation using different caecal content sources in broiler chicks. We hypothesized that chicks receiving at-hatch microbiota from organic hens would harbour a distinct microbiota from chicks receiving industry-raised broiler microbiota after six weeks of age. Three hundred Cobb broilers eggs were randomly assigned to one of four groups according to the caecal content received: organic laying hens (Organic); autoclaved caecal content of organic laying hens (Autoclaved); conventionally grown broilers (Conventional); and sterile saline (Control). caecal microbiota transplantation was given by gavage on day 1. Ten birds/group were euthanized on days 2, 7, 14, 28, and 42. The caecal tonsils and contents were collected for cytokines and microbiota analyses. The microbiota from chicks receiving live inocula resembled the donors' microbiota from day seven until day 42. The microbiota composition from the chickens who received the Organic inoculum remained markedly different. Starting on day 7, the Organic group had higher richness. Simpson and Shannon's indices were higher in the Conventional group on days 2 and 7. Chickens in the Conventional group presented higher production of IL-1β and IL-6 in plasma on days 2 and 28, increased IL-6 expression in the caecal tonsils at days 7 and 42, and increased IL-12 expression on day 7. However, the Conventional group was infected with Eimeria spp., which likely caused inflammation. In conclusion, microbiota transplantation using different microbiota profiles persistently colonized newly hatched broiler chicks. Future studies evaluating the importance of microbiota composition during infections with common enteropathogens are necessary. This study also highlights the need for a strict screening protocol for pathogens in the donors' intestinal content.

Cecal Microbiota Development and Physiological Responses of Broilers Following Early Life Microbial Inoculation Using Different Delivery Methods and Microbial Sources

Broilers in intensive systems may lack commensal microbes that have coevolved with chickens in nature. This study evaluated the effects of microbial inocula and delivery methods applied to day-old chicks on the development of the cecal microbiota. Specifically, chicks were inoculated with cecal contents or microbial cultures, and the efficacies of three delivery methods (oral gavage, spraying inoculum into the bedding, and cohousing) were evaluated. Also, a competitive study evaluated the colonization ability of bacteria sourced from extensive or intensive poultry production systems. The microbiota of inoculated birds presented higher phylogenetic diversity values (PD) and higher relative abundance values of Bacteroidetes, compared with a control. Additionally, a reduction in the ileal villus height/crypt depth ratio and increased cecal IL-6, IL-10, propionate, and valerate concentrations were observed in birds that were inoculated with cecal contents. Across the experiments, the chicks in the control groups presented higher relative abundance values of Escherichia/Shigella than did the inoculated birds. Specific microbes from intensively or extensively raised chickens were able to colonize the ceca, and inocula from intensive production systems promoted higher relative abundance values of Escherichia/Shigella. We concluded that Alistipes, Bacteroides, Barnesiella, Mediterranea, Parabacteroides, Megamonas, and Phascolarctobacterium are effective colonizers of the broiler ceca. In addition, oral gavage, spray, and cohousing can be used as delivery methods for microbial transplantation, as indicated by their effects on the cecal microbiota, intestinal morphology, short-chain fatty acids concentration, and cytokine/chemokine levels. These findings will guide future research on the development of next-generation probiotics that are able to colonize and persist in the chicken intestinal tract after a single exposure. IMPORTANCE The strict biosecurity procedures employed in the poultry industry may inadvertently hinder the transmission of beneficial commensal bacteria that chickens would encounter in natural environments. This research aims at identifying bacteria that can colonize and persist in the chicken gut after a single exposure. We evaluated different microbial inocula that were obtained from healthy adult chicken donors as well as three delivery methods for their effects on microbiota composition and bird physiology. In addition, we conducted a competitive assay to test the colonization abilities of bacteria sourced from intensively versus extensively raised chickens. Our results indicated that some bacteria are consistently increased in birds that are exposed to microbial inoculations. These bacteria can be isolated and employed in future research on the development of next-generation probiotics that contain species that are highly adapted to the chicken gut.

Mucosal and systemic lymphoid immune responses against Clostridium perfringens strains with variable virulence in the production of necrotic enteritis in broiler chickens

Necrotic enteritis (NE), caused by Clostridium perfringens, is an economically important disease of chickens. Although NE pathogenesis is moderately well studied, the host immune responses against C. perfringens are poorly understood. The present study used an experimental NE model to characterize lymphoid immune responses in the caecal tonsils (CT), bursa of Fabricius, Harderian gland (HG) and spleen tissues of broiler chickens infected with four netB+ C. perfringens strains (CP1, CP5, CP18, and CP26), of which CP18 and CP26 strains also carried the tpeL gene. The gross and histopathological lesions in chickens revealed CP5 to be avirulent, while CP1, CP18, and CP26 strains were virulent with CP26 being "very virulent". Gene expression analysis showed that, while the virulent strains induced a significantly upregulated expression of pro-inflammatory IL-1β gene in CT, the CP26-infected birds had significantly higher CT transcription of IFNγ and IL-6 pro-inflammatory genes compared to CP5-infected or uninfected chickens. Furthermore, CP26 infection also led to significantly increased bursal and HG expression of the anti-inflammatory/regulatory genes, IL-10 or TGFβ, compared to control, CP5 and CP1 groups. Additionally, the splenic pro- and anti-inflammatory transcriptional changes were observed only in the CP26-infected chickens. An antibody-mediated response, as characterized by increased IL-4 and/or IL-13 transcription and elevated IgM levels in birds infected with virulent strains, particularly in the CP26-infected group compared to uninfected controls, was also evident. Collectively, our findings suggest that lymphoid immune responses during NE in chickens are spatially regulated such that the inflammatory responses against C. perfringens depend on the virulence of the strain.

The control of poultry salmonellosis using organic agents: an updated overview

Salmonellosis is a severe problem that threatens the poultry sector worldwide right now. Salmonella gallinarium and Salmonella pullorum (Fowl typhoid) are the most pathogenic serovars in avian species leading to systemic infection resulting in severe economic losses in the poultry industry. Nontyphoidal serotypes of Salmonella (Paratyphoid disease) constitute a public health hazard for their involvement in food poisoning problems in addition to their zoonotic importance. Also, Salmonella species distribution is particularly extensive. They resisted environmental conditions that made it difficult to control their spread for a long time. Therefore, the current review aimed to through light on Salmonellosis in poultry with particular references to its pathogenesis, economic importance, immune response to Salmonella, Salmonella antibiotics resistance, possible methods for prevention and control of such problems using promising antibiotics alternatives including probiotics, prebiotics, symbiotics, organic acids, essential oils, cinnamaldehyde, chitosan, nanoparticles, and vaccines.

The immune response of pIgR and Ig to Flavobacterium columnare in grass carp (Ctenopharyngodon idellus)

The polymeric immunoglobulin receptor (pIgR) plays an important role in mediating the transcytosis of polymeric immunoglobulins (pIgs) to protect organisms against pathogen invasion. Here, a polyclonal antibody against grass carp (Ctenopharyngodon idellus) recombinant pIgR was developed by immunizing New Zealand white rabbit, and the responses of pIgR, IgM and IgZ were analyzed after bath immunization and intraperitoneal administration with Flavobacterium columnare. The results showed that pIgR transcription level was similar to IgM and IgZ, but pIgR rose much faster and peaked earlier than IgM and IgZ; the pIgR mRNA levels were higher in the skin and spleen for both immunized groups, while IgM and IgZ mRNA expression were higher in skin, gills, and intestines in bath immersion group, or spleen and head kidney in intraperitoneal immunization group. ELISA revealed that the IgM, IgZ and pIgR protein levels were up-regulated in skin mucus, gill mucus, gut mucus and bile, reaching a higher peak level earlier in skin mucus and gill mucus in bath immersion group, but a higher peak level in bile in injection group. Moreover, secretory component molecules were detected in grass carp's skin, gill and intestine mucus and bile, but not in serum, which molecular mass was near the theoretical mass obtained from the sequence of grass carp pIgR. These results demonstrated that bath and intraperitoneal immunization up-regulated pIgR and secretory Ig expression in secretions, which provided more insights into the role of pIgR in immunity and offer insight into ways of protecting teleost against pathogen invasion.

Effects of drinking water synbiotic supplementation in laying hens challenged with Salmonella

This experiment was conducted to study the effects of drinking water supplementation of synbiotic product PoultryStar®sol (containing Lactobacillus reuteri, Bifidobacterium animalis, Pediococcus acidilactici, Enterococcus faecium, and fructo-oligosaccharide) in laying hens with and without a Salmonella challenge. A total of 384 one-day-old layer chicks were randomly distributed to the drinking water synbiotic supplementation or control groups. At 14 wk of age, the birds were vaccinated with a Salmonella vaccine, resulting in a 2 (control and synbiotic) X 2 (non-vaccinated and vaccinated) factorial arrangement. At 24 wk of age, half of the birds in the vaccinated groups and all the birds that were not vaccinated were challenged with Salmonella Enterica serotype Enteritidis, resulting in a 3 (vaccinated, challenged, vaccinated+challenged) X 2 (control and synbiotic) factorial arrangment. At 8 d post-Salmonella challenge, synbiotic supplementation decreased (P = 0.04) cecal S. Enteritidis in the challenge group compared to the un-supplemented challenge group. Birds that were supplemented with synbiotic in the vaccine + challenge group had significantly greater cecal B. animalis and P. acidilactici percentage at 10 d post-Salmonella challenge than the birds in the vaccine + challenge group without synbiotic supplementation. At 3 d post-Salmonella challenge, birds that were supplemented with synbiotic in the challenge group had significantly greater cecal L. reuteri percentage than the birds in the challenge group without synbiotic supplementation. At 17 d post-Salmonella challenge, synbiotic supplementation increased bile anti-Salmonella IgA in the challenge group compared to the birds in the challenge group without synbiotic supplementation by 76.0%. At 10 d (P < 0.01) and 30 d (P = 0.05) post-Salmonella challenge, synbiotic supplementation decreased LITAF mRNA expression compared to the un-supplemented groups. At 3 d post-Salmonella challenge, synbiotic supplementation in the vaccine group had longer jejunal villi compared to the vaccine group without synbiotic supplementation. This experiment demonstrated that drinking water supplementation of the synbiotic product evaluated can significantly manipulate immune response and intestinal microbiota of laying hens post-Salmonella challenge to handle the challenge effectively.

Effect of synbiotic supplementation on layer production and cecal Salmonella load during a Salmonella challenge

This study analyzed the inhibitory effects of a synbiotic product (PoultryStar® me) on production parameters, intestinal microflora profile, and immune parameters in laying hens with and without a Salmonella challenge. The synbiotic product contained 4 probiotic bacterial strains (Lactobacillus reuteri, Enterococcus faecium, Bifidobacterium animalis, and Pediococcus acidilactici) and a prebiotic fructooligosaccharide. Layers were supplemented with the synbiotic from d of hatch to 28 wk of age. At 16 wk of age, birds were either vaccinated with Salmonella enterica Enteritidis (SE) vaccine or left unvaccinated. At 24 wk of age, a portion of the birds was challenged with 1 × 109 CFU of SE or left unchallenged, resulting in a 3 (vaccinated, challenged, or both vaccinated and challenged) X 2 (control and synbiotics) factorial arrangement of treatments. At 18 and 20 wk of age, birds fed synbiotics in both vaccinated and unvaccinated groups had increased (P < 0.05) BW more than those in the un-supplemented groups. Birds fed synbiotics had 0.7, 17.8, 21.7, 3, and 4.2% higher (P < 0.05) hen d egg production (HDEP) at 19, 20, 21, 22, and 23 wk of age, compared to the birds without supplementation, respectively. After administering the SE challenge, supplemented birds had 3, 6.7, 4.3, 12.5, and 14.4% higher (P < 0.05) HDEP at 24, 25, 26, 27, and 28 wk of age, compared to the birds not supplemented, respectively. Irrespective of the vaccination status, birds fed synbiotics and challenged with SE had a lower (P < 0.05) SE cecal load compared to the un-supplemented groups. At 22 d post Salmonella challenge, birds supplemented, vaccinated, and challenged had the highest bile IgA content. It can be concluded that supplementation of the synbiotic product could be beneficial to layer diets as a growth promoter, performance enhancer, and for protection against SE infection.

Comparison of polymeric immunoglobulin receptor between fish and mammals

Polymeric immunoglobulin receptor (pIgR) functions in transporting polymeric immunoglobulin across epithelial cells into external secretion in animals. During animal evolution, fish was situated at a transition point on the phylogenetic spectrum between species possessing only innate immunity (i.e., invertebrates) and species depending heavily on adaptive immunity (i.e., mammals). Previous studies reported that fish and mammals significantly differ in pIgR. This review summarized the differences in pIgR structure, function, and transcriptional regulation between fish and mammals. A model of the transcriptional regulation of the pIgR gene was suggested. In this model, microbes could activate Toll-like receptor, trigger the cascade reactions in the signaling pathway, and then activate transcription factors that regulate pIgR expression through combining with the pIgR promoter. This review provides some suggestions for further studies on the function and regulatory mechanism of pIgR in fish and other animals.

Effect of Salmonella infection on cecal tonsil regulatory T cell properties in chickens

Two studies were conducted to study regulatory T cell [Treg (CD4⁺CD25⁺)] properties during the establishment of a persistent intestinal infection in broiler chickens. Four-day-old broiler chicks were orally gavaged with 5 × 10⁶ CFU/mL Salmonella enteritidis (S. enteritidis) or sterile PBS (control). Samples were collected at 4, 7, 10, and 14 d postinfection. There was a significant (P < 0.05) increase in the number of CD4⁺CD25⁺ cells by d 4 postinfection that increased steadily throughout the course of the 14-d infection, whereas the number of CD4⁺CD25⁺ cells in the noninfected controls remained steady throughout the study. CD4⁺CD25⁺ cells from cecal tonsils of S. enteritidis-infected birds had a higher (P < 0.05) IL-10 mRNA content than CD4⁺CD25⁺ cells from the noninfected controls at all time-points studied. The amount of IL-2 mRNA content in the cecal tonsil CD4⁺CD25⁻ cells from the infected birds did not differ (P > 0.05) when compared to that of noninfected control birds. At a lower effector/responder cell ratio of 0.25:1, CD4⁺CD25⁺ cells from cecal tonsils of Salmonella-infected birds suppressed T cell proliferation at d 7 and 14 post-S. enteritidis infection, while CD4⁺CD25⁺ cells from noninfected control groups did not suppress T cell proliferation. In the second studu, 1-day-old chickens were orally gavaged with PBS (control) or 1.25 × 10⁸ CFU/bird S. enteritidis. At 7 and 21 d post-Salmonella infection, CD25⁺ cells collected from cecal tonsils of S. enteritidis-infected birds and restimulated in vitro with Salmonella antigen had higher (P < 0.05) IL-10 mRNA content compared to those in the control group. Spleen CD4⁺CD25⁺, CD4⁺, and CD8⁺ cell percentage did not differ (P > 0.05) between the Salmonella-infected and control birds. In conclusion, a persistent intestinal S. enteritidis infection increased the Treg percentage, suppressive properties, and IL-10 mRNA amounts in the cecal tonsils of broiler birds.

Genome-wide SNP analysis identifies major QTL for Salmonella colonization in the chicken

Salmonella-infected poultry products are a major source of human Salmonella infection. The prophylactic use of antimicrobials in poultry production was recently banned in the EU, increasing the need for alternative methods to control Salmonella infections in poultry flocks. Genetic selection of chickens more resistant to Salmonella colonization provides an attractive means of sustainably controlling the pathogen in commercial poultry flocks and its subsequent entry into the food chain. Analysis of different inbred chickens has shown that individual lines are consistently either susceptible or resistant to the many serovars of Salmonella that have been tested. In this study, two inbred chicken lines with differential susceptibility to Salmonella colonization (61 ((R)) and N((S)) ) were used in a backcross experimental design. Unlike previous studies that used a candidate gene approach or low-density genome-wide screens, we have exploited a high-density marker set of 1255 SNPs covering the whole genome to identify quantitative trait loci (QTL). Analysis of log-transformed caecal bacterial levels between the parental lines revealed a significant difference at 1, 2, 3 and 4 days post-infection (P < 0.05). Analysis of the genotypes of the backcross (F1  × N) population (n = 288) revealed four QTL on chromosomes 2, 3, 12 and 25 for the two traits examined in this study: log-transformed bacterial counts in the caeca and presence of a hardened caseous caecal core. These included one genome-wide significant QTL on chromosome 2 at 20 Mb and three additional QTL, on chromosomes 3, 12 and 25 at 96, 15 and 1 Mb, respectively, which were significant at the chromosome-wide level (P < 0.05). The results generated in this study will inform future breeding strategies to control these pathogens in commercial poultry flocks.

Avian CD4(+)CD25(+) regulatory T cells: properties and therapeutic applications

Regulatory T cells (Tregs) are a subset of T cells that specialize in immune suppression. CD4(+)CD25(+)FoxP3(+) T cells have been characterized as Tregs and extensively studied in mammals. In the absence of a putative FoxP3 ortholog in avians, CD4(+)CD25(+) cells is characterized as Tregs in avians. Avian CD4(+)CD25(+) cells produce high amounts of IL-10, TGF-β, CTLA-4, and LAG-3 mRNA; lack IL-2 mRNA; and suppress T cell proliferation in vitro through both contact-dependent and -independent pathways. Depleting avian CD4(+)CD25(+) cells increases the proliferation of, IL-2 amount, and IFNγ mRNA amount of CD4(+)CD25(-) cells. Avian CD4(+)CD25(+) cells lose their suppressive properties immediately after inflammation and acquire supersuppressive properties once inflammation subsides. Although Treg activity could be beneficial to the host, Tregs simultaneously inhibit host immunity and cause persistent infections of certain pathogens. Therapy targeted toward alleviating Treg mediated immune suppression can improve host immunity against those persistent pathogens and benefit poultry production.

Molecular cloning and expression analysis of polymeric immunoglobulin receptor in flounder (Paralichthys olivaceus)

The polymeric immunoglobulin receptor (pIgR) is one of the most important mucosal effectors mediating the transcytosis of polymeric immunoglobulins (pIgs) to protect the organisms. In this paper, a full-length cDNA of pIgR was firstly cloned from flounder (Paralichthys olivaceus) using rapid amplification of cDNA ends approaches, and it was of 1384 bp, containing an open reading frame (ORF) of 1005 bp encoding a polypeptide of 335 amino acids with the predicted molecular mass of 37.6 kDa. The flounder pIgR exhibited a unique structure containing only two immunoglobulin-like domains (ILD) corresponding to mammalian pIgR ILD1 and ILD5. The mRNA transcripts of pIgR were detected in all the tested tissues of flounder by semi-quantitative RT-PCR, and the pIgR was expressed at the highest level in liver and higher levels in intestine, gill, skin, spleen and head kidney than in stomach and muscle. The ORF was successfully expressed in Escherichia coli BL21 (DE3) and the recombinant protein displayed binding capability to the purified mucus IgM and serum IgM of flounder by ELISA. The polyclonal antibody against flounder recombinant pIgR was developed by immunization of Balb/C mice, which specifically reacted to the recombinant pIgR in Western blot. Moreover, a secretory component-like molecule was detected in the skin mucus but not in the serum of flounder, which molecular mass (about 37 kDa) was near the theoretical mass obtained from the sequence of flounder pIgR. All these results indicated that flounder pIgR probably involved in the pIgs transport and provided insights into the roles of fish pIgR in the mucosal immunity.

A mathematical model representing cellular immune development and response to Salmonella of chicken intestinal tissue

The aim of this study was to create a dynamic mathematical model of the development of the cellular branch of the intestinal immune system of poultry during the first 42 days of life and of its response towards an oral infection with Salmonella enterica serovar Enteritidis. The system elements were grouped in five important classes consisting of intra- and extracellular S. Enteritidis bacteria, macrophages, CD4+, and CD8+ cells. Twelve model variables were described by ordinary differential equations, including 50 parameters. Parameter values were estimated from literature or from own immunohistochemistry data. The model described the immune development in non-infected birds with an average R² of 0.87. The model showed less accuracy in reproducing the immune response to S. Enteritidis infection, with an average R² of 0.51, although model response did follow observed trends in time. Evaluation of the model against independent data derived from several infection trials showed strong/significant deviations from observed values. Nevertheless, it was shown that the model could be used to simulate the effect of varying input parameters on system elements response, such as the number of immune cells at hatch. Model simulations allowed one to study the sensitivity of the model outcome for varying model inputs. The initial number of immune cells at hatch was shown to have a profound impact on the predicted development in the number of systemic S. Enteritidis bacteria after infection. The theoretical contribution of this work is the identification of responses in system elements of the developing intestinal immune system of poultry obtaining a mathematical representation which allows one to explore the relationships between these elements under contrasting environmental conditions during different stages of intestinal development.

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.

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.

Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes

Food-borne salmonellosis is a major manifestation of gastrointestinal disease in humans across the globe. Accurate and rapid identification methods could positively impact the identification of isolates, enhance outbreak investigation, and aid infection control. The SNaPshot multiplex system is a primer extension-based method that enables multiplexing of single nucleotide polymorphisms (SNPs). Here the method has been developed for the identification of five Salmonella serotypes, commonly detected in the United Kingdom, based on serotype-specific SNPs identified in the multilocus sequence typing (MLST) database of Salmonella enterica. The SNPs, in genes hemD, thrA, purE, and sucA, acted as surrogate markers for S. enterica serovars Typhimurium, Enteritidis, Virchow, Infantis, and Braenderup. The multiplex primer extension assay (MPEA) was conducted in two separate panels and evaluated using 152 Salmonella enterica isolates that were characterized by MLST. The MPEA was shown to be 100% specific and sensitive, within this collection of isolates. The MPEA is a sensitive and specific method for the identification and detection of Salmonella serotypes based upon SNPs seen in MLST data. The method can be applied in less than 6 h and has the potential to improve patient care and source tracing. The utility of the assay for identification of Salmonella serotypes directly from clinical specimens and food samples warrants further investigation.

Across-line SNP association study of innate and adaptive immune response in laying hens

The aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in laying hens. For this purpose, the associations between 1022 single nucleotide polymorphism (SNP) markers and immune traits were studied in 583 hens from nine different layer lines. Immune traits were natural antibodies for keyhole limpet haemocyanin (KLH) and lipopolysaccharide (LPS) at 20, 40 and 65 weeks, acquired antibodies to the vaccinal virus of Newcastle disease at 20 weeks, and complement activity measured on sheep and bovine red blood cells at 20, 40 and 65 weeks. We adopted a novel approach based on across-line analysis and testing of the SNP-by-line interaction. Among lines, linkage disequilibrium is conserved at shorter distances than in individual lines; therefore, SNPs significantly associated with immune traits across lines are expected to be near the functional mutations. In the analysis, the SNPs that had a significant across-line effect but did not show significant SNP-by-line interaction were identified to test whether the association was consistent in the individual lines. Ultimately, 59 significant associations between SNPs and immune traits were detected. Our results confirmed some previously identified QTL and identified new QTL potentially involved in the immune function. We found evidence for a role of IL17A (chromosome 3) in natural and acquired antibody titres and in the classical and alternative pathways of complement activation. The major histocompatibility genes on chromosome 16 showed significant association with natural and acquired antibody titres and classical complement activity. The IL12B gene on chromosome 13 was associated with natural antibody titres.