Explore the vast range of titles available.

Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks. It is unclear how gut-dwelling E. coli bacteria often emerge to cause systemic infection in chickens. Here, Mageiros et al. use population genomics and pangenome-wide association studies to identify genetic elements associated with pathogenicity in avian E. coli .

Infectious animal diseases caused by pathogenic microorganisms such as bacteria and viruses threaten the health and well-being of wildlife, livestock, and human populations, limit productivity and increase significantly economic losses to each sector. The pathogen detection is an important step for the diagnostics, successful treatment of animal infection diseases and control management in farms and field conditions. Current techniques employed to diagnose pathogens in livestock and poultry include classical plate-based methods and conventional biochemical methods as enzyme-linked immunosorbent assays (ELISA). These methods are time-consuming and frequently incapable to distinguish between low and highly pathogenic strains. Molecular techniques such as polymerase chain reaction (PCR) and real time PCR (RT-PCR) have also been proposed to be used to diagnose and identify relevant infectious disease in animals. However these DNA-based methodologies need isolated genetic materials and sophisticated instruments, being not suitable for in field analysis. Consequently, there is strong interest for developing new swift point-of-care biosensing systems for early detection of animal diseases with high sensitivity and specificity. In this review, we provide an overview of the innovative biosensing systems that can be applied for livestock pathogen detection. Different sensing strategies based on DNA receptors, glycan, aptamers and antibodies are presented. Besides devices still at development level some are validated according to standards of the World Organization for Animal Health and are commercially available. Especially, paper-based platforms proposed as an affordable, rapid and easy to perform sensing systems for implementation in field condition are included in this review.

Newcastle disease (ND) is one of the most devastating diseases that considerably cripple the global poultry industry. Because of its enormous socioeconomic importance and potential to rapidly spread to naïve birds in the vicinity, ND is included among the list of avian diseases that must be notified to the OIE immediately upon recognition. Currently, virus isolation followed by its serological or molecular identification is regarded as the gold standard method of ND diagnosis. However, this method is generally slow and requires specialised laboratory with biosafety containment facilities, making it of little relevance under epidemic situations where rapid diagnosis is seriously needed. Thus, molecular based diagnostics have evolved to overcome some of these difficulties, but the extensive genetic diversity of the virus ensures that isolates with mutations at the primer/probe binding sites escape detection using these assays. This diagnostic dilemma leads to the emergence of cutting-edge technologies such as next-generation sequencing (NGS) which have so far proven to be promising in terms of rapid, sensitive, and accurate recognition of virulent Newcastle disease virus (NDV) isolates even in mixed infections. As regards disease control strategies, conventional ND vaccines have stood the test of time by demonstrating track record of protective efficacy in the last 60 years. However, these vaccines are unable to block the replication and shedding of most of the currently circulating phylogenetically divergent virulent NDV isolates. Hence, rationally designed vaccines targeting the prevailing genotypes, the so-called genotype-matched vaccines, are highly needed to overcome these vaccination related challenges. Among the recently evolving technologies for the development of genotype-matched vaccines, reverse genetics-based live attenuated vaccines obviously appeared to be the most promising candidates. In this review, a comprehensive description of the current and emerging trends in the detection, identification, and control of ND in poultry are provided. The strengths and weaknesses of each of those techniques are also emphasised.

Salmonella species are known to cause a significant decline in poultry production performance and to contaminate various stages of the breeding process, with Salmonella Pullorum ( S . Pullorum) and Salmonella Enteritidis ( S . Enteritidis) being the predominant serotypes responsible for infection in poultry. For rapid diagnosis at an early stage, we developed a method involving dual recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD) in this study, and primers were designed to target the traJ gene of S . Pullorum and the Sdf Ⅰ gene of S . Enteritidis. The primers and probes were screened, and the reaction conditions were optimized. The results showed that dual RPA successfully amplified S . Pullorum and S . Enteritidis DNA within 15 min at 37°C, and when combined with LFD, the entire process (amplification and detection) was completed within 20 min. The detection limits for S . Pullorum and S . Enteritidis were 1.56 × 10 2 CFU/mL and 1.38 × 10 2 CFU/mL, respectively. The developed dual RPA-LFD method specifically targets S . Pullorum and S . Enteritidis and exhibits no cross-reactivity with other common pathogenic microorganisms. The results for the clinical samples were fully consistent with those obtained using the Bacteriological Analytical Manual (BAM) method. The results of this study demonstrated that the developed dual RPA-LFD method is simple, rapid, specific, and highly sensitive for the simultaneous visual detection of S . Pullorum and S . Enteritidis, providing a technical reference for primary veterinary laboratories and veterinary field tests.

Avian pathogenic Escherichia coli causes septicemia in broiler chickens leading to high mortality and economic losses. Current diagnostic methods, such as serology and culture, cannot detect infections during early asymptomatic stages. Hence, this study focused on identifying novel serum metabolic biomarkers and pathways as an early detection prediction tool. Ross broiler chicks were challenged with E. coli at 3 or 5 d of age, and blood samples collected at 8 and 24 h following infection. Serum samples were analyzed for metabolite alterations using targeted The Metabolomics Innovation Centre (TMIC) mega metabolomics assay. Data was processed through comprehensive statistical analyses, including univariate, multivariate, and meta-analysis approaches. At 8 h post-infection, top metabolites like adenine, N-acetyl-alanine, N-acetyl-soleucine, N-acetyl-valine, and orotic acid related to nucleotide and amino acid metabolisms were downregulated ( p  = < 0.05). At 24 h, a distinct metabolic shift emerged with hippuric acid increasing, while adenine showed further depletion, accompanied by decreases in N1-acetylspermidine, N-acetylputrescine, and a modest increase in picolinic acid related to nucleotide, polyamine and immune response pathways ( p  = < 0.05). Correlation metabolite networks show that at 8 h post-infection, broiler chicken showed enhanced metabolic coordination, while at 24 h, disruptions in polyamine, nucleoside, and fatty acid pathways reflected systemic rewiring. The progressive depletion of adenine at both 8 and 24 h post-infection supports it as a novel metabolite signature for E. coli infection.

Background The conventional diagnosis in poultry disease enhances accuracy by combining clinical and necropsy observation with various molecular biological analysis. However, if the causative agents of a disease are not isolated and detected, accurate diagnosis and future disease management become challenging. The purpose of the present study aimed to diagnose and identify the causes of disease in broilers with novel petechial hepatitis by applying metagenomic analysis. Case presentation Through the necropsy, tracheal and pericardial congestion, and severe petechia and perihepatitis in the livers were observed. Histopathological examination revealed infiltration of lymphocytes and bacterial colonies in various organs, as well as severe sinusoidal congestion, hemorrhages and hepatocyte necrosis in the livers. E. coli was isolated and identified in the liver samples. Although FAdV, CkChpV, CAstV, IBV and IBDV were detected, no viral agents were detected in the livers. Metagenomic analysis of the livers showed a predominance of bacterial composition, followed by fungal and viral agents, with E. coli being the most abundant. Analysis of virulence factors in E. coli revealed the presence of those associated with APEC, as well as other IPEC and ExPEC pathotypes. Conclusion The present study identified a novel petechial hepatitis in broilers, associated with co-infections of antigenic variant IBDV, multiple pathotypes of E. coli , and possibly various causative. The application of metagenomic analysis proved valuable in identifying diverse potential pathogens when conventional methods were limited. These findings highlight the utility of metagenomic approaches as a complementary diagnostic tool and support their continued use in advancing poultry disease management.

Mycoplasma synoviae infection is a chronic disease of poultry with significant economic impacts. An efficient diagnostic tool for M. synoviae infection is in great demand. This study aimed to develop a novel indirect enzyme-linked immunosorbent assay (iELISA) method based on antigens identified by pull-down assay combined with mass spectrometry. Using these methods and anti- M. synoviae serum, we identified an uncharacterized protein with a molecular weight of 53 kDa (named P50 protein) and then established a recombinant P50 protein-based ELISA (rP50-ELISA) to detect antibodies against P50 protein. A receiver operating characteristic (ROC) analysis was performed to estimate the optical density (OD) cut-off value that maximized the sensitivity (Se) and specificity (Sp) of the rP50-ELISA, which had a mean Se of 93% (95% confidence interval (CI) = 86.25–96.57%) and a mean Sp of 100% (95% CI = 91.80–100%), with an area under the curve (AUC) of 0.9979 (95% CI = 99.41–100%). The rP50-ELISA showed no cross-reactivity with antibodies against other avian pathogens. Serum samples from 164 clinical chickens were tested with the rP50-ELISA, and the results revealed a high concordance rate of 93.29% with commercial diagnostic kits. Key points • Screening for the major antigen of M. synoviae for ELISA development. • The P50 protein was selected as a coating antigen for ELISA. • rP50-ELISA was successfully developed for detecting anti-M. synoviae antibodies with high sensitivity and specificity.

The broiler industry is facing an increasing prevalence of breast myopathies, such as white striping (WS) and wooden breast (WB), and the precise aetiology of these occurrences remains poorly understood. To progress our understanding of the structural changes and molecular pathways involved in these myopathies, a transcriptomic analysis was performed using an 8 × 60 K Agilent chicken microarray and histological study. The study used pectoralis major muscles from three groups: slow-growing animals (n = 8), fast-growing animals visually free from defects (n = 8), or severely affected by both WS and WB (n = 8). In addition, a weighted correlation network analysis was performed to investigate the relationship between modules of co-expressed genes and histological traits. Functional analysis suggested that selection for fast growing and breast meat yield has progressively led to conditions favouring metabolic shifts towards alternative catabolic pathways to produce energy, leading to an adaptive response to oxidative stress and the first signs of inflammatory, regeneration and fibrosis processes. All these processes are intensified in muscles affected by severe myopathies, in which new mechanisms related to cellular defences and remodelling seem also activated. Furthermore, our study opens new perspectives for myopathy diagnosis by highlighting fine histological phenotypes and genes whose expression was strongly correlated with defects.

Duck Tembusu virus (DTMUV) belongs to the family Flaviviridae and genus Orthoflavivirus . It causes disease in ducks, affecting the nervous system and significantly reducing egg production. The first outbreak of DTMUV in Thailand was reported in 2013, with widespread cases across various regions. However, serological diagnosis of DTMUV is challenging due to antibody cross-reactivity with other flaviviruses. To address this issue, we developed an ELISA based on subviral particles. The cassette encoding the membrane precursor and envelope genes of DTMUV (strain KPS54A61) were cloned into a pCAGGS vector with an OSF-tag and transfected into HEK-293T cells to generate subviral particles. The subviral particles were detected in the supernatant of the transfected cell via immunoblotting using anti-DTMUV E protein and anti-Strep-tag antibodies, which revealed a protein band of approximately 59 kDa. An electron microscopy confirmed the presence of particles approximately 35 nm in diameter. To optimize the SP-based ELISA, checkerboard titration identified the optimal antigen concentration as 70 µg/mL and the optimal serum dilution as 1:100,000. A cut-off value was established for the assay, and testing 300 duck serum samples using the SP-based ELISA identified 41 positive samples (14%) and 259 negative samples (86%). The SP-based ELISA exhibited 100% sensitivity and specificity, achieving a perfect agreement score of 1.0 in comparison with the serum neutralization test. Additionally, specificity testing using antibodies specific to Japanese Encephalitis virus (JEV) revealed no cross-reactivity in the ELISA test. Therefore, the developed SP-based ELISA is highly effective for screening and monitoring DTMUV outbreaks in duck farms, significantly reducing the risk of viral spread and enabling the timely implementation of disease control measures.

Infectious laryngotracheitis (ILT) is a highly contagious upper respiratory tract disease of chicken caused by a Gallid herpesvirus 1 (GaHV-1) belonging to the genus Iltovirus, and subfamily Alphaherpesvirinae within Herpesviridae family. The disease is characterized by conjunctivitis, sinusitis, oculo-nasal discharge, respiratory distress, bloody mucus, swollen orbital sinuses, high morbidity, considerable mortality and decreased egg production. It is well established in highly dense poultry producing areas of the world due to characteristic latency and carrier status of the virus. Co-infections with other respiratory pathogens and environmental factors adversely affect the respiratory system and prolong the course of the disease. Latently infected chickens are the primary source of ILT virus (ILTV) outbreaks irrespective of vaccination. Apart from conventional diagnostic methods including isolation and identification of ILTV, serological detection, advanced biotechnological tools such as PCR, quantitative real-time PCR, next generation sequencing, and others are being used in accurate diagnosis and epidemiological studies of ILTV. Vaccination is followed with the use of conventional vaccines including modified live attenuated ILTV vaccines, and advanced recombinant vector vaccines expressing different ILTV glycoproteins, but still these candidates frequently fail to reduce challenge virus shedding. Some herbal components have proved to be beneficial in reducing the severity of the clinical disease. The present review discusses ILT with respect to its current status, virus characteristics, epidemiology, transmission, pathobiology, and advances in diagnosis, vaccination and control strategies to counter this important disease of poultry.