Search Results (2,119)

Environmental stressors such as poor water quality, overstocking, and temperature spikes force shrimp to divert energy from growth and immunity to maintain homeostasis, increasing their susceptibility to opportunistic pathogens. Despite this risk, information on how these conditions affect viral and bacterial abundance, diversity, and community structure in shrimp farms remains scarce. To address this gap, this study offers a broad metagenomic analysis of the viral and bacterial communities in a shrimp farm, uncovering their diversity and ecological significance. In total, 13,572 viral operational taxonomic units (vOTUs) were recovered. Most viruses belonged to the realm Duplodnaviria, with Caudoviricetes dominating the libraries. Additionally, some contigs were linked to the Iridoviridae, a family that can affect fish and shrimp. Taken together, these findings highlight the critical role of virus–host interactions in marine environments and underscore the utility of metagenomic analysis for monitoring and safeguarding aquaculture health. Full article

Bacterial disease caused by Aeromonas hydrophila is a major constraint in intensive sturgeon aquaculture. This study examined the intestinal, humoral, and hepatic responses associated with dietary or waterborne pretreatment with the host-derived probiotic Bacillus subtilis Ya3.1 during A. hydrophila infection in hybrid sturgeon (Acipenser schrenckii ♂ × Huso dauricus ♀). Absolute taxon-targeted qPCR, serum innate immune assays, intestinal 16S rRNA gene sequencing, and untargeted liver metabolomics were integrated to evaluate probiotic-associated protective responses. Ya3.1 pretreatment increased intestinal B. subtilis-associated gene copy numbers before challenge and reduced the post-challenge A. hydrophila-associated burden. Among surviving fish at 10 days post-infection, both probiotic-pretreated groups showed significantly higher alkaline phosphatase activity than the infected control group; the dietary pretreatment group also exhibited a significantly higher complement C3 concentration. Microbiota analysis revealed marked community restructuring in untreated challenged fish, characterized by enrichment of Aeromonas and other opportunistic taxa, whereas probiotic-pretreated fish showed reduced challenge-associated compositional displacement and relative enrichment of Bacillus-related taxa. Liver metabolomics further indicated that Ya3.1 pretreatment was associated with altered hepatic metabolic profiles, with glycerophospholipid metabolism emerging as a recurrent candidate pathway. Overall, Ya3.1-associated protection was associated with a lower pathogen burden, reduced microbiota displacement, partial preservation of humoral immune indices, and altered hepatic metabolic responses. Full article

Monitoring immunosuppression in kidney transplant recipients remains challenging, as conventional therapeutic drug monitoring (TDM) reflects pharmacokinetic exposure rather than the overall functional immune state. Torque teno virus (TTV), a non-pathogenic virus, has emerged as a potential complementary biomarker of the net state of immunosuppression. This review evaluates the current evidence regarding the utility of TTV load in this context, focusing on its correlation with standard pharmacokinetic markers, the analytical performance of quantitative PCR assays, its role as an integrated marker of immunosuppression, and its predictive value for clinical outcomes. Available data indicate that TTV load shows weak and inconsistent correlations with individual drug levels, such as tacrolimus trough concentrations, supporting its role as a complementary rather than substitutive tool. qPCR-based assays demonstrate generally good sensitivity and reproducibility, although inter-assay variability and lack of standardization remain important limitations. Clinically, higher TTV levels have been associated with an increased risk of opportunistic infections, whereas lower levels have been linked to acute rejection, suggesting a potential association between TTV viremia and immune status. TTV monitoring may represent a promising complementary approach for a more individualized assessment of immunosuppression. However, further prospective and interventional studies are required to validate standardized thresholds and determine whether TTV-guided strategies improve transplant outcomes compared with conventional monitoring. Full article

Cytomegalovirus (CMV) is a major determinant of post-transplant morbidity in solid organ transplant recipients, not only through direct viral disease but also through a broad spectrum of indirect effects that may adversely influence graft and patient outcomes. This review summarizes current clinical and mechanistic evidence regarding the mechanisms of CMV-associated indirect injury in transplantation, drawing on human observational studies together with supporting in vitro and animal-model data. CMV establishes lifelong latency with intermittent reactivation and exerts sustained immunomodulatory effects on both innate and adaptive immunity, which may persist even during low-level viral replication. The mechanisms discussed include monocyte reprogramming, altered antigen presentation, T-cell and natural killer cell dysregulation, endothelial activation and dysfunction, chronic inflammatory signaling, impaired antimicrobial defense, and disturbances in metabolic regulation. The review considers how these mechanisms have been proposed to translate into major post-transplant complications, including acute rejection, chronic allograft dysfunction, cardiovascular and thrombotic disease, post-transplant diabetes, and increased susceptibility to secondary bacterial, fungal, and viral infections. It also addresses current preventive strategies, although evidence regarding their effectiveness in reducing indirect clinical outcomes remains limited and largely observational. Much of the supporting evidence is associative, and the contribution of CMV is often difficult to separate from that of the overall immunosuppressive burden and the comorbidities of transplant recipients. With these considerations, the available evidence supports regarding CMV not merely as an opportunistic pathogen, but as a persistent immunobiological driver of long-term transplant injury. Improved understanding of these indirect effects may enhance risk stratification, support biomarker-guided prevention, and inform future strategies aimed at reducing long-term graft dysfunction and patient morbidity after transplantation. Full article

Background/Objectives: Opportunistic infections remain clinically important after kidney transplantation and may contribute to morbidity and graft dysfunction in pediatric recipients. Data regarding their timing, spectrum and clinical course in children remain limited. Methods: We retrospectively reviewed pediatric kidney transplant recipients followed at a single tertiary center between 2014 and 2024. Demographic and clinical characteristics, infection type, timing after transplantation, management and outcomes were recorded. Infection incidence was assessed at the patient level, whereas pathogen distribution and timing were analyzed per infection episode. Results: Twenty-seven pediatric kidney transplant recipients were included, with a mean follow-up of 5.6 years. Ten patients (37.0%) developed at least one clinically significant opportunistic infection, and one patient experienced two distinct episodes, resulting in 11 infection events. BK virus was the most frequent pathogen, followed by fungal infections and cytomegalovirus (CMV). Five episodes (45.5%) occurred within the first post-transplant year, whereas six (54.5%) occurred later during follow-up. Late infections included CMV, fungal infections, BK virus and West Nile virus. Most infections resolved after targeted management without persistent graft impairment; however, one patient developed biopsy-confirmed BK virus-associated nephropathy with sustained graft dysfunction. No infection-related mortality was observed. Conclusions: Clinically significant opportunistic infections occurred both early and late after pediatric kidney transplantation, with more than half of all infectious episodes developing beyond the first post-transplant year. Although overall outcomes were favorable, BK virus-associated nephropathy remained clinically relevant because of its impact on graft function. Full article

Pseudomonas aeruginosa (P. aeruginosa) is a multidrug-resistant opportunistic pathogen that causes both acute and chronic infections and is known for its ability to form biofilms. In the current study, we applied a hypothesis-generating framework primarily based on integrating four different datasets and applying batch correction. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed in parallel with differential expression analysis using limma. Therefore, we aimed to identify potential biofilm-associated gene candidates. Significant candidate genes were subjected to functional analysis and gene ontology, followed by the construction of a protein–protein interaction network using STRING. The Pseudomonas Genome Database was used to highlight the candidate genes. A total of 271, 687, 533, and 277 significantly up-regulated differentially expressed genes (DEGs), as well as 306, 985, 472, and 312 significantly down-regulated DEGs, resulted from the exploratory analysis. Through WGCNA/limma integration, 223 common significantly up-regulated/positively correlated gene candidates were identified. Functional analysis results showed significant enrichment in virulence-related pathways, such as biofilm formation (PA0083, PA0084, hcp1, hcpC, pilH, pilI, pilJ, vfr, pqsA, pqsB, pqsC, pqsE, PA1657, and PA1658). In addition, other virulence-related pathways, such as quorum sensing, phenazine biosynthesis, the bacterial secretion system, and secondary metabolite biosynthesis, were enriched. In conclusion, our hypothesis-generating integrative analysis identifies candidate genes and potential pathways associated with biofilm formation, virulence, and other processes in P. aeruginosa. In light of this, we point out that all candidate genes presented in this study remain hypothesis-generating. Further validation is recommended, including large-scale in silico analyses and in vitro experimental studies. Full article

Pseudomonas aeruginosa, an opportunistic pathogen, is a major threat to hospital infection control and global public health due to its strong environmental adaptability, complex virulence systems, efficient biofilm formation capability, and widespread multidrug resistance. Traditional single-target antibiotics are often inadequate for clinical treatment. The research into Plant-Derived Bioactive Compounds for combating P. aeruginosa infections is reviewed, highlighting their advantages (many of which are extensively studied in Traditional Chinese Medicine) over conventional antibiotics. The antimicrobial mechanisms of these compounds include the inhibition of bacterial quorum sensing (QS) systems to suppress virulence factor expression rather than direct anti-bactericidal effects, delaying the development of resistance. The abundant natural medicinal plants and their diverse chemical structures provide ample material for active compound screening to identify unique chemical compositions with specific binding to pathogen targets. Plant-Derived Bioactive Compounds exhibit excellent safety profiles, targeting bacterial-specific pathways or host immune regulation, resulting in minimal off-target toxicity. Plant-Derived Bioactive Compounds exert anti-P. aeruginosa effects via inhibition of QS systems to reduce pathogenicity by disrupting intercellular signaling, suppressing biofilm formation/maturity to overcome biofilm-associated resistance, directly interacting with bacterial structure. Plant-Derived Bioactive Compounds are promising treatments for drug-resistant P. aeruginosa infections, providing lead compounds for novel anti-infective drug development. Full article

Introduction: Stenotrophomonas maltophilia (S. maltophilia) has emerged as an important opportunistic pathogen. It is resistant to most available antibiotics due to its intrinsic resistance, leaving only some antibacterial agents as possible therapeutic options, which is further complicated by acquired mechanisms of antimicrobial resistance. This study aimed to provide a comprehensive genomic characterization of clinical S. maltophilia complex (Smc) isolates, focusing on molecular characterization of its resistance and virulence, since studies tackling this are scarce in Oman. Methods: This study is a prospective cross-sectional study, in which a total of 21 clinical isolates of Smc were collected from different clinical samples and further characterized using Whole Genome Sequencing. Results: Besides S. maltophilia, the isolates included S. hibiscicola, S. pavanii, and S. muris for the first time in Oman. All isolates were found to be susceptible to cefiderocol, levofloxacin, and minocycline. Sequence types (STs) were diverse among the isolates, with more than half of the isolates showing new STs with novel alleles. Additionally, blaOXA-2, sul1, and the recently described aac(6′)-Iap and aph(9)-Ic were detected among the isolates. Moreover, virulence-associated genes (smf-1, pilT, pilQ, gpmA, rmlA, spgM, stmPr1, plcN, clpP, and katE) were highly conserved across all isolates. Mobile genetic elements were detected in most of the isolates (76.20%). Conclusions: The collected isolates showed high ST diversity and showed no specific pattern in terms of antibiotic susceptibility and resistance genes. More studies are needed to establish relationships between the different members of the Smc and the different molecular resistome and virulome. Full article

Cronobacter spp. are opportunistic foodborne pathogens that can cause neonatal meningitis, necrotizing enterocolitis, and sepsis. This study conducted a systematic contamination survey and whole-genome epidemiological analysis of 562 low-water-activity food samples in Hunan Province of China. The results showed an overall Cronobacter spp. detection rate of 41.99% (236/562), with spices exhibiting the highest contamination rate (60.06%), and with high-level contamination samples (>110 MPN/g) concentrated in this category. The 236 isolates comprised 6 species, 120 sequence types, and 39 clonal complexes, with C. sakazakii being the most frequently isolated species (64.83%) and high-risk clones ST4, ST1, ST148, and ST64 prevailing. Multiple virulence genes (TraJ, fur, rcsAB, rpoS) and antimicrobial resistance genes (qnrS1, blaTEM-1, blaCTX-M-55, blaLAP-2, aac(3)-IId, aadA2, tet(A), floR, mcr-9.1, sul2) were detected. Core genome multilocus sequence typing (cgMLST) identified two clustering patterns: Cluster C, whose genetic clustering was consistent with transmission associated with potential common upstream raw materials across different brands and provinces, and Cluster G, whose clustering suggested potential persistent colonization in the production environment across multiple batches of the same brand. This study elucidates the contamination characteristics of Cronobacter spp. in low-water-activity foods from Hunan Province and provides a basis for WGS-based active surveillance and supply chain traceability. Full article

Pseudomonas aeruginosa is a major opportunistic pathogen frequently associated with nosocomial infections, such as pneumonia, urinary tract infections, and wound infections, particularly in immunocompromised or hospitalized patients. These infections are often difficult to treat due to the pathogen’s intrinsic antibiotic resistance and biofilm-forming ability. Therefore, rapid and selective detection of P. aeruginosa is essential for early diagnosis and effective infection control. In this study, a novel surface-imprinted MIP design uniquely combines methacrylamide (MAM), acrylamide (AAM), and vinylpyrrolidone (VP) monomers to generate recognition cavities that are complementary to the surface morphology and physicochemical properties of Pseudomonas aeruginosa cells. Unlike traditional MIP approaches, this surface imprinting strategy provides improved stability and reproducibility, without relying on biological recognition elements like antibodies or aptamers. This novel approach enabled us to achieve an ultralow LOD of 1 CFU/mL over a linear range of 1–10⁴ CFU/mL, demonstrating excellent analytical performance. In addition, the sensor exhibited good reproducibility with an RSD of 5–12%. The novelty of this work lies in the use of a surface-imprinted MIP strategy combined with a multi-monomer system to enhance bacterial recognition and sensing performance. Overall, the proposed MIP-based electrochemical biomimetic sensor offers a rapid, cost-effective, and portable platform with strong potential for the detection of P. aeruginosa in clinical and environmental applications. Full article

The mitigation of anthropogenic climate change caused by fossil fuel combustion is a critical global challenge that necessitates a transition to renewable energy systems. Bioethanol represents a major renewable fuel, but first-generation production relies on edible feedstocks, which raises concerns regarding food security. Consequently, research is shifting toward second-generation bioethanol produced from abundant non-edible lignocellulosic biomass sources. This review comprehensively examines the potential of Candida krusei (synonyms: Pichia kudriavzevii, Issatchenkia orientalis) to serve as an alternative biocatalyst for second-generation bioethanol production. Compared with the first-generation bioethanol-producing yeast Saccharomyces cerevisiae, C. krusei exhibits superior physiological traits, such as thermo, acid, and inhibitor tolerances, enabling the utilization of several lignocellulosic feedstocks. This review summarizes the taxonomic and physiological characteristics of C. krusei, describes case studies on bioethanol production, and discusses strategies for reducing production costs. Furthermore, the technical and biosafety challenges associated with the industrial deployment of C. krusei are critically examined, including xylose metabolism limitations, scale-up constraints, and the management of its opportunistic pathogenic nature. A life cycle assessment perspective suggests that the unique physiological properties of C. krusei contribute to reducing greenhouse gas emissions and energy consumption throughout the entire production process, from pretreatment to downstream ethanol recovery. Full article

Pneumocystis is an opportunistic fungal pathogen that causes severe Pneumocystis pneumonia (PCP) in immunocompromised individuals and laboratory animals. Three host-specific species—Pneumocystis murina (P. murina), Pneumocystis carinii (P. carinii), and Pneumocystis jirovecii (P. jirovecii)—are closely associated with infections in humans and laboratory animals. However, the conventional method, microscopic staining, suffers from low sensitivity, operator-dependent subjectivity, and inability to differentiate species, highlighting the urgent need for a multiplex qPCR assay. In this study, we established a multiplex qPCR method targeting the mtLSUrRNA gene of P. murina, the TS gene of P. carinii, and the mtSSUrRNA gene of P. jirovecii. Primers and probes were designed and optimized using a matrix approach. The method was systematically evaluated for sensitivity, specificity, and reproducibility using recombinant plasmid standards and laboratory animal samples. Validation was performed on 260 mouse lung samples, 30 P. murina-positive samples, 25 rat lung samples, 6 rat bronchoalveolar lavage fluid (BALF) samples, and 8 P. carinii-positive samples. Results were compared with single-plex qPCR and staining microscopy (performed on 68 mouse lung samples, 38 Pneumocystis-positive samples). The limits of detection (LOD) were 5 copies/μL for P. murina, 6 copies/μL for P. carinii, and 8 copies/μL for P. jirovecii. Standard curves showed excellent linearity (R² ≥ 0.999) with amplification efficiencies of 90–110%. No non-specific reactions were observed with 22 common pathogens, and intra-/inter-group coefficients of variation (CV%) were below 1%. Moreover, interference testing revealed minimal matrix effects on the amplification system and no mutual interference among the primers and probes. The multiplex qPCR detected all 38 positive samples (100%), showing 100% concordance with single-plex qPCR, whereas Giemsa staining detected none (0%) and toluidine blue staining only 60% (3/5) of the tested positives, suggesting that the multiplex qPCR achieved higher detection rates than staining microscopy. In conclusion, this novel multiplex qPCR method offers high sensitivity, specificity, and reproducibility, providing a sensitive and specific tool for laboratory animal health monitoring and epidemiological surveillance. Its clinical application for human PCP diagnosis requires further validation with authentic human specimens. Full article

Rapid and accurate diagnosis of infectious diseases in aquaculture is essential for preventing major economic and ecological losses. Traditional culture-based methods focus on isolation of individual pathogens, and often are burdened with extended processing times, particularly during investigations of polymicrobial infections. Application of Oxford Nanopore Technologies (ONT) sequencing offers a rapid, culture-independent workflow for the identification of bacterial and fungal pathogens directly from fish tissues. Swab and organ samples from four cases (1: Salmo spp.; 2: Cyprinus carpio; 3: Salvelinus fontinalis; 4: Heniochus acuminatus) were analyzed using ONT long-read sequencing for metagenomic screening and bioinformatic classification. The results revealed case-, species-, and tissue-specific microbial profiles, with external tissues showing higher microbial diversity and internal organs enriched in pathogenic taxa. Dominant pathogens included Streptococcus iniae, Aeromonas hydrophila, Pseudomonas spp., and Saprolegnia parasitica, alongside opportunistic zoonotic bacteria such as Escherichia coli and Acinetobacter baumannii. We demonstrate the potential for diagnostic application of ONT sequencing in investigations and detection of multi-pathogen infections, including assessments of microbial community structure changes during disease outbreaks in aquatic species. The presented workflow enables rapid, cost-effective, and comprehensive pathogen profiling, supporting early disease surveillance and improved management in aquatic veterinary practice. Full article

The COVID-19 pandemic has highlighted the increased vulnerability of hospitalized patients to healthcare-associated infections (HAIs), which significantly impact patient safety and clinical outcomes. This narrative review summarizes the main opportunistic pathogens associated with HAIs in COVID-19 patients, with particular focus on multidrug-resistant organisms such as Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, and Candida spp. The review also examines key aspects of antimicrobial resistance, prevention and control strategies, and medico-legal implications. The evidence supports the need for a multifaceted approach based on antibiotic stewardship, infection prevention guidelines, and multidisciplinary clinical risk management. Full article

Heat shock proteins (HSPs) are highly conserved molecular chaperones that play a key role in maintaining protein homeostasis and cellular survival under stress conditions. Clinically relevant human pathogenic fungi include opportunistic fungi, dimorphic fungi, dermatophytes, Mucorales, and other pathogenic groups. HSPs, including Hsp90, Hsp70, Hsp60, Hsp40, and Hsp110, are essential for the correct nascent protein folding, aggregation prevention, and degradation of misfolded polypeptides. Fungal pathogens frequently encounter environmental and host-imposed stresses, including oxidative stress, temperature fluctuations, and antifungal treatments. This review synthesizes and critically analyzes current evidence on the role of HSP families in essential processes linked to fungal virulence, including morphogenetic transitions, biofilm formation, maintenance of cell wall integrity, and interactions with host immune cells. Beyond their canonical chaperone functions, HSPs act as central mediators in pathogenic processes, such as morphogenesis transitions, biofilm formation, cell wall integrity, and interactions with host immune cells. Hsp90 stabilizes key signaling proteins involved in stress responses, morphogenesis, and antifungal resistance, while Hsp60 and Hsp70 contribute to mitochondrial function, cell wall integrity, and immune modulation. Disruption of these chaperones impairs growth, reduces virulence, and increases susceptibility to antifungal agents. The rise of antifungal resistance underscores the urgent need for new therapeutic strategies. Targeting fungal HSPs has emerged as a promising approach due to their essential roles in stress tolerance and pathogenesis. Hsp90 inhibitors, including geldanamycin derivatives and other small molecules, have demonstrated the ability to impair fungal growth, reduce virulence traits, and sensitize resistant strains to conventional antifungal drugs. Combining HSP inhibitors with existing antifungal drugs represents a potential strategy to overcome resistance and improve treatment outcomes. This review summarizes the current knowledge on HSPs in pathogenic fungi, focusing on their roles in stress adaptation, virulence, host-pathogen interaction, antifungal resistance, and their potential as targets for novel antifungal therapies. Full article