Search Results (343)

Porcine epidemic diarrhea virus (PEDV) is a major pathogen responsible for viral diarrhea in pigs, causing particularly high mortality in neonatal piglets. In recent years, genetic variations in PEDV have resulted in alterations in both its virulence and antigenicity, leading to a reduced efficacy of existing vaccines. In this study, diarrheal samples were collected from four commercial pig farms in the Hubei, Guangxi, and Jiangxi provinces, China, which experienced vaccine failure. RT-qPCR confirmed PEDV infection, and three PEDV strains, 2021-HBMC, 2024-JXYX, and 2024-JXNC, were successfully isolated. Sequence analysis and phylogenetic tree construction classified these strains into the G2c genotype, the predominant subtype in China. The neutralization assays revealed a significant reduction in the neutralizing titers of these strains against the immune serum compared with the AJ1102 reference strain. Further amino acid sequence analysis of the spike (S) protein identified several mutations in key neutralizing epitopes compared with the AJ1102 strain, including S27L, E57A, N139D, M214T, and P229L in the S-NTD epitope; A520S, F539L, K566N, D569E, G612V, P634S, E636V/K in the COE epitope; and Y1376H in the 2C10 epitope, along with several deletions at N-glycosylation sites (347NSSD and 510NITV). Additionally, whole-genome sequencing and recombination analysis indicated that the 2021-HBMC strain may have resulted from a recombination event. The findings of this study underscore the challenge posed by the continuous genetic evolution of PEDV to vaccine efficacy and provide valuable insights for future vaccine development and control strategies. Full article

Insects are among the most diverse and abundant organisms on Earth, and their population dynamics are strongly influenced by entomopathogenic fungi. This study examines the role of carbon and nitrogen metabolism in the virulence of the entomopathogenic fungus Metarhizium rileyi against the migratory locust, Locusta migratoria. The findings demonstrate that the capacity of M. rileyi to utilize different carbon and nitrogen sources is a key factor in its virulence. Specifically, two strains of M. rileyi (PPDB201006 and SZCY201010) exhibited distinct metabolic abilities, with PPDB201006 displaying superior growth and enzyme activities on various carbon and nitrogen sources compared to SZCY201010. These metabolic differences were associated with significant variations in virulence, as PPDB201006 induced higher mortality rates in L. migratoria than SZCY201010. Metabolomics analysis revealed that infection by M. rileyi led to substantial alterations in the hemolymph metabolites of L. migratoria, particularly in organic acids, amino acids, sugars, and lipids. These results emphasize the significance of carbon and nitrogen metabolism in the pathogenicity of entomopathogenic fungi and offer new perspectives for optimizing their application as biological control agents. This study not only improves our understanding of fungal virulence mechanisms but also contributes to the development of more effective and sustainable pest management strategies. Full article

Effective control of bacterial infections remains a significant challenge in aquaculture. The marine bacterium Piscirickettsia salmonis (P. salmonis), responsible for piscirickettsiosis, causes widespread infections in various salmon species, leading to substantial mortality and economic losses. Despite efforts to genetically characterize P. salmonis, critical gaps persist in understanding its virulence factors, antimicrobial resistance genes, and single-nucleotide polymorphisms (SNPs). This study addresses these gaps through a comparative analysis of the pan-genome and core genomes of 80 P. salmonis strains from different geographical regions and genogroups. P. salmonis had an open pan-genome consisting of 14,564 genes, with a core genome of 1257 conserved genes. Eleven virulence-related genes were identified in the pan-genome, categorized into five functional groups, providing new insights into the pathogenicity of P. salmonis. Unique SNPs were detected in four key genes (gyrA, dnaK, rpoB, and ftsZ), serving as robust molecular markers for distinguishing the LF and EM genogroups. Notably, AMR genes identified in four LF strains suggest evolutionary adaptations under selective pressure. Functional annotation of the core genomes using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases demonstrated conserved gene clusters linked to essential intracellular survival mechanisms and bacterial pathogenicity. These findings suggest a direct association between core genome features and variations in pathogenesis and host–pathogen interactions across genogroups. Phylogenetic reconstruction further highlighted the influence of AMR genes on strain divergence. Collectively, this study enhances the genomic understanding of P. salmonis and lays the groundwork for improved diagnostic tools and targeted therapeutics to manage piscirickettsiosis in aquaculture. Full article

The avirulence (AVR) genes of the filamentous ascomycete fungus Magnaporthe oryzae (M. oryzae) are known to mutate rapidly under a higher selection pressure, allowing the pathogen to evade recognition by rice resistance (R) genes. Understanding the geographic distribution and natural variation of AVR genes is critical for the rational utilization and prolonging of the effectiveness of R genes. In this study, a total of 1060 M. oryzae strains collected from 19 rice blast nurseries in 13 provinces across southern China were subjected to presence/absence variation (PAV), genetic variation, and virulence analyses of the AVR-Pita1 gene. PCR amplification results indicated that AVR-Pita1 was present in only 57.45% of the blast strains, with significant geographic variation in distribution frequency. Specifically, the highest frequency (100%) was observed in strains from Chengmai, Hainan, while the lowest (1.79%) was observed in strains from Baoshan, Yunnan. A sequencing analysis identified 29 haplotypes of AVR-Pita1, characterized by insertions, deletions, and base substitutions. A phylogenetic analysis indicated that haplotypes of AVR-Pita1 identified in this study were clustered into one clade. A further amino acid sequence analysis of these haplotypes led to the identification of 25 protein variants. Notably, four haplotypes of AVR-Pita1 exhibited pathogenicity toward its corresponding rice R gene, PtrA. Additionally, we performed allele profiling of Ptr in a collection of elite parental lines that are widely used in rice breeding in southern China and found that the functional Ptr alleles (PtrA, PtrB, and PtrC) accounted for over 70%. Full article

Background/Objectives: Porcine reproductive and respiratory syndrome virus (PRRSV) significantly impedes swine production due to rapid genetic variation and suppression of antiviral interferon (IFN) responses, leading to ineffective immunity. To address this, we developed IFNmix, a replication-competent PRRSV modified live vaccine (MLV) candidate co-expressing three Type I IFN subclasses (IFNα, IFNβ, IFNδ) to enhance antiviral immunity. Methods: In two independent in vivo experiments, we compared the protection of IFNmix and a commercial PRRSV MLV vaccine during challenge with a virulent PRRSV strain. Clinical signs, antibody and cytokine production, viral replication, and lung pathology in IFNmix-vaccinated pigs were compared to those of commercial PRRSV vaccines and controls. Results: Pigs vaccinated with IFNmix exhibited similar anti-PRRSV antibody development, serum viral loads, lung lesions, and cytokine responses post-challenge with the virulent NADC34 strain, with comparable or lower body temperatures and weight gain, to pigs vaccinated with the commercial vaccines. While IFNmix showed early viral load reduction compared to the commercial vaccine (Days 7–14 post-challenge), it demonstrated similar efficacy in controlling PRRSV replication and lung pathology. Conclusions: These findings suggest that IFNmix, by expressing multiple IFNs, can potentially enhance innate and adaptive immune responses, offering a promising approach to improving PRRSV vaccine efficacy. Further studies are needed to evaluate IFNmix against a broader range of PRRSV strains and to optimize its attenuation and immunogenicity. Full article

Salmonella Dublin (S. Dublin) and Salmonella Typhimurium (S. Typhimurium) are commonly linked to bovine salmonellosis. S. Dublin is, however, considered a bovine-adapted serovar for primarily infecting and thriving in cattle. Using S. Typhimurium (a generalist serovar) as a benchmark, this study investigates genomic factors contributing to S. Dublin’s adaptation to cattle hosts in the U.S. A total of 1337 S. Dublin and 787 S. Typhimurium whole-genome sequences from bovine sources were analyzed with CARD (version 4.0.0), ARG-NOTT (version 6), and AMRfinderPlus (version 4.0.3) for antimicrobial resistance (AMR) genes; VFDB and AMRfinderPlus for virulence genes; AMRFinderPlus for stress genes; and Plasmidfinder for plasmids. Existing clonal groups among isolates of the two serovars were also investigated using the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) model. The results revealed minimal genomic variation among S. Dublin isolates. Comparatively, the IncX1 plasmid was somewhat exclusively identified in S. Dublin isolates and each carried an average of four plasmids (p-value < 0.05). Furthermore, S. Dublin isolates exhibited a higher prevalence of AMR genes against key antimicrobials, including aminoglycosides, beta-lactams, tetracyclines, and sulfonamides, commonly used in U.S. cattle production. Additionally, Type VI secretion system genes tssJKLM and hcp2/tssD2, essential for colonization, were found exclusively in S. Dublin isolates with over 50% of these isolates possessing genes that confer resistance to heavy metal stressors, like mercury. These findings suggest that S. Dublin’s adaptation to bovine hosts in the U.S. is supported by a conserved genetic makeup enriched with AMR genes, virulence factors, and stress-related genes, enabling it to colonize and persist in the bovine gut. Full article

Pseudorabies virus (PRV) remains a critical threat for the global swine industry, with heightened attention due to the emergence of variant strains since late 2011 in China. Emergent viral variants generally undergo three to four years of adaptation to present new phenotypes. However, limited investigations have been performed on the evolution and pathogenicity of variant PRV strains in growing pigs after 2015. In this study, three PRV field strains, named SD1501, SD1701, and SD1801, were isolated and their genetic characteristics and pathogenicity on 9-week-old pigs were analyzed. Nucleotide identity and phylogenetic analyses based on the complete genome sequence, as well as major immunogenic and virulence-related genes revealed that all three isolates clustered closely with genotype II variant strains prevalent in China. The pathogenicity analysis demonstrated that the three isolates exhibited moderate pathogenicity in growing pigs with a TCID₅₀ of 10⁷. Infected pigs displayed transient fever and reduced appetite, with only one pig in each challenge group showing typical neurological symptoms and succumbing within 6 days post infection. These findings enrich the epidemiological data of PRV and provide direct evidence for the phenotypic variations caused by PRV infection, which enhances our understanding of PRV evolution in China and contributes to PRV control in the field. Full article

Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition, primarily affecting young individuals, with a significant impact on their quality of life due to recurrent, painful nodules, abscesses, and oozing sinus tracts, primarily affecting intertriginous areas. The pathogenesis of HS is multifactorial, involving a complex interplay between genetic predisposition, immune dysregulation, microbial, and environmental factors. While it is known that cutaneous and gut microbiome contribute to innate immune dysregulation in HS, their precise involvement in disease pathogenesis remains unclear. Despite several studies investigating the microbiome of HS lesions, either by culture-dependent or independent methods, there is no data available on the interplay between bacterial virulence profiles, clinical manifestations, and the host immune response. This study aimed to explore the phenotypic and genotypic resistance and virulence profiles of microorganisms isolated from HS lesions (including the expression of soluble virulence factors and the ability to develop biofilms), with a special focus on Staphylococcus aureus (S. aureus), one of the most frequent infectious agents of HS. A total of 92 bacterial strains, belonging to 20 different bacterial species, were isolated from the HS lesions of 23 patients. The strains of Staphylococcus, Corynebacterium, and Enterococcus expressed the highest levels of soluble virulence factors, such as hemolysins, lecithinase, and lipase, which are involved in bacterial persistence, local invasivity, and tissue damage. Moreover, a significant variation among bacterial species was noted regarding the capacity to develop biofilms, with a potential impact on disease chronicization, bacterial tolerance to antibiotics, and immune defense mechanisms. The genetic characterization of methicillin-resistant staphylococci revealed the presence of adhesins, hemolysin and enterotoxin genes as well as methicillin and macrolides resistance genes. Our findings highlight the critical role of virulence determinants, including bacterial biofilms, in HS pathogenesis, emphasizing the need for targeted therapeutic strategies to disrupt biofilms and mitigate infection severity. Full article

Alternaria species produce diverse secondary metabolites that act as critical virulence factors during plant pathogenesis. In cultivation areas of Chrysanthemum morifolium ‘Fubai’—a key cultivar for herbal tea—black spot disease caused by A. alternata manifests as necrotic leaf lesions progressing to wilting. Despite this disease’s economic impact, information on its associated toxins is limited, and the types of toxins produced by the black spot pathogen of Chrysanthemum morifolium ‘Fubai’ in particular remain unclear. Furthermore, whether toxins are present in the flowers when the leaves show symptoms is uncertain, but their inflorescence is not visibly infected. Using two previously characterized A. alternata strains (F16/F20) isolated from ‘Fubai’ in earlier studies, we demonstrated the concomitant production of altenuene (ALT) and tenuazonic acid (TeA) in both strains, with strain-specific yield variations (F20 TeA: 342.16 µg/mL vs. F16: 21.84 µg/mL; ALT: 0.28 µg/mL vs. 0.90 µg/mL). Time-course monitoring revealed coordinated accumulation of both toxins in inoculated petals, reaching 18.07 μg/g ALT and 2.59 µg/g TeA by day 9. Notably, these two toxins were detected only in flower samples from black spot-infected plants, and their concentrations correlated closely with disease severity in the leaves. Moreover, although the inflorescences did not display symptoms, both fresh and dried flowers retained detectable toxin levels. We established a technical system for the extraction and quantitative detection of the toxins ALT and TeA produced by the black spot pathogen in tea chrysanthemum. This work provides the first confirmation of ALT/TeA co-contamination in Chrysanthemum morifolium ‘Fubai’, revealing substantial dietary exposure risks through tea consumption. Our findings suggest that, from a food safety risk reduction perspective, integrated management strategies should be developed to minimize toxin contamination in tea chrysanthemum, including improved disease prevention measures and potential regulatory considerations. Full article

The banana pseudostem weevil (BPW), Odoiporus longicollis (Oliver), is one of the most destructive pests of bananas that is seriously affecting the yield and quality of bananas. We isolated pathogens from banana pseudostem weevils in Xishuangbanna and Dongchuan, Yunnan, China, and explored their biological characteristics. The pathogenicity of the strains was verified through laboratory and greenhouse inoculation experiments. The results showed that four strains of fungi were identified and confirmed as Beauveria caledonica (Bc) via ITS-rDNA sequencing. Optimal in vitro culture conditions were found to be a photoperiod of 24 h light, 25 °C temperature, and 18 days on potato dextrose agar (PDA) medium with insect meal. Under these conditions, the Cs-1 strain achieved a colony diameter of 65.17 ± 0.74 mm and spore production of 1.24 × 10⁸ cfu/cm². The Cs-1 strain had the shortest lethal time (LT₅₀) of 9.36 days at an inoculum of 1.00 × 10⁹ cfu/mL, with a lethality of 86.67% after 20 days. The Cs-3 strain showed 77.78% lethality at 1.00 × 10⁸ cfu/mL after 20 days. Despite variations in virulence, lethality did not correlate with major cuticle-degrading enzymes. The Cs-3 strain demonstrated effective biocontrol in greenhouse tests. Banana plants suffered significant damage without Bc-treated BPW, while the treated plantlets thrived. The mortality rate reached 82.78% after 35 days. This study marks the first identification of these entomopathogenic fungi (EPF) in Yunnan, China, highlighting B. caledonica’s potential for biocontrol application. Full article

SARS-CoV-2 virus and its variants remain a global health threat, due to their capacity for rapid evolution. Variants throughout the COVID-19 pandemic exhibited variations in virulence, impacting vaccine protection and disease severity. Investigating nonstructural protein variants is critical to understanding viral evolution and manipulation of host protein interactions. We focus on nonstructural protein 3 (nsp3), with multiple domains with different activities, including viral polyprotein cleavage, host deubiquitylation, de-ISGylation, and double-membrane vesicle formation. Using affinity purification–mass spectrometry (AP-MS), we identify differential protein interactions in nsp3 caused by mutations found in variants identified between 2019 and 2024: Alpha 20I, Beta 20H, Delta 21I, Delta 21J, Gamma 20J, Kappa 21B, Lambda 21G, Omicron 21K, and Omicron 21L. A small set of amino acid substitutions in the N-terminal region of nsp3 (nsp3.1) could be traced to increased interactions with RNA-binding proteins, which are vital in viral replication. Meanwhile, variants of the central region of nsp3 (nsp3.2) were found to share interactions with protein quality control machinery, including ER-associated degradation. In this construct, shared trends in interactor enrichment are observed between Omicron 21K and Delta 21I. These results underscore how minor mutations reshape host interactions, emphasizing the evolutionary arms race between the host and virus. We provide a roadmap to track the interaction changes driven by SARS-CoV-2 variant evolution. Full article

Escherichia coli (E. coli) is a Gram-negative, commensal/pathogenic bacteria found in human intestines and the natural environment. Pathogenic E. coli is known as extra-intestinal pathogenic E. coli (ExPEC) or intestinal pathogenic E. coli (InPEC). InPEC E. coli strains are separated into six pathogenic groups, known as enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroinvasive (EIEC), enteroaggregative (EAEC), enterohaemorrhagic (EHEC), and diffusely adherent (DAEC), that have various virulence factors that cause infection. Virulence factors refer to a combination of distinctive accessory traits that affect a broad range of cellular processes in pathogens. There are two important virulence factors that directly interact with cells to cause diarrhoeal diseases within the intestines: adhesion and colonization factors and exotoxins. Virulence factors are crucial for bacteria to overcome the host’s immune system and result in antibiotic resistance. Antibiotics are used to combat the symptoms and duration of infection by pathogenic E. coli. However, the misuse and overuse of antibiotics have led to the global concern of antibiotic resistance. Currently, the antibiotic colistin is the last-resort drug to fight infection caused by this bacterium. Antibiotic resistance can be achieved in two main ways: horizontal gene transfer and mutation in different genes. The genetic basis for developing antibiotic resistance in E. coli occurs through four mechanisms: limiting drug uptake, modification of the drug target, inactivation of the drug, and active efflux of the drug. These mechanisms use different processes to remove the antibiotic from the bacterial cell or prevent the antibiotic from entering the bacterial cell or binding to targets. This prevents drugs from working effectively, and bacteria can acquire antibiotic resistance. E. coli is classified into different phylogenetic groups (A, B1, B2, D1, D2, E, and clade I). It is a very versatile bacterium that can easily adapt to different environmental factors. The present review gathered information about the pathogenicity, antimicrobial resistance, and phylogenetics of E. coli. These aspects are interconnected; thus, it will provide information on tracking the spread of pathogenic strains and antibiotic resistance genes of different strains using phylogenetics and how antibiotic resistance genes evolve. Understanding genetic variation in E. coli will help in monitoring and controlling outbreaks and in developing novel antibiotics and treatment. The increasing rate of antibiotic resistance, and the ability of E. coli to evolve rapidly, suggest that in-depth research is needed in these areas. Full article

The porcine reproductive and respiratory syndrome virus (PRRSV) possesses an inherent ability to adapt to environmental transformations and undergo evolutionary changes, which has imposed significant economic pressure on the global pig industry. Given the potential for recombination among PRRSV genomes and variations in pathogenicity, newly emerging PRRSV isolates are of considerable clinical importance. In this study, we successfully isolated a novel strain named XJ-Z5 from PRRSV-positive samples collected in Xinjiang province in 2022. Through comprehensive genomic sequencing, phylogenetic analysis, and recombination analysis, we confirmed that this strain belongs to the NADC30-like recombinant PRRSV. During pathogenicity tests in piglets, this strain exhibited moderate virulence, causing symptoms such as reduced appetite, persistent fever, and weight loss; however, no mortality cases were observed. Tests conducted at various time points detected the presence of PRRSV nucleic acid in nasal swabs, rectal swabs, tissue samples, and blood, with the highest viral loads found in lung tissue and blood. Serum biochemical tests indicated significant impairment of liver and kidney function. PRRSV antibodies began to appear gradually after 10 days post infection. Hematoxylin and eosin staining revealed substantial pathological changes in lung tissue and lymph nodes. This study enhances our understanding of the epidemiology of PRRSV and underscores the importance of ongoing monitoring and research in light of the challenges posed by the continuous evolution of viral strains. Furthermore, the research emphasizes the urgency of the rapid genomic analysis of emerging viral strains. Through these comprehensive research and monitoring strategies, we aimed to curb the spread of PRRSV more effectively and thus reduce the huge economic losses it caused to the pig industry. Full article

Background/Objectives: Feline coronavirus (FCoV) belongs to the family Coronaviridae and includes two pathotypes, the less virulent feline enteric coronavirus (FECV), which replicates in the enteric epithelial cells, and feline infectious peritonitis virus (FIPV), which is more virulent, replicates efficiently within monocytes/macrophages with systemic involvement and may cause feline infectious peritonitis (FIP), a progressive and often fatal disease. The diagnosis of FIP is complex and requires different examinations. Among serological tests, the indirect immunofluorescent antibody test (IFAT), considered the gold standard, and the enzyme-linked immunosorbent assay (ELISA) are the most widely used to detect FCoV antibodies. The aim of this work was the development of FCoVCHECK Ab ELISA, a new rapid indirect test for the detection of FCoV antibodies in feline serum/plasma samples. Methods: FCoVCHECK Ab ELISA was developed after a meticulous set-up and cut-off analysis through several methods, including the Youden’s index and ROC curve, to achieve the best test performance. It was validated by testing 110 feline sera (62 positives and 48 negatives) against the reference IFAT and compared with two other rapid ELISA tests, INgezim Corona Felino (Gold Standard Diagnostics) and ImmunoComb Feline Coronavirus (FCoV) [FIP] Antibody Test Kit (Biogal). Conclusions: FCoVCHECK Ab ELISA agreed with IFAT at 96.4% (93.5% sensitivity, 95% confidence interval (CI): 83.5–97.9%; 100% specificity, 95% CI: 90.8–100%), with ImmunoComb FCoV at 93.6% and with INgezim Corona Felino at 82.7%. Intra- and inter-assay accuracy and precision gave coefficients of variation lower than 20%. Compared to IFAT, the new assay correctly identifies positive and negative samples with a good correlation, and, in addition, it is simpler, faster and provides a less subjective reading of the results. Full article

Fluorescent protein-tagged bacterial strains are widely used tools for studying host-pathogen interactions and microbial dynamics. In this study, we developed and characterized Vibrio harveyi strains genetically modified to express green fluorescent protein (GFP) and red fluorescent protein (RFP). These strains were constructed using triparental mating and evaluated for phenotypic, genomic, and virulence attributes. Genomic analyses revealed strain-specific variations, including mutations in key regulatory and metabolic genes, such as luxO and transketolase. While plasmid acquisition imposed metabolic costs, resulting in altered growth and antibiotic sensitivities in certain transconjugants, others demonstrated robust phenotypic stability. Virulence assays using gilthead seabream larvae revealed that most tagged strains retained moderate pathogenicity, with visualization of co-infections highlighting the potential for studying strain-specific interactions. Furthermore, fluorescent microscopy confirmed the successful colonization and localization of tagged bacteria within host tissues. These findings underscore the utility of GFP- and RFP-tagged Vibrio harveyi as versatile tools for infection dynamics, offering a foundation for future research on strain interactions and pathogen-host relationships. Full article