Search Results (253)

Broodiness is a natural behavior whereby female birds stop laying eggs to sit on and hatch them. This behavior is regulated through genetic, hormonal, and environmental factors. The Taihe Black-Boned Silky Fowl (TBSF), a Chinese traditional domestic breed, exhibits a strong brooding tendency; however, the molecular mechanisms underlying this trait remain unclear. In this study, we performed an integrated multi-omics analysis to characterize differences between two groups of TBSF hens: 8 individuals undergoing 30 days of active brooding (BR30) and 8 individuals in the normal laying egg stage (NB), selected from a total group of 230 hens. We combined 16S rRNA sequencing, untargeted metabolomics, and hepatic transcriptome sequencing, with statistical analyses including QIIME 1.9.1, OPLS-DA (VIP > 1), Student’s t-test (p ≤ 0.05), and DESeq2 (|log₂FC| ≥ 1, FDR < 0.05) for differentially expressed genes (DEGs), respectively, and Pearson’s correlation analysis for multi-omics integration. Phenotypically, brooder hens showed significantly reduced feed intake, body weight, and main digestive tissue indices, alongside altered liver and blood biochemical parameters. Hepatic transcriptome analysis identified 1582 DEGs between groups, enriched in pathways related to fatty acid oxidation and the amino acid degradation pathway. In addition, 16S rRNA sequencing revealed distinct gut microbial community structures: the NB group was enriched in Bacilliota and Pseudomonadota, while the BR30 group was enriched in Spirochaetota and Synergistota. Metabolomic profiling identified a total of 143 differential metabolites, which were enriched in lipid and amino acid metabolites, including alpha-linolenic acid and pyruvate metabolites. Multi-omics correlation analysis revealed tight associations between gut microbial taxa, circulating metabolites, and hepatic gene expression. Specifically, beneficial lipid metabolites, including phospholipids, lysophosphatidylcholines, and sphingomyelins, were positively correlated with Synergistes and the Christensenellaceae R-7, as well as with key hepatic lipid metabolism genes FABP1, LPL, and FADS2. In summary, this study reveals that the gut–liver axis plays a critical part in the modulation of energy metabolism during broodiness, and further highlights new insights into metabolic targets that could optimize reproductive behavior and enhance poultry production. Full article

Highly pathogenic avian influenza (HPAI) is a transboundary disease of birds with zoonotic potential. Since 2021, H5 HPAI virus variants have spread globally, with migratory waterfowl playing a key role in transcontinental dissemination. Kazakhstan lies at the intersection of major flyways, creating a persistent risk of virus introduction into domestic poultry. While HPAI risk in wild birds has been explored in Kazakhstan, the spatial risk for poultry has remained underassessed. Here, we present a risk map for HPAI in poultry across 174 administrative districts of Kazakhstan, using a multi-criteria decision analysis (TOPSIS) that integrates five quantitative risk indicators that relate to wild bird habitat, virus survival in the environment and poultry farm census. The obtained district-level risk index agreed well with historical outbreak data (2005–2025), with an area under the receiver operating characteristic (ROC) curve of 0.899 (95% CI: 0.846–0.952). Most districts (56%) were at negligible risk, whereas medium- and high-risk clusters occurred in the north, central, and southern regions, and near the Caspian Sea. These findings provide an operational, spatially explicit tool for targeting surveillance and biosecurity measures to high-risk areas, ultimately helping to mitigate the impact of one of the most devastating transboundary poultry diseases in Central Asia. Full article

Toxoplasma gondii is a cosmopolitan zoonotic parasite for which free-range poultry can act as sentinels of oocyst contamination. Romanian avian data on toxoplasmosis are limited to extensive systems and wildlife, while poultry seropositivity in intensive systems has not been previously characterized. In this study, 1940 domestic birds from intensive and extensive production systems were tested for T. gondii IgG antibodies by the Modified Agglutination Test (MAT). The descriptive dataset included data on 813 intensive broiler chickens and 1127 backyard birds. Backyard chickens had roughly twice the MAT seroprevalence of intensive broilers (31.2% vs. 14.1%, p < 0.001), rising to more than a tenfold difference at ≥1:48 (18.7% vs. 1.7%, p < 0.001). Seroprevalence varied among counties and farms, but intensive broilers were sampled in a very delimited area, so geographic and production-system patterns partly overlapped and should not be interpreted independently. In models adjusting for county and age, intensive production remained associated with lower odds of infection. These findings establish the first Romanian seroprevalence baseline for intensive poultry and support risk-based surveillance focused on backyard flocks and counties with high extensive-system prevalence. Full article

The H5N1 highly pathogenic avian influenza (HPAI) virus has caused severe global losses, reaching South America in 2022 and Antarctica in 2024. Here, we synthesize outbreak reports submitted to the World Organization for Animal Health by South American countries and overseas territories in this continent, and document the virus’s unprecedented expansion into Antarctica, affecting wild birds, wild mammals, and domestic poultry. Phylogenetic and time-calibrated Bayesian analyses were performed on available genomic sequences. Over 6 million domestic birds were lost, mostly from commercial operations. Of the 11 South American countries and overseas territories that reported H5N1 to WOAH, 10 reported infections in wild birds, spanning 104 species, 59.62% of which are migratory and predominantly non-trans-equatorial. Marine mammal outbreaks followed wild bird detections, with the South American sea lion (Otaria flavescens) being the most reported species. Several Antarctic bird species with migratory behavior were also reported in South America. Genomic analyses revealed multiple introduction events, regional viral diversification, and patterns consistent with repeated cross-species spillover events. These findings highlight H5N1’s extensive ecological reach in the Southern Hemisphere and underscore the urgent need for a One Health approach that strengthens wildlife and backyard-poultry surveillance, alongside coordinated regional action to control and prevent further HPAI spread. Full article

Global food trade exposes sharp differences in food safety regulation, especially between the EU and the US. The EU follows a precautionary, hazard-based model, allowing intervention under scientific uncertainty to protect consumers, maintain public trust, and avoid long-term risks. The US applies a science-based, proof-of-harm approach, requiring clearer evidence of risk before limiting market access, supporting innovation and regulatory efficiency. These contrasting philosophies create trade tensions and non-tariff barriers, as seen in disputes over hormone-treated beef, genetically modified organisms, and chlorine-washed poultry. Beyond the transatlantic context, countries adopt precautionary, science-based, or hybrid systems depending on domestic priorities, institutional capacity, and trade commitments. Hybrid models in India, China, and parts of Africa combine precautionary safeguards with evidence-based risk assessment to balance consumer protection and market access. International bodies such as Codex Alimentarius, the WHO, and the WTO help manage regulatory divergence through standards, guidance, and dispute resolution, while recognising precaution under uncertainty. Recent EU agreements with Mercosur and India show pragmatic cooperation through transparency, safeguards, and sanitary and phytosanitary commitments. Overall, effective global food governance depends on hybrid, coordinated, and adaptive approaches that reconcile health protection, trade facilitation, and innovation. Full article

Avian influenza remains a major threat to poultry production, wildlife conservation, and public health in Asia, where migratory birds, wetlands, rice paddies, domestic ducks, and live poultry trade often intersect. This Asia-focused review synthesizes ecological, epidemiological, surveillance, tracking, phylogenetic, and environmental evidence from 1996 to 2025, with particular emphasis on China, to clarify how risk develops at the wild bird–domestic poultry interface. The reviewed evidence suggests three broad epidemic phases: early Goose/Guangdong-lineage H5N1 outbreaks before 2014, recurrent clade 2.3.4.4 H5Nx expansions during 2014–2019, and the widespread clade 2.3.4.4b H5N1 period since 2020. Spatial risk is concentrated around major stopover wetlands and rice-paddy–duck landscapes, including Qinghai Lake, Poyang Lake, Sanmenxia, the Sanjiang Plain, and peri-urban market belts. Wetlands and paddies can maintain viruses environmentally, free-grazing ducks and bridge hosts can facilitate introduction, and live poultry markets and trade networks can amplify and export risk. By organizing these processes through an Interface–Amplifier–Conduit evidence-mapping approach, this review highlights setting-specific priorities, including seasonal wetland surveillance, closed farm-water systems, improved market hygiene, and better integration of ecological and genomic data for early warning and control. Full article

Fatty liver disease represents a major metabolic disorder affecting domestic animals worldwide, with significant implications for animal health, welfare, and agricultural productivity. Disrupted communication between mitochondria and other organelles—particularly the endoplasmic reticulum, lipid droplets, and lysosomes—plays a critical role in disease pathogenesis. This review synthesizes knowledge on inter-organellar communication across domestic animals, with emphasis on species-specific adaptations. We address the “Dairy Cow Paradox”—periparturient dairy cows develop severe hepatic steatosis (>30% liver fat), yet under sterile conditions, they have a higher threshold for progressing to sterile steatohepatitis compared to rodents and humans. However, it is critical to note that severe fatty liver in dairy cows is indeed associated with impaired autophagy, inflammation, and liver damage, particularly when accompanied by ketosis or concurrent infections, and 39% of transition cows exhibit moderate to severe lymphocytic hepatitis. We propose that the tolerance to severe steatosis in dairy cows arises from three adaptations: (1) attenuated innate immune sensing via the cGAS-STING pathway; (2) enhanced lipid buffering from perilipin 5 (PLIN5) with a hypothesized ruminant-specific Val152 substitution that may stabilize lipid droplet–mitochondria contacts; and (3) dampened calcium signaling due to ER–mitochondria membrane lipid raft rigidity, elevated inositol 1,4,5-trisphosphate receptor 2 (IP₃R2) expression, and reduced mitochondrial calcium uniporter (MCU) conductance. We contrast this with the inflammatory steatohepatitis common in rodent models driven by calcium overload and mitochondrial DNA (mtDNA) release, and glucocorticoid-mediated mitofusin 1 (MFN1) suppression, causing mitochondrial fragmentation in poultry. We identify critical knowledge gaps, including the need to define bovine and avian mitochondria-associated endoplasmic reticulum membrane (MAM) proteomes and spatially resolve hepatic zonal communication patterns. Targeting organellar communication hubs with nutraceuticals or pharmacological agents offers promising therapeutic strategies. Full article

The National Special Pathogens System (NSPS) stratifies U.S. healthcare facilities by their readiness level to care for patients with high-consequence infectious diseases (HCIDs). While NSPS Level 1 and 2 facilities possess advanced biocontainment capabilities to care for patients for the duration of their illness, most U.S. hospitals fall under a NSPS Level 3 or 4 designation, with limited resources to manage patients with a suspected or confirmed HCID. However, emerging zoonotic threats like H5N1 underscore the need to bolster HCID preparedness across all NSPS Levels. Beginning in March 2024, the U.S. H5N1 outbreak has primarily impacted wild bird flocks, poultry, and cattle, along with some human infections. The continuation of this outbreak in wild and domesticated animals increases the likelihood of further human spillover and eventual viral evolution in human hosts. At the frontlines, rural farming communities are likely to be most affected, with potential outbreaks exacerbated by a lack of accessible NSPS Level 1, 2, or 3 facilities in these regions. Thus, strengthening the HCID preparedness of local NSPS Level 4 facilities is critical to preventing transmission, minimizing societal disruption, protecting communities and the healthcare workforce, along with ensuring an equitable, coordinated response to future emerging infectious disease threats. This manuscript explores the financial, societal and health system impacts of HCID outbreaks to delineate the necessity of strengthening the preparedness of NSPS Level 4 facilities. Full article

Avian haemosporidian parasites, especially Plasmodium juxtanucleare, Leucocytozoon caulleryi, and Leucocytozoon sabrazesi, represent major threats to poultry health and production. However, there is limited epidemiological information about these pathogens in domestic chickens in Southern China, which hinders effective disease prevention and control. The objective of this study was to conduct a cross-sectional survey to investigate the epidemiological characteristics of these three parasites in Guangxi and Hunan Provinces between June 2024 and December 2025. A total of 941 blood samples were collected from domestic chickens and analyzed using both nested PCR targeting the cytb gene and species-specific PCR assays targeting the coxI gene. The overall detection rate of haemosporidian infection was 25.40% (239/941). P. juxtanucleare was the most commonly detected species, with a detection rate of 23.59% (222/941), followed by L. caulleryi at 1.81% (17/941), while no L. sabrazesi infections were identified. Analysis of risk factors showed that chickens older than 90 days had significantly higher detection rates for both P. juxtanucleare and L. caulleryi compared to younger birds. Additionally, breed-specific differences were noted, with black-bone and partridge chickens showing higher susceptibility to P. juxtanucleare than three-yellow chickens. Genetic analysis of coxI sequences demonstrated high conservation among P. juxtanucleare isolates (99.7–100% similarity) and complete identity among L. caulleryi strains. Phylogenetic analysis confirmed that all sequences clustered with the corresponding reference strains from GenBank. This study presents an epidemiological evaluation of these three haemosporidian parasites in domestic chickens from Guangxi and Hunan Provinces, identifying P. juxtanucleare as a widespread pathogen and highlighting age and breed as important risk factors. These results emphasize the importance of ongoing monitoring and targeted control measures in the area. Full article

Chicken (Gallus gallus domesticus) domestication, likely associated with dry-rice farming in central Thailand, has led to substantial loss of ancestral immune-related genetic diversity in commercial chicken lineages. This study addresses allelic loss by providing the first comprehensive analysis of the highly polymorphic BG1 gene, an MHC-linked marker across the wild–domestic interface in Thailand and Vietnam, using high-depth Illumina amplicon sequencing. Genomic DNA from 47 Thai and Vietnamese chicken populations was extracted using a salting-out protocol following ethical sampling. Allelic variation was examined by targeting the BG1 intron 15–exon 16 region using triplicate PCR and Salus Pro NGS sequencing. Evolutionary dynamics and selection pressures were analyzed using AmpliSAS, MrBayes, and Datamonkey, while AlphaFold 3 was used to predict and validate 3D protein structures. We identified 98 novel alleles and 172 polymorphic sites within the BG1 intron 15–exon 16 region encoding an Ig-like domain. Extensive allele sharing between indigenous chickens and red junglefowl indicated strong balancing selection and trans-species polymorphism. Selection analyses showed that purifying selection conserved structural integrity at codons 9, 13, and 18, while variation at other sites enhanced immune recognition. AlphaFold 3 modeling confirmed conservation of the β-sandwich fold across variants, maintaining stability of the Immunoreceptor Tyrosine-based Inhibition Motif (ITIM). Thus, despite the regional gene flow, geographic isolation has shaped distinct signatures, as evidenced by the presence of 38 unique Thai and 9 unique Vietnamese alleles in addition to breed-specific private markers in the Betong (BG1*TH88), Decoy (BG1*TH91), and Tre (BG1*VN54) populations. A notable adaptive outlier under positive selection (ω = 1.357) was detected in the Dong Tao population, suggesting a recent selective sweep. These findings support the mission of the Siam Chicken Bioresource Project (SCBP) to utilize indigenous breeds as genetic reservoirs and provide a molecular basis for restoring resilience traits in domestic poultry to enhance global food security. Full article

The 2022 highly pathogenic avian influenza (HPAI) outbreak of H5N1 clade 2.3.4.4b was one of the major avian influenza outbreaks, leading to multiple spillover events infecting domestic and wild bird flocks, as well as mammals. The sustained spread was a result of viral circulation in wild birds across migratory flyways in North America. Pennsylvania has a significant poultry population that supports both retail and live bird markets. The state also features migratory bird stopovers on the Atlantic flyway, increasing exposure to HPAI infections. This study investigates clinical presentation and sequence data from H5N1 clade 2.3.4.4b viruses during the 2022 outbreak in Pennsylvania. Eight different H5N1 clade 2.3.4.4b genotypes were detected (A1, B1.1, B1.2, B1.3, B2.2, B3.3, B3.5, and one minor genotype) during the first year. The earliest detection was genotype A1, a fully Eurasian virus, in commercial poultry in April 2022. All other genotypes identified were reassortants of A1 with North American avian influenza gene segments (denoted with “B”). Genotype B3.3 was a rare genotype prior to the initial spillover into the live bird market system, but remained predominant among backyard flocks in Pennsylvania and surrounding states until September 2023. Genotype B3.3 has not been detected in migratory waterfowl since, suggesting the genotype has waned and is no longer in circulation. This study sheds light on the genotype diversity of H5N1 during the 2022 outbreak in Pennsylvania poultry, contributing to the understanding of virus evolution and its potential impacts. Full article

Campylobacter spp. constitutes a significant global public health hazard as it is a leading cause of reported foodborne diseases. Human infection is predominantly acquired through the ingestion of contaminated food, unpasteurized milk and untreated water, prompting the widespread implementation of chemical disinfection across several sectors, from healthcare, domestic environments, and food-processing to animal husbandry. While these biocidal agents encompass multiples classes with different modes of action and efficacy, growing evidence suggests that their extensive and repeated use may unintentionally promote bacterial persistence, tolerance and adaptive responses. Although biocide resistance has been documented in several foodborne pathogens, data on biocide tolerance in Campylobacter spp. remain limited. Available studies report variable degrees of reduced susceptibility to commonly used biocides among isolates originating from poultry production, food-processing environments, and water systems. Importantly, while biocide-induced adaptive responses in Campylobacter spp. may potentially overlap with antimicrobial resistance mechanisms, the extent to which these agents drive co-selection, persistence, or dissemination requires further elucidation. Evidence remains limited on the effects of long-term and repeated exposure under realistic processing conditions, the interplay between stress-induced gene regulation and stable genetic changes, and the contribution of mobile genetic elements, biofilm formation, and microbial communities in shaping antimicrobial resistance evolution. In light of the global health burden imposed by campylobacteriosis and the rising challenge of antimicrobial-resistant Campylobacter, this review brings together current evidence on the role of biocides in shaping bacterial survival, adaptation, and resistance mechanisms. Full article

The guinea fowl (Numida meleagris), a thermo-tolerant and disease-resilient poultry species, holds great potential for sustainable poultry production in climate-vulnerable regions. The genomic aspects of this species remain largely understudied. The present study aims to delineate the patterns of domestication and understand the evolutionary dynamics of guinea fowl populations (wild and domestic) across three continents, utilizing whole-genome sequencing data from 122 genomes. The population structure analyses (ADMIXTURE, PCA, phylogeny, F_ST, LD, and MAF) revealed that Indian guinea fowl (CARI) shared close ancestry with Iranian (IRAD) and Chinese (CHID) domesticated populations while remaining distinct from wild lineages. The runs of homozygosity (ROH) identified 49,088 segments, with short fragments (ROHs) preponderant in Indian and domestic populations, reflecting historical inbreeding and effects of domestication cum selection. Copy number variation (CNV) analysis revealed 105,178 CNVs concatenated into 40,067 CNV regions (CNVRs) across 11 populations, establishing the first CNV atlas for guinea fowl at the global level. Gene annotation of overlapping ROH and CNVRs revealed 1080 common candidates across Asian guinea fowl populations, i.e., the Indian guinea fowl (CARI), IRAD, and CHID, including FOS, EPAS1, CD74, and CSF1R. These genes have earlier been associated with immune regulation, stress response, and thermal adaptation. Selection signature scans, integrating intra-population (iHS) and inter-population (XP-EHH) approaches, uncovered genes under positive selection linked to immune response (like BCL11B, IL18, and GPC3), thermo-tolerance (like TRPV4 and BAG3), lipid metabolism (like AACS and ELOVL4), and pigmentation (BCO2). These signatures highlight the molecular basis of resilience in guinea fowl and their potential to withstand climate-induced stresses. This study presents the first global CNV atlas for guinea fowl and provides the first comprehensive genomic characterization of the Indian domestic population, integrating ROH, CNV, and selection signature analyses. It offers a comprehensive assessment of guinea fowl genomes (wild and domesticated) across three continents, offering insights into domestication, evolutionary dynamics, and the genetic basis of their adaptation and resilience. Full article

Background/Objectives: We analyzed the whole-genome sequences of ciprofloxacin-resistant (CIP-R) enteropathogenic Escherichia coli (EPEC) ST752 isolates in South Korea to characterize their molecular epidemiology. This lineage has emerged as the predominant CIP-R EPEC clone in South Korea, accounting for 28.8% of human clinical isolates and circulating within the One Health interface. Methods: We performed whole-genome sequencing (WGS) and reference-based core-genome single-nucleotide polymorphism (SNP) analysis on 26 CIP-R EPEC ST752 isolates (19 human clinical and 7 poultry-derived isolates). To elucidate their evolutionary history and transmission dynamics, Bayesian phylodynamic and phylogeographic reconstructions were implemented by integrating domestic isolates with a global genome dataset (n = 508). Results: Isolates from human and poultry sources clustered together with an identical virulence profile and minimal genetic distance. The Bayesian molecular clock analysis estimated that the time to the most recent common ancestor of the South Korean clade was 2000.65. Moreover, the phylogeographic analysis supported statistical evidence (Bayes factor 32.16) for the introduction of this lineage into South Korea from Denmark and revealed a strongly supported host transition from humans to poultry (Bayes factor > 10,000), although this requires cautious interpretation due to limited temporal sampling of poultry isolates. Conclusions: Continued integrated One Health surveillance across human, animal, and environmental reservoirs is needed to monitor and prevent the spread of high-risk antimicrobial-resistant clones. Full article

Botulism is a neuroparalytic disease caused by exposure to botulinum neurotoxins produced by anaerobic spore-forming bacteria of the genus Clostridium. This disease occurs in both humans and wild and domestic animals, and is currently becoming an increasingly serious problem worldwide due to high animal mortality and economic losses. The clinical signs observed during the progression of botulism are nonspecific and difficult to unequivocally associate with this disease entity. The aim of this study is to present laboratory diagnostics of suspected botulism cases reported in Poland in 2022–2024, as well as to present the challenges encountered during laboratory investigations. The material for the study consisted of samples of liver, serum, digestive tract, feed, feces, straw, and water from drinking lines, sent to the National Veterinary Research Institute (NVRI) in relation to thirteen suspected cases of botulism, predominantly reported in poultry, but also in mink and cattle farms. The samples were analyzed using a mouse bioassay and conventional culture methods, as well as real-time PCR methods aimed at detecting the ntnh and bont genes, which determine the production of botulinum neurotoxins. Of the thirteen suspected cases analyzed, ten were confirmed by the detection of botulinum toxin (BoNTs) and/or the presence of the ntnh and bont genes in the tested material. Based on the results obtained, it was concluded that botulinum toxin type C was the etiological factor of botulism poisoning in most of the analyzed cases. In one case reported in cattle, poisoning occurred as a result of the mosaic variant of BoNT D/C. Due to the nonspecific signs of botulism and the time required for them to appear, laboratory diagnostics play a key role in detecting the disease. However, this process is complicated due to the high heterogeneity observed among Clostridium spp. strains, as well as difficulties encountered during the isolation of the microorganism and the possibility of loss of toxin-producing capacity at later stages of analysis. Full article