Pathogens最新文献

Interest in Zika virus (ZIKV, Orthoflavivirus zikaense) evolution and pathogenicity has attracted the attention of a wider circle of the research community ever since ZIKV emerged on the South American continent in 2015, after more or less island hopping across the Pacific Ocean from Southeast Asia on its way from Africa where it was first described in Uganda in 1947 [...].

Arthropod-borne viruses (arboviruses) such as dengue, chikungunya, Zika, and yellow fever pose significant global health risks, with mosquitoes from the Aedes genus as the primary vectors responsible for human transmission. The Republic of the Marshall Islands (RMI), particularly the urbanized areas of Kwajalein and Majuro atolls, has experienced multiple outbreaks of dengue, Zika, and chikungunya with substantial health and economic impacts. Vector control remains the most effective method for reducing disease risk, but comprehensive data on local mosquito vector composition, distribution, and abundance are needed to guide new, effective control efforts. From 2022 to 2024, we conducted a longitudinal baseline assessment of mosquito abundance and species composition on Ebeye and nearby islets in Kwajalein Atoll, RMI, using BG-Sentinel traps and ovitraps. Aedes aegypti was the most prevalent species, accounting for 58% of all adult females collected across study locations, with higher relative abundances on Ebeye than on northern islets (4.7 vs. 2.3 per trap/night). Aedes albopictus was more abundant on northern islets (0.7 vs. 3.2 per trap/night), and Culex quinquefasciatus showed similar abundances (1.2 vs. 1.7 per trap/night). Rainfall and anthropogenic factors, including water storage practices and housing density, influenced mosquito abundance. These findings provide multi-seasonal baseline data to support targeted vector control strategies in RMI.

Pseudomonas aeruginosa bloodstream infections (PABSIs) are a major clinical challenge due to their association with significant mortality and antimicrobial resistance mechanisms. The COVID-19 pandemic changed antimicrobial practices, intensive care management, and patient risk profiles, potentially influencing the epidemiology and outcomes of PABSIs. In the post-pandemic period, practices were expected to revert to normal. The objective of this scoping review was to identify and summarize reported mortality rates and risk factors for PABSIs in studies published between 2023 and 2025. Literature searches were conducted across PubMed, Web of Science, Embase, and Scopus. Screening was performed in accordance with PRISMA-ScR guidelines. Twenty-two eligible studies were included. Mortality rates varied across the study setting and populations; however, several consistent predictors were consistently identified, including carbapenem exposure, multidrug-resistant Pseudomonas aeruginosa, hematologic disease or malignancy, corticosteroid therapy, sepsis or septic shock, mechanical ventilation, and higher severity-of-illness scores. Few studies have linked molecular mechanisms to patient outcomes, highlighting important gaps in knowledge. Notably, only a small number of studies included the post-pandemic period but did not analyze the data separately. Despite limited available evidence, critically ill and immunocompromised patients remain at greatest risk of death from PABSIs. This review highlights the need for a broader comparative analysis in future.

The need for contrasting Healthcare-Associated Infections requires the promotion and support of alternative disinfection techniques. Due to the antimicrobial potential of UV, devices equipped with UVC, UVB and UVA lamps or LEDs have been developed in recent years for domestic, everyday use. In this study, four bacterial strains (S. aureus, E. faecalis, E. coli, and P. aeruginosa) were exposed to different doses of near-UVA radiation at 405 nm, with an average irradiance of 21 mW/cm², using an experimental multi-LED device. Bacterial suspensions were irradiated under both sub-lethal and non-sub-lethal stress conditions. When using only near-UVA light, the highest abatement effect was observed on P. aeruginosa (2.4 log₁₀). Treatment with osmotic stress, in combination with light irradiation, was effective on all bacterial strains (mean abatement of 2.76, 5.46, 5.31, and 1.5 log₁₀ on E. coli, E. faecalis, P. aeruginosa, and S. aureus, respectively). In heat stress conditions at 4 °C, P. aeruginosa and S. aureus species were the most susceptible (2.76 and 5.5 log₁₀), whereas at 45 °C all species, except E. faecalis (0.58 log₁₀), achieved significant reduction. The addition of exogenous photosensitive porphyrins produced a reduction in total concentrations from the lowest doses for S. aureus and P. aeruginosa, while for E. coli and E. faecalis, the reductions did not exceed 1 log₁₀ abatement. Near-UVA radiation at 405 nm has a high disinfectant potential when combined with certain sub-lethal stress conditions. The most significant germicidal effect was achieved with the use of exogenous porphyrins in S. aureus and P. aeruginosa species. This study opens perspectives on the possible future application of near-UVA radiation in disinfection in order to limit the spread of healthcare-related infections.

This study investigates the codon usage characteristics of Japanese encephalitis virus (JEV) genotype 5 (G5). Based on 339 complete JEV genome sequences, we systematically compared the codon usage patterns of G5 with other genotypes (G1-G4) using a multi-faceted approach, including evolutionary analysis, nucleotide composition, Relative Synonymous Codon Usage (RSCU), Principal Component Analysis (PCA), Effective Number of Codons Plot analysis (ENC-Plot), Parity Rule 2 analysis (PR2), Neutrality plot analysis, dinucleotide abundance analysis and Codon Adaptation Index analysis (CAI). The results indicate that G5 forms a distinct evolutionary branch, with both its overall GC content (50%) and GC content at the third codon position (GC3, 53%) being lower than those of other genotypes. RSCU analysis revealed a preferential use of A/U-ended codons in G5, indicating a trend towards reduced GC3 usage. ENC analysis demonstrated a stronger codon usage bias in G5 (mean ENC = 54.2). Furthermore, ENC-plot, PR2, and neutrality plot analyses collectively suggested that G5 is subject to stronger natural selection pressure. Analysis of dinucleotide abundance showed a significant increase in CA values in G5, while CAI analysis indicated higher translational efficiency in human hosts compared to Culex mosquito hosts. Our findings suggest that G5 JEV, potentially through reduced Cytosine-phosphate-Guanine (CpG) usage and optimized codon preference, may enhance its capabilities for immune evasion and host adaptation, and could possess the potential for efficient replication in humans or other mammalian hosts. This research provides crucial theoretical insights into the molecular evolutionary mechanisms of G5 JEV and informs related vaccine development.

Osteoarthritis (OA) is one of the most common and burdensome musculoskeletal disorders and a major cause of pain, disability, and reduced quality of life worldwide. In recent years, increasing attention has been paid to extra-articular factors influencing its development and progression, opening new avenues of research into pathophysiological mechanisms and potential therapies. One of the most promising areas concerns the role of the gut-joint axis and related alterations in the gut microbiome. Numerous studies indicate that an imbalance of gut bacteria, increased intestinal permeability, and low-grade inflammation may contribute to the progression of degenerative joint processes. The mechanisms through which the microbiota influences the immune system and host metabolism are becoming increasingly well understood, including pathways involving short-chain fatty acids, tryptophan metabolites, and bile acids. Despite growing evidence linking dysbiosis to the pathogenesis of OA, effective therapeutic strategies based on microbiome modulation remain under active investigation. Among the most frequently studied approaches are probiotics, dietary interventions, and more advanced strategies such as gut microbiota transplantation and targeted modulation of microbial metabolites. However, before these methods can become part of routine treatment, extensive clinical trials and a clearer understanding of causal relationships between the microbiome and joint degeneration are required. This article summarises the current state of knowledge regarding the role of the gut microbiome in osteoarthritis, outlines key research findings, and highlights current and potential therapeutic directions.

Protozoa use iron to grow, feed, and cause harm through elaborate mechanisms to obtain it from the host. In addition, expression of virulence genes is affected by iron. In Entamoeba histolytica, the parasite that causes amoebic dysentery and complications in human organs, our group have previously reported the presence of an IRE/IRP-like (Iron Responsive Element/Iron Regulatory Protein) mechanism. Giardia duodenalis is another parasite of medical interest that causes giardiasis, including nutrient malabsorption syndrome and dysbiosis, among other complications, such as anemia in children with giardiasis. Moreover, expression of many putative giardial virulence factors by free-iron levels has been reported. Recently, we have reported stem-loop structures in some mRNAs coding virulence proteins from both parasites. However, much remains to be studied about the role of iron in pathogenesis. In this review, we summarize several aspects of gene expression regulation by iron in these protozoa as well as an iron regulatory mechanism in E. histolytica and discuss the possibility of an iron regulatory IRE/IRP-like mechanism in G. duodenalis.

Outcomes of influenza virus infection vary widely across individuals, reflecting not only viral genetics and host factors but also the composition and function of the airway microbiome. Over the past few years, mechanistic work has clarified how specific commensals (for example, Staphylococcus epidermidis and Streptococcus oralis) restrict influenza replication by priming epithelial interferon-λ programs, reshaping intracellular metabolite pools (notably polyamines), dampening host protease activity, and maintaining barrier integrity; meanwhile, pathobionts (notably Staphylococcus aureus and Streptococcus pneumoniae) can enhance viral fitness via secreted proteases and neuraminidases that activate hemagglutinin and remodel sialylated glycoconjugates and mucus, setting the stage for secondary bacterial disease. Recent studies also highlight the gut-lung axis: gut microbiota-derived short-chain fatty acids (SCFAs), especially acetate, protect tight junctions and modulate antiviral immunity in influenza models. Together, these insights motivate translational strategies-from intranasal live biotherapeutics (LBPs) to metabolite sprays and decoy/dual neuraminidase approaches-that complement vaccines and antivirals. We synthesize recent evidence and outline a framework for leveraging the airway microbiome to prevent infection, blunt severity, and reduce transmission. Key priorities include strain-level resolution of commensal effects, timing/dosing windows for metabolites and LBPs, and microbiome-aware clinical pathways for anticipating and averting bacterial coinfection. Overall, the airway microbiome emerges as a tractable lever for influenza control at the site of viral entry, with several candidates moving toward clinical testing.

The skin of turtles, particularly aquatic species, can harbor a diverse range of bacteria, including Citrobacter species, which are recognized as causative agents of Septicemic Cutaneous Ulcerative Disease. Consequently, turtles may act as reservoirs of pathogenic and multidrug-resistant bacteria, posing a potential public health concern. This case-based study investigated the presence of Citrobacter spp. in a loggerhead sea turtle (Caretta caretta) housed at the Livorno Aquarium, Italy. Nine swabs were collected from skin lesions (plastron, carapace, nuchal mass), the oral cavity, and the cloaca. The isolated strains were identified by MALDI-TOF MS and tested for their susceptibility to 12 antimicrobials, belonging to eight antimicrobial classes, by the disc diffusion method. Isolates were investigated genotypically for extended-spectrum-β-lactamase (ESBL) bla_CTX-M, bla_TEM, bla_SHV, bla_PER, and metallo-β-lactamase (MBL) bla_IMP, bla_OXA-48, bla_VIM, bla_NDM, bla_GES genes. Biofilm production ability was also evaluated. Fifteen Citrobacter spp. strains were recovered from the analyzed samples. Complete resistance was recorded for ampicillin, followed by high levels of resistance to imipenem, tetracycline and piperacillin-tazobactam. Worryingly, 86.7% were classified as multidrug-resistant. The most common ESBL-genotype combination was bla_SHV and bla_PER genes (60%), while the most frequently detected MBL gene was bla_NDM (46.7%), followed by bla_GES (40%). Most isolates were classified as weak biofilm producers (80%). The findings of this study demonstrate the presence of Citrobacter spp., an opportunistic pathogen, with a notable prevalence of multidrug-resistant strains carrying beta-lactamase-encoding genes, in a loggerhead sea turtle in Italy, across both lesioned and healthy anatomical sites.

Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.