Poultry Science

Campylobacter is the leading cause of bacterial foodborne gastroenteritis in many countries. Source attribution studies unequivocally identify the handling or consumption of contaminated poultry meat as the primary risk factor. One potential strategy to control Campylobacter is to select poultry with increased resistance to colonisation. We conducted genomic and transcriptomic analyses of commercial pedigree broilers exposed to Campylobacter to examine persistent colonisation of the caecum as a quantitative trait. 3,000 broilers were genotyped using a 50K single nucleotide polymorphism (SNP) array and imputed to 600K SNPs. Genotypes were analysed for associations with the number of viable Campylobacter in the caeca. Heritability of the trait was modest but significantly greater than zero (h2=0.11 {+/-} 0.03). Genome-wide association analyses confirmed quantitative trait loci (QTL) on chromosomes 14 and 16 previously identified using the progeny of crosses of inbred lines differing in resistance, and detected two additional genome-wide significant QTLs on chromosomes 19 and 26. RNA-Seq analysis of the transcriptome of caecal tonsils from birds at the low and high extremes of C. jejuni colonisation phenotype identified differentially transcribed genes, mainly located within the QTL on chromosome 16 and proximal to the major histocompatibility complex (MHC) locus. We also identified strong cis-QTLs located within the MHC suggesting the presence of cis-acting variation in both MHC class I, class II and BG genes. Multiple other cis-acting variants were identified in association with key immune genes (COPS3, CCL4, CR1L, C4BP, PLGR) in the other QTLs. Pathway and network analysis implicated cooperative functional pathways and networks in colonisation, including those related to antigen presentation, innate and adaptive immune responses, calcium, and renin-angiotensin signalling. While co-selection for enhanced resistance and other breeding goal traits is feasible, the frequency of resistance-associated alleles was high in the population studied and non-genetic factors significantly influence Campylobacter colonisation in poultry. Author summaryCampylobacter infection is estimated to cause 95 million illnesses in people worldwide each year. Human infections mostly involve gastroenteritis, but can have severe complications. The handling or consumption of contaminated poultry meat is a key risk factor for human campylobacteriosis. The bacteria reach high numbers in the intestines of chickens reared for meat (broilers) and are frequently found on carcasses after slaughter. Effective vaccines against Campylobacter are not yet available, and treatments to reduce carcass contamination (e.g. chlorination) are not acceptable in some markets. One alternative is to breed for chickens with improved resistance to Campylobacter colonisation. To test the feasibility of this option in commercial birds, we analysed the genetic make-up of 3,000 pedigree broilers and determined the number of Campylobacter in their gut. There were associations between specific regions of the chicken genome and resistance to Campylobacter. Within some of these regions, expression of certain genes differed between birds at the low and high extremes of Campylobacter colonisation, providing a potential explanation for genetic variation in resistance. Selection of poultry with increased resistance to Campylobacter colonisation may be a complementary strategy to improved biosecurity, management, handling and processing procedures to reduce the burden of Campylobacter on human health.

ABSTRACTThe rapid increase in antibiotic resistance poses a global threat to public health, necessitating the development of effective antimicrobial alternatives. This study compared an indigenous probiotic mix containing Lactobacillus reuteri and two strains of Enterococcus faecium to a commercial probiotic blend ProtexinR on the growth performance, mortality rate, histomorphology, serum immunoglobulins, and intestinal microflora of broiler chickens challenged with two multi drug resistant Salmonella serovars, Typhimurium and Enteritidis. Two hundred and forty day-old broiler chicks were randomly assigned to six treatment groups for 4 weeks: the treatment groups were; birds continuously supplemented with only indigenous probiotic strains (108 CFU/mL) (IPRO-); birds challenged with Salmonella serovars 106 (CFU/mL) (PC+); birds continuously supplemented with indigenous probiotic strains and challenged with Salmonella serovars (IPRO+); birds supplemented with ProtexinR and challenged with Salmonella serovars (CM+); birds supplemented with only ProtexinR (CM-); and birds with no Salmonella challenge or probiotics (negative control; PC-). The results revealed that IPRO- diets significantly improved feed conversion ratio (FCR) and increased body weight (BW) (P [≤] 0.05). No effect of probiotic treatments was observed on IPRO- and CM- on relative organ weights as compared to the negative control (PC-). The Salmonella- challenged group PC+ had the highest (20%) mortality rate and lowest BW. The IPRO- had significantly lower FCR (1.55) compared to PC- (1.86) and PC+ (1.95). The broilers in the IPRO- group showed significantly increased serum concentrations of IgA and IgG relative to both control groups (P [≤] 0.05). Morphological analysis of the ileum revealed significant increases (P [≤] 0.05) in the villus height and villus height/crypt depth in birds fed IPRO- compared with the PC+. Cecal Lactobacillus and Enterococcus counts were the highest (P [≤] 0.05) and Salmonella counts were the lowest (P [≤] 0.05) in the IPRO- group compared to the Salmonella infected group PC+. These results indicated that indigenous probiotic strains Lactobacillus reuteri and Enterococcus faecium can be an effective and low-cost alternative compared to commercial probiotics in the Pakistan poultry industry.

Probiotics were introduced as a spray directly in the hatcher when chickens started to leave the eggs which potentially could reduce the horizontal transmission and colonization with pathogenic bacteria. The single introduction of probiotics could limit the cost compared to multiple introductions with feed and/or water. A mixture of five probiotic strains belonging to Escherichia coli, Enterococcus faecalis, Lactobacillus agilis and Lactobacillus rhamnosus was tested with two independent flocks of broilers (Ross 308). For each experiment, a comparison was made to an untreated control flock on the same farm. At day 14 of production the probiotic strains were re-isolated from ileum of euthanized chickens. The first week mortality was slightly increased in the probiotic flock (0.42%) compared to the control (0.35%) in experiment 1, however, it was higher in the control flock (1.45%) compared to the probiotic flock (1.12%) in experiment 2. The average weight of chickens that could be slaughtered for consumption was increased by 3.5% in the probiotic flocks compared to the control flocks, resulting in a 1.9% higher total weight of slaughtered chickens in the probiotics treated flocks compared to the control as a mean of the two experiments. The number of condemned animals was within the normal range for the production system and could not directly be related to effects of probiotics. Although one probiotic strain of E. coli was isolated from dead animals, the probiotics did not affect the proportion of chickens which died due to E. coli during the first week compared to the control. Primary audienceplant managers, veterinarians, nutritionists

Intensive broiler production practices impair the transmission of commensal microbes from hens to offspring, resulting in a lower abundance of non-spore-forming strict anaerobic bacteria. We evaluated the effects of colonization by a defined community (DC) of bacteria including and excluding Megamonas hypermegale in chicks challenged with Salmonella. Inoculation with DC resulted in higher phylogenetic diversity and the dominance of Bacteroidetes species in the cecal microbiota, with a decrease in the relative abundance of Salmonella and Escherichia/Shigella, as well as a lower Enterobacteriaceae load. Substantial shifts in microbiota composition were coupled with subtle changes in metabolites and host responses, including changes in interferon-{gamma}, macrophage colony-stimulating factor, propionate, valerate, and isovalerate concentrations in the ceca. We identified bacterial species that were able to establish and persist after a single exposure, many of which were members of Bacteroidetes. Although co-culture with M. hypermegale reduced Salmonella counts by 99.3% in vitro, in vivo inoculation of M. hypermegale increased splenic Salmonella counts in inoculated chicks. The use of DC containing bacteria isolates harvested from the cecal contents of mature chickens can recapitulate the changes in volatile fatty acid concentrations observed in birds colonized with complex communities, and the presence of M. hypermegale specifically enhances the production of propionate. Our findings suggest that the use of DC can be explored as a strategy to control disease occurrence in broiler production; however, further research is warranted to properly understand the role of individual species in the broiler cecal community aiding the formulation of appropriate DCs. ImportanceIntensive production practices can reduce beneficial gut bacteria in broiler chickens, potentially leading to higher disease risk. We investigated whether introducing a defined community (DC) of beneficial bacteria, along with M. hypermegale, could improve gut health and resistance to Salmonella in broiler chicks. Our findings show that DC increases microbial diversity and reduces the relative abundance of potential pathogens, like Salmonella and Escherichia/Shigella, which was coupled with subtle changes in the immune responses of the birds and higher concentration of volatile fatty acids in the ceca. This study suggests that using DC can enhance poultry health and reduce disease, providing a potential strategy to improve broiler production. However, further research is needed to understand the roles of individual bacteria and refine these bacterial communities for practical use in farming. This work holds promise for developing natural methods to enhance poultry health and safety.

The widespread use of antibiotics in broiler production has contributed to antimicrobial resistance, necessitating the development of sustainable alternatives. Synbiotics, combining probiotics and prebiotics in a synergistic formulation, have emerged as promising candidates to replace antibiotics. This study evaluated the efficacy of dietary synbiotics as alternatives to early-life antibiotic supplementation in broiler chickens, examining their effects on growth performance, gut morphology, and welfare. A total of 80 mixed-sex Cobb 500 broiler chickens were allocated to a 2 x 2 factorial design investigating synbiotic supplementation (Bacillus subtilis and dried fermented Saccharomyces cerevisiae extract) and enrofloxacin treatment (days 0-5) administered via drinking water. During the initial growth period (days 0-7), synbiotic supplementation reduced body weight gain compared to controls. However, synbiotic x antibiotic interactions were observed during days 7-14 and 14-21, where synbiotics without antibiotics produced the highest weight gain in the second week, while controls without either treatment achieved superior performance in the third week. Feed intake was increased by synbiotic supplementation during days 7-14, while antibiotic treatment consistently elevated feed consumption throughout multiple periods and overall trial duration. Feed conversion efficiency was initially impaired by synbiotics (days 0-7) but improved during days 14-21. Antibiotic supplementation resulted in a poorer overall feed conversion ratio. Gut morphological analysis revealed significant synbiotic x antibiotic interactions for duodenal length and empty weights of duodenum and caeca, with synbiotics enhancing these parameters only when combined with antibiotic treatment. Both synbiotic and antibiotic supplementation independently reduced ileal content weight, while antibiotic treatment specifically decreased ileal weight and caecal length. Immune function evaluation through heterophil-to-lymphocyte ratios demonstrated a tendency for interaction, where synbiotics reduced this ratio in the absence of antibiotics but showed no effect when combined with antibiotic treatment. Neither treatment affected spleen or bursa weights, indicating minimal impact on immune organ development. These findings suggest that while dietary synbiotics show promise as alternatives to antibiotics in broiler production, their efficacy varies depending on concurrent antibiotic exposure and growth phase. Synbiotics demonstrated beneficial effects on gut morphology and stress markers, particularly when administered without concurrent antibiotic treatment, supporting their potential as functional alternatives in antimicrobial-free poultry production.

Managing Salmonella enterica Enteritidis (SE) carriage in chicken is necessary to ensure human food safety and enhance chicken breeding viability. Salmonella can contaminate poultry products, causing human foodborne disease and economic losses for farmers. Both genetic selection for a decreased carriage and gut microbiota modulation strategies could reduce Salmonella propagation in farms. Two-hundred and twenty animals from the White Leghorn inbred lines N and 61 were raised together on floor, infected by SE at 7 days of age, transferred into isolators to prevent oro-fecal recontamination and euthanized at 19 days. Caecal content DNA was used to measure individual Salmonella counts (ISC) by droplet digital PCR. A RNA sequencing approach was used to measure gene expression levels in caecal tonsils after infection of 48 chicks with low or high ISC. The analysis between lines identified 7516 differentially expressed genes (DEGs) corresponding to 62 enriched Gene Ontology (GO) Biological Processes (BP) terms. A comparison between low and high carriers allowed us to identify 97 DEGs and 23 enriched GO BP terms within line 61, and 1034 DEGs and 288 enriched GO BP terms within line N. Among these genes, we identified several candidate genes based on their putative functions, including FUT2 or MUC4, which could be involved in the control of SE infection, maybe through interactions with commensal bacteria. Altogether, we were able to identify several genes and pathways associated with differences in SE carriage level. These results are discussed in relation to individual caecal microbiota compositions, obtained for the same animals in a previous study, which may interact with host gene expression levels for the control of the caecal SE load.

Breeding programs using genomic information have become common in broilers. In broilers, the main traits for selection are body weight and feed efficiency. These traits are measured in both sexes and before sexual maturity. Thus, increases in genetic gain in broiler breeding programs due to the use of genomic information are attributable primarily to the increased accuracy of predicted breeding values of potential parents. As not all birds can be genotyped due to economic constraints, an optimal genotyping strategy needs to be chosen. The objective of this study was to investigate the rates of genetic gain and inbreeding obtained by varying three factors: the percentage of birds genotyped (PG), the percentage of birds genotyped randomly (PRG) or selectively, and the percentage of males among genotyped birds (PMG). Stochastic computer simulation with a full factorial experimental design was used. Significant interaction among the factors (PG, PRG, and PMG) was observed for the rate of genetic gain in body weight and aggregate breeding value, but not for the gain in residual feed intake or the rate of inbreeding per generation. Our findings indicate that the PG, PRG, and PMG need to be considered when selecting a genotyping strategy for a broiler breeding program. If available resources allow only to genotype a small percentage (e.g., 2.5% or 5%) of all birds, the genotyping of 50-100% of male birds and selection of birds to be genotyped using phenotypic information is best. If resources allow to genotype more (e.g., [≥]20%) candidates, genotyping of equal numbers of each sex, and low PRG level (i.e., preselection of the majority of candidate based on performance) is best. Provided that a proper genotyping strategy is chosen, we conclude that the incorporation of genomic information in broiler breeding programs can substantially increase the rate of genetic gain.

BackgroundThe laying hen industry aims to extend production for the economic and environmental benefits it offers, while at the same time facing the challenges of declining egg production and quality in aging hens. To explore trait persistence, we studied 998 Rhode Island Red purebred hens from the Novogen nucleus. We recorded daily egg production from 70 to 92 weeks of age and measured individual feed intake twice a week for three weeks, starting at 70, 80, and 90 weeks, as well as body weight at the start and at the end of each feed intake recording period. Random regression models were used to study trait trajectories over time, and PCA and hierarchical clustering were applied to identify groups of hens based on estimated breeding values for the intercept and slope of traits trajectory. ResultsResults showed different aging trajectories among traits. Daily body weight variation, Feed conversion ratio, Haugh unit and yolk percentage showed persistence (i.e., stability) over the measured period. On the contrary, daily feed intake, residual feed intake, laying rate, egg mass, eggshell breaking strength and stiffness decreased over time, while body weight, mean egg weight and eggshell colour increased. To assess the feasibility of selecting for trait persistence, we estimated the genetic variance of the slope and its correlation with the intercept. We found that, for egg weight and eggshell colour, genetic variance of the slope was negligible, indicating that selection for persistence on these traits requires other means. On the contrary, the slope for other traits such as laying rate and residual feed intake showed significant additive genetic variance. Strong genetic correlations between trait estimates at different ages were also observed and heritabilities estimates were low to high depending of the traits and period. ConclusionThe study explores hens trait persistence from 70 to 92 weeks, suggesting potential for improved egg production persistence. Challenges arise from low genetic variances impacting the efficiency of the potential selection on persistence. Clustering analysis reveals distinctive response patterns to elongation of production and underlined that selecting for enhanced persistence of different traits will necessitate compromises in breeding goals.

Modern broiler breeds allow for high feed efficiency and rapid growth, but come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are furthermore affected by the composition of the gut microbiota, which in turn is influenced by diet composition. In this study we therefore assessed how diet composition alters the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content jejunum was used for metagenomic shotgun sequencing to determine the microbiota composition on species level. Among all diet groups, a total of 104 differential abundant bacterial species were detected. Most notably were the changes in the jejunal microbiota induced by butyrate supplementation when compared to the control diet, resulting in the reduced relative abundance of mainly Enterococcus faecium and the opportunistic pathogen Enterococcus hirae in broilers 4 days post-hatch. At this early stage of development, the immune system is still immature thereby highlighting the importance to study the relation of diet and the jejunal microbiota. Future studies should furthermore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.

BackgroundExcessive and irrational use of antibiotics as growth promoters in poultry has been one of key factors contributing to increased emergence of antibiotics resistant bacteria. Drug resistant infections are becoming major concerns in poultry production impacting both human and poultry health. Several alternatives for antibiotic growth promoters are being sought, and the search for effective probiotics to be used as feed additives is amongst the promising ones. Our study aimed to isolate and test potential probiotics bacteria from cloacal swabs of various indigenous chicken (Gallus domesticus) breeds from rural outskirts of the Kathmandu valley (Nepal). MethodsSelective isolation of probiotics was conducted by micro-aerophilic enrichment of sample in MRS Broth at 37{degrees}C, followed by culturing on MRS agar supplemented with 5 g/L of CaCO3. Isolated bacterial colonies producing transparent halo were selected as potential lactic acid bacteria (LAB), and tested for their antibacterial activity, phenotypic and biochemical characteristics, acidic yield, and tolerance to acid and bile. ResultsA total of 90 potential LAB were isolated from cloacal samples collected from 41 free-ranging chickens of indigenous breeds. Of these, 52 LAB isolates (57%) showed variable antibacterial activity to at least one bacterial pathogen. Of 52 LAB, 46 isolates fulfilled phenotypic and biochemical criteria of Lactobacillus spp. Of these, 37 isolates produced varying percentage yields of lactic acid, 27 isolates showed survival at pH 3.0, and 17 isolates showed survival tolerances in the presence of 0.3% and 0.5% bile salts for 24 hours. Phylogenetic analysis of 16SrDNA sequencing of LAB isolates fulfilling in vitro probiotics properties showed that 3 isolates had genetic identity of 99.38% with Lactobacillus plantarum, while one isolate was genetically similar (99.85%) with the clade of L. reuteri, L. antri and L. panis. ConclusionsOur study identified four Lactobacillus spp. strains having potential probiotics properties. Further investigations are needed to evaluate these isolates to be used as poultry probiotics feed supplement.

The implementation of the T-ARMS PCR method in the detection of single nucleotide polymorphisms (SNPs) in the LEPR gene in chicken DNA samples has never been conducted. This research aims to design a specific protocol for exon 9 LEPR gene SNPs detection and detect LEPR gene expression or LEPR SNPs in Pelung chicken samples, F1 Pelung, Layer, Broiler Cobb 500, F1 Kambro chicken and F2 Kambro chicken using the T-ARMS PCR method. Determination of LEPR gene correlation degree on Body Weight (BT) and Egg Productivity (PT) in F1 Kambro population and F2 Kambro. Qualitative phenotype parameters showed six groups of segregated phenotypes compared to F1 Kambro chicken. Growth of F2 Kambro chicken weight reached 753.36 {+/-} 155.31 grams in 8 weeks was not significant for F1 Kambro chicken due to inbreeding depression (Fx = 25%, IR = 4.925%) and transversion of A LEPR allele mutations. Specific protocol detection of exon 9 LEPR gene SNPs using the T-ARMS PCR method can detect C127A LEPR mutations with IP: OP ratio 10:1 pmol / {micro}M, chicken DNA template concentration of 100 ng / {micro}L with annealing temperature of 55.7{degrees} C / 30s. The transversion mutation of C127A of LEPR exon 9 SNP were detected in DNA samples of F1 Kambro hens (80%), F2 Kambro roosters (20%), Broiler Cobb 500 hens (75%). The mutations were not detected in Layer, Pelung Blirik Hitam chicken and F1 Pelung populations.

This study examined the effects of short-term dietary zinc (Zn) and phosphorus (P) variations on the mobilizable bone Zn pool and overall Zn status in adult laying hens. Forty-eight hens (50% Lohmann Brown Classic, 50% Lohmann LSL Classic) were housed in pairs (one hen per breed per pen) across 24 pens. The pens were randomly assigned to one of two dietary P levels (0.37% or 0.84% in DM) using a high-protein corn-soybean diet (11.4 MJ AME/kg, 21.5% CP) during a 14-day acclimatization period. Following acclimatization, pens from both P groups were further randomized into four dietary treatments in a 2 x 2 factorial design, varying in P levels (low vs. high) and Zn supplementation (28 vs. 131 mg/kg) over an 8-day experimental feeding phase. Performance metrics, egg production and quality, and tissue mineral concentrations (plasma, liver, bone, and eggs) were measured. Statistical analyses were performed using linear mixed models in SAS 9.4, incorporating random effects of pen nested within treatment group and fixed effects of dietary P, dietary Zn, breed, and their interactions. Tukey-corrected 95% confidence intervals were used to estimate effect differences, with significance set at P < 0.05. Performance metrics, including egg production and body weight, were unaffected by dietary treatments (P > 0.1), indicating no clinical symptoms of Zn deficiency. However, hens on low-Zn diets exhibited significant reductions in plasma Zn concentration (-0.83 mg/L; P = 0.0008) and liver Zn concentration (-6.78 mg/kg DM; P = 0.01), confirming subclinical Zn deficiency. Low-Zn diets also increased the femoral molar Ca:P ratio by 0.15 (P = 0.01), irrespective of dietary P supply. Interestingly, low-P diets led to a significant reduction in femur Zn content (-0.46 mg; P = 0.0009), regardless of Zn supplementation, following 21 days of reduced P feeding. These findings highlight the higher susceptibility of laying hens to phytate antagonism compared to broilers, as evidenced by measurable subclinical Zn deficiency under short-term Zn deprivation. Additionally, a temporary suspension of mineral P supply appeared to impair the mobilizable bone Zn pool. The underlying functional mechanisms driving these interactions remain unclear and warrant further investigation.

The current study investigated the genomic selection accuracies and biases estimates from two commercial Pekin duck lines reared under commercial breeding practices. A large dataset of 26K duck records comprising both phenotype and imputed genotype information (60K chip) were analysed for growth, welfare and primary feather length traits. First, we employed mixed linear models with relationship matrices computed from the pedigree (BLUP) or markers (GBLUP) to estimate the variance components and breeding values. Then, we estimated the selection accuracies and selection biases to assess the more appropriate models. Our results showed moderately high imputation accuracies of 0.93 and 0.92 for lines A and D respectively. In both lines, the heritability estimates obtained using the pedigree were generally higher than using genomic markers in all traits considered. These ranged for juvenile weight (JW) from 0.22{+/-}0.01 vs 0.25{+/-}0.01 in line A vs line D using marker information to 0.39{+/-}0.02 to 0.50{+/-}0.02 using the pedigree in line A vs line D for slaughter body weight (BW). We observed very low estimates of heritability for gait 0.07{+/-}0.01 using markers in both lines. Breast muscle depth (BD) also had lower estimates of 0.15-0.16 using markers. For line A, the genomic predictions were generally higher when using the G-matrix than the A-matrix with the highest prediction was for BW (r2=0.68-0.70) and JW with r2 of 0.49. The estimates for gait and foot pad dermatitis (FPD) were greatly improved by using the G-Matrix at 0.58 vs 0.24 and 0.68 vs 0.44 respectively for markers vs pedigree information. For line D, the same improvements for G-Matrix vs A-Matrix were observed with estimates for BD being similar in the two lines. However, for BD the G-Matrix greatly improved the estimates from 0.50 to 0.71 unlike in line A where they remained at 0.50. The bias in line A were minimal (0.01- 0.19) using the G-Matrix compared to 0.02- 0.41 when using A-Matrix. The highest observed bias was for JW followed by BD for the G-matrix whereas when using the A-matrix we observed higher biases in many traits (JW, BW, BD and gait). The biases for line D were generally lower for the G-matrix (0.02 - 0.17 vs 0.00 - 0.19) than those observed in line A using markers whereas higher biases were observed using the pedigree (0.01 - 0.37). Current findings pinpointed that all traits were heritable with higher prediction accuracies and lower biases when using GBLUP as opposed to traditional BLUP. The present study demonstrates the effectiveness of GBLUP for improving prediction accuracy and reducing bias in selection traits of Pekin ducks, particularly for traits with low heritability. Author SummaryThe study explored genomic selection in two commercial Pekin duck lines. Using a large dataset of 26,000 records, including phenotype and genotype data, researchers analyzed growth, welfare, and feather length traits. They applied statistical models to assess variance components and breeding values, comparing traditional pedigree-based methods (BLUP) with genomic marker-based methods (GBLUP). Results showed high imputation accuracies (93% for line A and 92% for line D). Heritability estimates varied, with genomic markers generally producing lower estimates than pedigrees, except for traits like gait and breast muscle depth where genomic predictions were superior. For example, line A showed higher accuracy using genomic data for body weight and juvenile weight. Overall, genomic predictions (GBLUP) provided higher accuracy and lower bias compared to traditional methods, especially for traits with low heritability. This highlights the effectiveness of GBLUP in improving selection processes in Pekin ducks.

This is an anecdotal observation of an intervention study involving laying hens from a commercial farm in the city of Chincha, Peru, who suffered an outbreak caused by Newcastle disease virus (NDV) and infectious laryngotracheitis virus (ILTV), confirmed by clinical observations, serological and molecular tests (PCR). In addition to receiving standard treatment appropriate to the state of health at the time of the operation, a group of birds were treated with a single dose of ivermectin administered subcutaneously (0.2 mL of a 1% solution equivalent to 200 {micro}g/kg body weight), with a group of control birds not receiving the treatment being reserved. The results showed a remarkable recovery of symptoms after 24 hours of treatment among the birds that received ivermectin. At 4 days after treatment, the birds that received ivermectin showed visibly greater mobility and vivacity, as well as a recovery in egg production. PCR tests after 4 days of treatment with ivermectin were negative for NDV and ILTV. These results are interesting and suggest a possible effect of ivermectin against NDV and ILTV in birds. More controlled studies are needed to confirm this hypothesis.

The comb is an accessory organ on the head of chicken which is influenced by testosterone hormone and can be used as an indicator of chickens fertility. Comb shape is related to climate adaptation and associated with a dominant mutation in chicken chromosome 1. Therefore this research was aimed to study the association between Pea-comb shape and SOX5 gene polymorphism in the population of progenies (BC-III Kambro) derived from a crossbreed between females Pelung and males second backcross generation Kampong Broiler-Type (BC-II Kambro). Chicken (Gallus gallus) SOX5 gene was acquired from NCBI GenBank with the Ref. Seq. 418195. Primers used to amplify the SOX5 gene are (F):5-AGGTAGCCATGGTGACAAGC-3,(R):5-GATCTGTGAGGCAGCCAGTT-3. Progenies showed 100% Pea-comb shape, while parental generation composed of Pea-comb shape and Single-comb shape. PCR-RFLP and endonuclease restriction enzyme HindIII were unable to determine the genotype of the female parent with Pea-comb. The result of SOX5 gene polymorphism showed the comb shape uniformity between progenies and parental of Kambro backcross generation. This study concluded that the genotype of Pea-comb shape female Pelung was undetermined and there was no polymorphism of the SOX5 gene between pea and single comb. PCR-RFLP using endonuclease restriction enzyme HindIII produced both target products and non-target/artifact products. The sequencing procedure was required to provide nucleotide sequences.

The internationally recognised method for diagnosis of avian influenza (AI) is virus isolation (VI) in specific pathogen-free embryonated fowls eggs (EFEs). In Great Britain (GB), AI virus isolation currently involves two passages in EFEs; the first typically of two days duration followed by a second lasting up to four days meaning that premises may remain under restriction for up to six days. Shorter time lengths for AIV isolation were investigated to reduce the time that businesses remain under official restrictions to safely negate AI infection, whilst maintaining test sensitivity. Both experimental inoculations of EFEs and analyses of VI attempts from high pathogenicity (HP) AI disease incursions in GB since 2016 demonstrated that HP viruses were isolated during first passage while for low pathogenicity AI outbreaks, the second passage could be reduced to two days. Power analysis showed that the benefit of reducing the number of days outweighed the risk of missing a positive isolate. This approach will substantially reduce costs to government and industry by releasing restrictions at least two days earlier where samples are negative for viral nucleic acid. Critically, it will reduce welfare implications of housing birds under restriction and improve international standards without loss of test performance.

Poultry industry in Nepal has experienced remarkable growth in the last decade, but farm biosafety and biosecurity measures are often overlooked by farmers due to lack of knowledge or to save cost. As a result, farms often suffer from sporadic and regular outbreaks of many zoonotic diseases such as highly pathogenic avian influenza (HPAI), impacting production and creating public health challenges. Poor farm management practices, including overuse of antibiotics for prophylaxis and therapeutics, can complicate the spread of poultry diseases by creating and enhancing antimicrobial resistance (AMR) that is threating to both, poultry, and human health. We assessed biosafety, biosecurity risks and AMR stewardship in sixteen poultry farms located in four districts (Ramechhap, Nuwakot, Sindhupalchowk, and Kavre) surrounding densely populated Kathmandu valley. Risk assessment and AMR stewardship evaluation questionnaire were administered to formulate biosafety and biosecurity compliance matrix (BBCM). Risk assessment checklist assessed facility operations, personnel and standard operating procedures, water supply, cleaning and maintenance, rodent/pest control and farm record keeping. Oral and cloacal samples from the poultry were collected, pooled, and screened for eight poultry pathogens using Polymerase Chain Reaction (PCR) tests. Based on BBCM, we identified one of the farms in Sindhupalchowk (Farm 4) having the most (BBCM score= 67%) and a farm in Kavre (Farm 3) to having the least (BBCM score= 12%) biosafety and biosecurity compliance. Although most of the farms (61.6%) followed general poultry farming practices, only half had clean and well-maintained farms. Personal safety standard procedure compliance (BBCM score = 42.4%) and rodent control (BBCM score = 3.1%) were the biggest gaps. At least one of either bacterial or viral pathogen was detected in all farms. Mycoplasma gallisepticum was the most common disease detected in all but one farm, followed by Mycoplasma synoviae. Although more than half of the farmers considered AMR a threat, over 26% of them used antibiotics as a preventive measure and 81% did not consider withdrawal period for antibiotics prior to processing of their meat products. Additionally, antibiotics classified as Watch and Restrict by the WHO were frequently used by the farmers to treat bacterial infections in their farms. Lack of awareness and inadequate enforcement of regulations have exacerbated the risk of disease transmission in farms and compromised antimicrobial stewardship.

Anas platyrynchos (ducks) are reared mostly for egg, which are very nutritious, that fetch better prices, however duck meat possess rich nutrient content. They possess the unique characteristics of disease resistance to the common avian diseases, even asymptomatic to avian influenza, with a scopeto evolve as one of the best poultry species The major limitation encountered is the lowered average egg production as well as higher age at first egg (an indicator for sexual maturity) for the indigenous ducks compared to that of exotic ones. In this current study, we attempt to explore the genes responsible for duck reproduction in terms of sexual maturity,egg production and fertility of the ducks. We had compared the genomic constitution for the Bengal duck with highest egg production with that of non-layer (infertile or sexually immature) ducks. We characterized the genes in indigenous ducks from ovarian tissues, identified important domains for characterized genes for the first time, and studied differential mRNA expression profiling for these genes with respect to layer and non-layer groups. Upregulation was observed for ESR2, DIAPH2, KMT2E, ASCF2 genes for Bengal duck in highest egg producing duck in comparison to non-layer duck, whereas downregulation was observed for KSR1, A2M, BMPR1B, ACVR1. In the next step, we explored the association with the genes which were actually responsible for egg production. Thus, duck may be utilized as a model for studying the molecular aspect of reproduction. Genes upregulated may be utilized for knock in of gene, whereas down regulated genes may be knocked out or knocked down through gene editing technologies for the improvement of reproductive performance of the duck in future. Molecular biomarkers may be developed with these genes for early selection of better reproducing ducks at day of hatch or even earlier.

Ayam Cemani is a local Indonesian chicken with heavy pigmentation in plumage colour, skin, eyes, and inner body organs. This trait with dermal hyperpigmentation is identical to Fibromelanosis (Fm) mutation in a Silkie chicken. The causal mutation of the Fm trait is due to an inverted duplication and junction of two genomic regions involving the Endothelin3 (EDN3) gene on chromosome 20. There are two duplication boundaries; one is specific to the Fm allele, the other is common for both Fm and fm+ allele. Determining birds that are homozygous or heterozygous at this locus is useful for unifying the Fm trait of Cemani populations. This study develops a method for determining the presence or absence of Fm mutation by PCR amplification using the inverted sequences specific to the Fm allele. Further, it develops the restriction fragment length polymorphism (RFLP) method in regions common to the Fm and wild-type fm+ allele. We aim to establish a simple method for detecting homozygous (Fm/Fm) and heterozygous (Fm/fm+) individuals with Fm mutation and to clarify the degree of fixation of the Fm trait in the Ayam Cemani populations and the association between the phenotype and genotype. The result showed that mostly, the phenotype for Cemani with Fm/ fm+ genotype is reddish black in their comb; meanwhile, the Cemani with (Fm/Fm) genotype showed heavy black pigmentation. Our study concluded that using the PCR-RFLP method. We can discriminate between Fm homozygous and heterozygous birds in the Cemani population. Thus, this briefly genotyping method effectively maintains and protects the pure line of Cemani chicken.

This study leverages Convolutional Neural Networks (CNN) and Mel Frequency Cepstral Coefficients (MFCC) to analyze the vocalization patterns of laying hens, focusing on their responses to both visual (umbrella opening) and auditory (dog barking) stressors at different ages. The aim is to understand how these diverse stressors, along with the hens age and the timing of stress application, affect their vocal behavior. Utilizing a comprehensive dataset of chicken vocal recordings, both from stress-exposed and control groups, the research enables a detailed comparative analysis of vocal responses to varied environmental stimuli. A significant outcome of this study is the distinct vocal patterns exhibited by younger chickens compared to older ones, suggesting developmental variations in stress response. This finding contributes to a deeper understanding of poultry welfare, demon-strating the potential of non-invasive vocalization analysis for early stress detection and aligning with ethical live-stock management practices. The CNN models ability to distinguish between pre- and post-stress vocalizations highlights the substantial impact of stressor application on chicken vocal behavior. This study not only sheds light on the nuanced interactions between stress stimuli and animal behavior but also marks a significant advancement in smart farming. It paves the way for real-time welfare assessments and more informed decision-making in poultry management. Looking forward, the study suggests avenues for longitudinal research on chronic stress and the application of these methodologies across different species and farming contexts. Ultimately, this research represents a pivotal step in integrating technology with animal welfare, offering a promising approach to transforming welfare assessments in animal husbandry.