Search Results (128)

Syndromic multiplex-PCR panels deliver rapid, comprehensive detection of pathogens and resistance determinants in acute infections, but their unrestricted use can generate a high proportion of negative results with substantial economic and stewardship implications. We retrospectively analysed all BioFire FilmArray meningitis/encephalitis (ME), upper-respiratory (RP2.1), pneumonia (PN) and gastrointestinal (GI) determinations performed at the UOSD Microbiology and Virology of P.O. “Vito Fazzi”, ASL Lecce (Apulia, Italy) between 1 July 2024 and 30 April 2026. Repeat determinations from the same patient with the same panel were identified in the laboratory information system and removed before any analysis, so that each determination analysed corresponds to a distinct diagnostic episode. Across 5381 determinations (CNS, n = 761; upper respiratory, n = 2601; lower respiratory, n = 399; gastrointestinal, n = 1620), 59.3% were negative for every target, with a steep appropriateness gradient: 90.0% negativity for the ME panel and 77.1% for the gastrointestinal panel versus 44.2% for the upper-respiratory and 26.6% for the pneumonia panel. CNS positives were predominantly viral (75%), led by enterovirus; Streptococcus pneumoniae was the only consistent bacterial agent. Human rhinovirus/enterovirus dominated the respiratory ecology; influenza A was almost entirely H3 and H1N1pdm09, but 8.1% of influenza-A–positive specimens were equivocal or non-subtypeable and were never referred for sequencing, an avoidable surveillance blind spot for novel/zoonotic (avian) influenza. Pneumonia-panel resistance markers (mecA/C–MREJ, CTX-M, KPC, NDM) clustered in Enterobacterales co-infections. The gastrointestinal panel was dominated by diarrhoeagenic Escherichia coli pathotypes (chiefly EPEC and EAEC) and Clostridioides difficile toxin, its 77% negativity identifying a second over-utilised stream. We argue for CSF-pleocytosis gating, tiered/reflex respiratory algorithms, gastrointestinal-panel gating to community-onset diarrhoea, and mandatory reflex sequencing of unsubtypeable influenza A. Full article

To address the lack of a commercially available vaccine for goose circovirus (GoCV), we developed and evaluated a prokaryotically expressed subunit vaccine targeting the viral capsid (Cap) protein. A truncated Cap protein (GoCV-ΔCap) was expressed in Escherichia coli (E. coli) and formulated with aluminum hydroxide as a subunit vaccine (GoCVsubvac). Goslings were primed intramuscularly (i.m.) with high (75 µg) or low (15 µg) doses GoCVsubvac, followed by a boost 14 days later. At 14 days post-boost, goslings were challenged with GoCV and were administered a bivalent inactivated vaccine against Newcastle disease virus (NDV) and H9-subtype Avian influenza virus (AIV). Using our established gosling pathogenicity model, vaccine efficacy was evaluated via body weight, lesions, viral load, antibody titers, cytokine responses, and interference with NDV/AIV immunity. Results demonstrated that the GoCV-ΔCap vaccine, especially the high-dose formulation, provided effective immunoprotection. It elicited robust humoral and cellular immune responses, reduced lymphoid pathology, and decreased the viral detection rate in lymphoid tissues from 100% (5/5) in infected controls to 40% (2/5). Importantly, it alleviated GoCV-induced immunosuppression and preserved the immunogenicity of co-administered vaccines. This novel subunit vaccine is a promising candidate for controlling GoCV disease (GoCVD). Full article

Background/Objectives: Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are priority antimicrobial-resistant pathogens with significant implications for food safety and public health. Food-producing animals and their derived products represent a key interface for zoonotic transmission, yet prevalence data across Nigeria remain fragmented and unsynthesized. This systematic review and meta-analysis assessed the prevalence, species distribution, geographical patterns, and detection methods of ESBL-producing E. coli in food-producing animals and animal-derived food products across Nigeria. Methods: A comprehensive search of PubMed, Web of Science, Scopus, and African journals online was conducted for studies published between January 2000 and January 2026, following PRISMA 2020 guidelines. Twenty eligible studies collectively analyzed 5104 samples, and 984 ESBL-positive isolates were included in the meta-analysis. Results: The overall pooled prevalence of ESBL-producing E. coli was 17.0% (95% CI: 13.0–21.0%; I² = 89.4%). Subgroup analysis by animal species revealed the highest pooled prevalence among caprine (32.0%, 95% CI: 17.0–52.0%), bovine (24.0%, 95% CI: 17.0–33.0%), porcine (17.0%, 95% CI: 7.0–36.0%) and avian species (13.0%, 95% CI: 9.0–19.0%). Animal-derived food products showed a pooled prevalence of 19.0% (95% CI: 17.0–21.0%). Regional analysis showed the highest pooled prevalence in South-West (19.0%, 95% CI: 13.0–27.0%) and South-South (19.0%, 95% CI: 9.0–34.0%). Studies using combined culture and molecular methods reported higher pooled prevalence (19.0%, 95% CI: 14.0–25.0%) than culture alone (12.0%, 95% CI: 8.0–18.0%). However, the difference between subgroups was not statistically significant (test for subgroup differences: p = 0.0563). Conclusions: These findings confirm extensive ESBL-producing E. coli circulation in Nigerian food-producing animals and highlight critical gaps in antimicrobial stewardship, veterinary surveillance, and food safety infrastructure, underscoring the urgent need for coordinated One Health strategies to contain the spread of resistant strains through the food chain. Full article

To characterize the ecological and genomic architecture of temperate bacteriophages in Escherichia coli isolated from Brazilian broiler chickens, we analyzed 63 femur-derived genomes, most fulfilling molecular avian pathogenic E. coli (APEC) criteria, and tested whether temperate phage regions are enriched for antimicrobial resistance genes (ARGs), virulence factors, plasmid markers, and other mobilome components. Diversity was summarized using incidence-based richness estimators and bootstrap confidence intervals, and positional enrichment was assessed using permutation-based statistical analysis. We detected 1164 phage-like elements, including 188 medium- and high-quality phages, of which 93.6% were temperate. Median temperate diversity per genome was three phage genera and three temperate regions. At the population level, 19 temperate genera were observed, with a Chao2 estimate of 21.2, indicating near-saturated genus-level diversity. Positional mobilome analysis showed significant enrichment of insertion sequences within temperate regions (p < 0.05), while ARGs, virulence factors, and plasmid markers were not significantly enriched inside temperate phage coordinates (p > 0.05). The surrounding genomic neighborhood (±20 kb) accumulated mobile elements but showed no significant enrichment. CRISPR spacer matches further supported ongoing host–phage interactions. Overall, temperate phages are widespread and ecologically structured in Brazilian broiler-associated E. coli, but they are not preferential hotspots for ARG, virulence, or plasmid gene enrichment; instead, they are chiefly associated with insertion-sequence enrichment. Full article

The increasing prevalence of multidrug-resistant (MDR) pathogens, particularly avian pathogenic Escherichia coli (APEC) and methicillin-resistant Staphylococcus aureus (MRSA), poses a severe threat to the breeding industry and human health. To develop novel antibiotic alternatives, we adopted a “converting virulence into therapy” strategy by leveraging the type VI secretion system (T6SS) of the APEC strain ACN17-20. Guided by the structural analysis of T6SS Protein 00145, we rationally designed a series of amphipathic α-helical polypeptides. Among them, polypeptide A7 emerged as a lead candidate, exhibiting potent broad-spectrum antibacterial activity with negligible cytotoxicity against mammalian cells. Mechanistic studies revealed that A7 exerts a rapid bactericidal effect through a dual mode of action: physical disruption of bacterial membrane integrity leading to cytoplasmic leakage, and induction of lethal oxidative stress via reactive oxygen species (ROS) accumulation. Furthermore, A7 demonstrated excellent efficacy in eradicating pre-formed bacterial biofilms, addressing the challenge of persistent infections in breeding environments. In a mouse sepsis model induced by APEC and MRSA, A7 treatment significantly improved survival rates (60–80%), reduced bacterial loads in vital organs, and attenuated the systemic cytokine storm (TNF-α and IL-1β), thereby alleviating immune-mediated tissue damage. In conclusion, this study identifies polypeptide A7 as a safe therapeutic agent with a dual mechanism of action, providing a promising strategy to combat MDR infections and reduce antibiotic dependence. Full article

Background/Objectives: Spotty liver disease (SLD), caused by Campylobacter hepaticus, is an emerging disease that leads to substantial production losses in the egg industry. The shift toward antibiotic-free and cage-free production systems has further intensified the impact of SLD. The current control measures largely rely on autogenous killed vaccines; however, their use is constrained by the slow and fastidious growth of C. hepaticus and inconsistent efficacy. To overcome these limitations, this study aimed to identify immunogenic mimotopes as vaccine candidates and express them on the surface of an avian pathogenic Escherichia coli (APEC) vector. Methods: To identify immunogenic mimotopes, Ph.D.-12 phage display peptide library was screened using the hyperimmune serum raised against killed whole-cell C. hepaticus in specific pathogen-free chickens. Subsequently, the outer membrane protein C (OmpC) of E. coli was used as a scaffold for constructing a surface display library. A single restriction site, PstI, located in the seventh external loop of OmpC, was strategically utilized to insert each 12-amino-acid mimotope with a six-histidine (6xHis) tag sequence at its N-terminus, generating ompC + mimotope fusion constructs. These constructs were cloned into the inducible expression vector pTrc and electroporated into an E. coli DH5α ∆ompC strain, which lacked ompC. The surface expression of the mimotopes was confirmed in vitro. The verified ompC + mimotope constructs were subsequently subcloned into the pYA3422 constitutive expression vector and electroporated into the APEC PSUO78 ∆aroA ∆asd vaccine vector strain. A chicken vaccination–challenge trial was conducted using nine groups of chickens, including an unvaccinated challenged control and an unvaccinated–unchallenged negative control. Each experimental group received a mixture of two recombinant E. coli strains carrying different mimotopes at a dose of 1 × 10⁹ CFU, which were administered orally twice at 16 and 18 weeks of age. Results: Fourteen immunogenic mimotopes corresponding to 13 different C. hepaticus proteins were identified as potential vaccine candidates. The expression of these mimotopes on the surface of the E. coli was successfully demonstrated using the OmpC-mediated surface display system. Of the 14 mimotopes tested, two flagellar-related peptides and one major outer membrane protein (MOMP)-derived peptide elicited significant immune responses and conferred protection against the C. hepaticus challenge. Conclusions: We successfully developed a functional E. coli surface display system that was capable of expressing 12-amino-acid mimotopes of C. hepaticus, providing a robust platform for evaluating vaccine candidates against SLD. Immunogenicity and efficacy studies in chickens demonstrated that three identified mimotopes conferred protection against C. hepaticus colonization of the bile and liver. Future in vivo investigations are necessary to develop and evaluate the immunogenicity and protective efficacy of a multivalent mimotope vaccine consisting of three identified mimotopes against both C. hepaticus and APEC, utilizing the ΔaroA Δasd APEC PSU078 strain as the vaccine vector. Full article

Background: Avian pathogenic Escherichia coli (APEC) contributes substantially to colibacillosis outbreaks in chickens. Because APEC cells readily attach to surfaces and develop biofilms, they pose a notable hazard to poultry production and food safety. This study investigated the antibiofilm and anti-adhesion activities of deep eutectic solvent-based emulsion containing Piper betle L. extract (DEPE) and hydroxychavicol, a pure compound isolated from P. betle leaves against APEC. Methods: Antibiofilm and anti-adhesion activities of DEPE and hydroxychavicol against APEC were investigated. Molecular docking and dynamics simulation of DEPE and hydroxychavicol was conducted. In addition, anti-adhesion activity of DEPE on chicken meat during storage was evaluated. Results: DEPE and hydroxychavicol significantly inhibited biofilm formation at sub-MIC, with DEPE achieving up to 80% inhibition and hydroxychavicol up to 69%. At 8 × MIC, DEPE and hydroxychavicol diminished the viability of both early and established biofilms. Furthermore, DEPE and hydroxychavicol reduced APEC adhesion on the surface as observed by SEM. In silico analyses demonstrated the stable binding of hydroxychavicol to adhesion-related proteins, particularly EcpA and FimH, suggesting a possible mechanism for its anti-adhesion activity. At day 5, DEPE at 4 × MIC significantly reduced 63% bacterial adhesion to chicken meat surfaces during storage, while maintaining the meat’s color. Conclusions: These findings indicate that DEPE and hydroxychavicol are promising candidates for limiting APEC biofilm formation and surface attachment and may serve as alternative antibacterial agents in poultry-related food safety applications. Full article

Background: Avian pathogenic Escherichia coli (APEC) are significant bacterial pathogens that cause economic losses in the poultry industry and can pose a potential foodborne zoonotic risk. Herein, we examined APEC distribution and antimicrobial resistance in E. coli isolated from slaughtered broiler chickens in northern Thailand. Methods: PCR was used to classify APEC as either virulent or avirulent on 108 stored E. coli strains, as well as to perform Clermont phylotyping. Antimicrobial susceptibility to ciprofloxacin, cefotaxime, ceftazidime, imipenem, and colistin was examined. Results: Of the 108 E. coli strains, 101 (93.5%) isolates were APEC, and the remaining isolates were non-APEC. Among the APEC isolates, 58.4% were classified as virulent APEC; these isolates showed a statistically significant association with phylogroups F and C and (n = 54, 56.8%) more frequently exhibited a ciprofloxacin-resistant phenotype than avirulent APEC (n = 35, 36.8%). Among the ten APEC virulence genes, hlyF, iroC, iroN, iutA, O78, and ompT were significantly associated with virulent APEC. Conclusions: This study reveals a high prevalence of virulent APEC with fluoroquinolone resistance in slaughtered broiler chickens. Almost all virulent APEC strains belong to phylogroups F and C. The prediction of virulent APEC using hlyF, iroC, iroN, iutA, O78, and ompT may be useful. Full article

Nucleated erythroid cells (NECs) have emerged as active participants in immune responses in addition to their canonical oxygen transport function. The subpopulations and immune heterogeneity of chick erythroid cells (ch-ECs) upon infection have not been fully characterized. Single-cell RNA sequencing (scRNA-seq) was used to profile ch-ECs in chicks infected with avian pathogenic Escherichia coli (APEC). Unsupervised clustering uncovered ten distinct ch-EC subpopulations (C1–C10), with significant compositional shifts between infected and control groups. Pseudotime analysis revealed a developmental continuum: C1, C3, C5, and C9 as early progenitors; C2, C4, C6, C7, and C10 as mature erythroid cells; and C8 as a naive population. We revealed 62 immune-related genes, including protein kinases and heat shock proteins, and subpopulation-specific differentially expressed genes (DEGs) linked to immune functions. SCENIC analysis revealed Fos, Srf, and Stat3 as key transcription factors with elevated regulon activity and specificity following infection. Subpopulations C2, C4, C6, and C7, which exhibited marked abundance changes, were scrutinized for immune relevance through integrated multi-omics analysis. Immune-related genes including FOS, AKAP9, HS6ST1, GAB3, TFRC, HSPA8, HSP90AA1, and DNAJB6 were identified. Enrichment analysis indicated activation of the MHC class I antigen presentation pathway, while pathways such as Mitogen-Activated Protein Kinase (MAPK) signaling, NOD-like receptor (NLR) signaling, and the heat shock response were found to be suppressed. In conclusion, this study delineates the immune gene repertoire and signaling networks of ch-ECs during APEC infection, offering new perspectives on NEC immunoregulatory functions. Full article

Chicken respiratory diseases represent multifactorial conditions resulting from viral, bacterial, mycoplasmal pathogens, and environmental factors, causing significant economic losses within the poultry industry. A specific respiratory disease characterized by breathing difficulties and bronchial occlusion due to caseous exudates is termed chicken bronchial obstruction. However, the absence of rapid, precise, and highly sensitive diagnostic methods for differentiation of primary respiratory disease pathogens or opportunistic pathogens, including avian influenza virus (AIV), infectious bronchitis virus (IBV), Pseudomonas aeruginosa (P. aeruginosa), and Escherichia coli (E. coli), constitutes a substantial challenge. This study developed a quadruplex droplet digital polymerase chain reaction (ddPCR) method that targeted the HA gene of H9 subtype AIV, the M gene of IBV, the Pal gene of P. aeruginosa, and the UidA gene of E. coli. Following the optimization of annealing temperature, sensitivity, and repeatability, the minimum detectable concentrations were determined as 3.02 copies/μL for the HA gene of H9 subtype AIV, 3.08 copies/μL for the M gene of IBV, 3.19 copies/μL for the Pal gene of P. aeruginosa, 3.39 copies/μL for the UidA gene of E. coli. No cross-reactivity was observed with Newcastle disease virus (NDV), H5 subtype AIV, H7 subtype AIV, fowl adenovirus serotype 4 (FAdV-4), infectious laryngotracheitis virus (ILTV), Avibacterium paragallinarum, Streptococcus, Salmonella, Pasteurella multocida, and Staphylococcus aureus. The method demonstrated excellent repeatability, with a coefficient of variation (CV) below 9%. The 185 clinical samples collected in Hebei Province China are tested by both quadruplex ddPCR and quadruplex qPCR method and the results compared. The sensitivity of the quadruplex ddPCR method (57.30%; 106/185) slightly exceeded that of the quadruplex qPCR method (49.73%; 92/185). Pathogens or opportunistic pathogens positive rates obtained via the quadruplex ddPCR were 40.00% for H9 subtype AIV, 33.51% for IBV, 24.32% for P. aeruginosa, and 27.57% for E. coli. In comparison, the positive rates of H9 subtypes AIV, IBV, P. aeruginosa, and E. coli from the quadruplex qPCR were 36.22%, 30.81%, 21.62%, and 24.32%, respectively. The coincidence rates between the two methods were 96.22% for H9 AIV, 97.30% for IBV, 97.30% for P. aeruginosa, and 96.76% for E. coli. These results demonstrated that the quadruplex ddPCR method represented a highly sensitive, specific, and rapid technique for identifying H9 subtype AIV, IBV, P. aeruginosa, and E. coli. Full article

Avian pathogenic Escherichia coli (E. coli) impairs poultry production and causes substantial economic losses. This study investigated the effects of Lactobacillus reuteri postbiotics (LR) on growth performance and intestinal health of broiler chickens challenged with E. coli. A total of 180 one-day-old Arbor Acres+ broilers were allocated into three groups (six replicates per group and 10 chicks each replicate): CTR, control group; E. coli-infected group, orally challenged with a mixture of E. coli O₁, O₂, and O₇₈ at a dose of 10⁹ CFU/mL; LR + E. coli-infected group, challenged with E. coli and fed a basal diet supplemented with 100 mg/kg LR. The results showed that dietary LR significantly improved the average daily gain (ADG) in the LR + E. coli group compared to the E. coli-infected group from days 1 to 18 (p < 0.05). However, no significant differences in average daily feed intake (ADFI) or feed conversion ratio (FCR) were observed among the CTR, E. coli, and LR + E. coli groups. Infection with E. coli led to lower total antioxidant capacity in jejunum and activity of total superoxide dismutase in ileum. Moreover, dietary LR significantly alleviated the down-regulation of Mucin2 and Aquaporin-3 gene expression in jejunum and ileum caused by E. coli infection and up-regulated the gene expression of Claudin-1 and Zonula occludens 1 in the ileum. In addition, dietary LR treatment led to the up-regulation of interleukin-10 mRNA transcripts in the jejunum. Further analysis demonstrated that dietary supplementation with LR reshaped the ileal flora of birds challenged with E. coli via elevating the relative abundance of Romboutsia and Bacteroidota, while reducing the abundance of Candidatus_Arthromitus and Escherichia-Shigella. In conclusion, dietary LR supplementation improved the expression of intestinal barrier and anti-inflammatory genes and reshaped the intestinal flora in E. coli-infected broilers. Full article

Avian colibacillosis is a significant disease in poultry caused by avian pathogenic Escherichia coli (APEC). APEC affects birds of all ages and leads to severe lesions in multiple organ systems, including the respiratory, digestive, and reproductive tracts. The disease imposes a substantial economic burden on poultry production due to increased mortality and decreased meat and egg production associated with the disease. Moreover, there is growing concern about the potential transmission of APEC to humans via contaminated poultry products, where it may cause extraintestinal infections. Given these implications for both animal welfare and public health, a thorough understanding of the pathogen is essential for developing effective control strategies. This review seeks to discuss the major facets of colibacillosis and outlines key considerations for advancing its diagnosis and effective management. Full article

Avian pathogenic Escherichia coli (APEC) infections cause substantial economic losses in the poultry industry, primarily due to high mortality rates, reduced productivity, and increased treatment costs. With the emergence of antibiotic-resistant APEC strains, including multidrug-resistant (MDR) variants, alternative therapeutic strategies have gained increasing attention. This study reports the isolation and characterization of an Escherichia phage, vB_EcoG_APECPW12 (phage vAPECPW12), which specifically targets MDR APEC. Both antibacterial and antibiofilm activities of the phage were evaluated. Phage vAPECPW12 produced small plaques with halos and exhibited strong lytic activity against MDR APEC. Whole-genome sequencing revealed a genome size of 77,812 base pairs with 123 open reading frames. No tRNA, antibiotic-resistant, or lysogenic genes were identified. Phylogenetic analysis and genome comparison suggest that phage vAPECPW12 is a novel member of the genus Kuravirus within the Gordonclarkvirinae family. It also demonstrated good stability across a range of temperatures and pH levels and remained viable after exposure to UV radiation. Phage vAPECPW12 showed a high adsorption rate, a short latent period of 10 min, and a burst size of 258 plaque-forming units per cell. A depolymerase domain was identified in the genome, prompting investigation of its antibiofilm efficacy. Results showed that vAPECPW12 significantly inhibited biofilm formation and removed preformed biofilms, indicating its potential as an alternative antimicrobial agent for controlling MDR APEC and their biofilms in poultry farming. Full article

The diseases caused by genotype VII Newcastle disease virus (NDV), H9N2 avian influenza virus (AIV), and fowl adenovirus serotype 4 (FAdV-4) continue to threaten the global poultry industry. However, no broad-spectrum vaccines provide simultaneous protection against these three pathogens. This study employed bioinformatics and immunoinformatics approaches to design a multi-epitope vaccine, named NFAF, which consists of B-cell, cytotoxic T lymphocyte (CTL) epitopes, and helper T lymphocyte (HTL) epitopes derived from hemagglutinin-neuraminidase (HN) and fusion (F) proteins of genotype VII NDV, hemagglutinin (HA) protein of H9N2, and Fiber2 protein of FAdV-4. The vaccine candidate was predicted to have non-allergenic properties, non-toxicity, high antigenicity, and favorable solubility. Each of its constituent antigenic epitopes has a high degree of conservation. Molecular docking demonstrated stable binding between NFAF and chicken Toll-like receptor (TLRs) and major histocompatibility complex (MHC) molecules. NFAF was expressed in soluble form in Escherichia coli and purified. Polyclonal antibodies against all three target viruses showed specific binding to NFAF. In vitro experiments revealed that NFAF effectively stimulated chicken peripheral blood mononuclear cells (PBMCs) and induced Th1, Th2, and pro-inflammatory cytokine production, confirming its immunogenicity, and increased the mRNA expression of the key signaling molecules MyD88 and NF-κB. These results suggested that NFAF could therefore be an efficacious multi-epitope vaccine against genotype VII NDV, H9N2, and FAdV-4 infections. Full article

As a core strategy for antibiotic replacement, probiotics have two advantages insofar as they enhance both animal productivity and pathogen suppression. In this study, we screened the intestines of antibiotic-naïve chickens for broad-spectrum antimicrobial lactic acid bacteria (LAB) with natural adaptability, based on the host–microbiota coevolution theory, and systematically evaluated their potential for development as poultry probiotics. We isolated a LAB strain, Lactiplantibacillus plantarum Y300, from traditional native free-range chickens, which showed strong inhibitory activity against avian pathogenic Salmonella, Escherichia coli, and Staphylococcus aureus. In vitro experiments indicated that the Lpb. plantarum strain Y300 had no hemolytic activity; excellent acid-producing ability;an outstanding tolerance to bile salts, low-pH environments, and simulated gastrointestinal fluids; a positive hydrophobic interaction with xylene, and good auto-aggregation characteristics. It also displayed a relatively high antioxidant capacity. Whole-genome sequencing revealed that the genome of Lpb. plantarum Y300 was approximately 3.05 mb, with a GC content of 44.74%. The main carbohydrate-active enzyme and bacteriocin genes were predicted in the Y300 genome, and no virulence genes or drug-resistance genes were detected. In summary, this study suggests that Lpb. plantarum Y300 has potential utility as a probiotic, and lays the theoretical foundation for the further development of microecological preparations of avian-sourced LAB. Full article