MicrobiologyOpen最新文献

Pseudomonas aeruginosa poses a significant therapeutic challenge in pediatric patients with cystic fibrosis (CF) due to increasing multidrug resistance (MDR) and carbapenem resistance, underscoring the need for surveillance to guide treatment strategies. In this study, sputum and throat swab samples were collected from inpatient and outpatient CF children with pulmonary infection at the Children's Medical Center in Tehran, Iran. Isolates were identified using standard culture and biochemical methods, followed by antimicrobial susceptibility testing. Carbapenemase production was assessed phenotypically and by molecular detection of resistance genes, and genetic diversity was also evaluated using Random Amplified Polymorphic DNA (RAPD)–polymerase chain reaction (PCR). A total of 117 P. aeruginosa isolates were recovered (prevalence 17.41%), of which 94.9% were nonsusceptible to at least one antimicrobial agent. Carbapenem-resistant P. aeruginosa (CRPA) and MDR isolates accounted for 24.8% and 23.1% of isolates, respectively. Carbapenemase gene coexistence was significantly associated with MDR (ρ = 0.227, p = 0.014) and CRPA (ρ = 0.314, p = 0.001). Metallo-β-lactamase production was detected in 13.7% of isolates, while blaVIM was the most frequently identified carbapenemase gene (59%). RAPD–PCR demonstrated marked genetic heterogeneity, grouping isolates into 24 distinct clusters. Overall, the substantial burden of MDR and CRPA identified at this tertiary pediatric center highlights an urgent need for stricter antimicrobial stewardship, enhanced infection control measures, and ongoing surveillance to mitigate resistance spread and preserve therapeutic effectiveness in this vulnerable population. These findings warrant multicenter investigation to determine whether similar patterns exist across other Iranian pediatric CF facilities.

Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.

Stenotrophomonas maltophilia is a nosocomial and opportunistic microorganism with increasing antibiotic resistance rates. This study aimed to assess its biofilm production capacity, antibiotic resistance distribution, and the prevalence of biofilm- and resistance-related genes in clinical isolates. In this multiinstitutional study, 230 isolates were collected from hospitals across Iran between 2022 and 2024. Resistance trends were evaluated using disc diffusion and minimal inhibitory concentration E test methods, per Clinical and Laboratory Standards Institute guidelines. Crystal violet staining assessed biofilm production, while polymerase chain reaction (PCR) sequencing identified biofilm- and resistance-related genes. Real-time PCR was used to evaluate the relative expression of the smeD, smeE, and smeT genes, calibrated against TMP/SMX-sensitive control strains. Susceptibility rates to trimethoprim/sulfamethoxazole (TMP/SMX), levofloxacin, and minocycline were 97.39%, 93.47%, and 93.04%, respectively. TMP/SMX-resistant strains showed 19.8- and 16-fold higher expression of smeD and smeE, compared with sensitive isolates. The spgM gene was detected in all isolates, and 93.04% (n = 214) were biofilm producers, with most showing moderate-biofilm formation (n = 89, 38.70%). Additionally, the rpfF gene was closely associated with strong-biofilm formation (p ≤ 0.05). The L2, L1, smqnr, sul2, and sul1 resistance genes were identified in 214 (93.04%), 181 (78.69%), 135 (58.7%), 136 (59.1%), and 127 (55.2%) isolates, respectively. Our findings demonstrate that most isolates remain sensitive to TMP/SMX, while resistance to alternative antibiotics is rising. Moreover, biofilm production appears significantly associated with the rpfF gene.

Gallid alphaherpesvirus 1 (GaAHV-1), also referred to as infectious laryngotracheitis virus (ILTV), primarily targets the upper respiratory tract of chickens. This infection leads to significant economic setbacks worldwide in the poultry sector, driven by reductions in egg output, weight gain, and increased mortality rates. Even with the broad implementation of vaccination programs, ILTV outbreaks remain a challenge, as vaccine strains can revert to a virulent form under field conditions. This underscores the need to explore targeted therapeutic options, including a deeper understanding of GaAHV-1's nuclear trafficking mechanisms, critical for viral replication. The herpesvirus large tegument protein UL36 contains N-terminal nuclear localization signals (NLSs) that are essential for capsid routing to the nuclear pore complex (NPC). However, the mechanisms by which UL36 of GaAHV-1 mediates nuclear import remain poorly understood. In this study, we identified the NLS of GaAHV-1 UL36 and elucidated their binding mechanism with human nuclear import proteins. Using high-resolution crystal structures and quantitative assays, we mapped the specific residues and regions within UL36's N-terminal domain that facilitate binding to importin (IMP) α. Moreover, we revealed variations in binding affinities among different importin isoforms. Our biochemical and structural analyses demonstrate that the predicted N-terminal NLS of GaAHV-1 UL36 is critical for IMPα binding. These findings provide detailed molecular insights into the interaction between the GaAHV-1 large tegument protein and IMPs, paving the way for the development of targeted antiviral therapies.

Brucella-induced neuroinflammation represents a key mechanism in the development of neurobrucellosis. The objective of this investigation was to clarify the molecular pathways through which the BvrR contributes to neuroinflammation and cognitive dysfunction. Human microglial clone 3 (HMC3) cells were transfected with pcDNA3.1-BvrR-His to examine the effects of BvrR from Brucella abortus on endoplasmic reticulum (ER) function and the activation of activating transcription factor 2 (ATF2) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) p65. The role of phosphorylated inositol-requiring enzyme 1 (p-IRE1) in mediating BvrR-induced activation of ATF2 and NF-κB p65 was assessed by applying the IRE1 activator IXA4 and the IRE1 inhibitor GSK2850163, followed by evaluation with western blotting and RT-qPCR. Interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) concentrations in cell culture supernatants were quantified using ELISA. For in vivo analysis, HBAAV2/9-IBA-1-BvrR-6*HIS-ZsGreen was stereotactically delivered into the right hippocampus of mice. Expression of BvrR in HMC3 cells induced phosphorylation of IRE1 and expansion of the ER. This activation enhanced ATF2 and NF-κB p65 phosphorylation, facilitated their nuclear translocation, and significantly increased IL-6 and TNF-α expression at both the protein and mRNA levels. Inhibition of IRE1 with GSK2850163 suppressed these responses, whereas IRE1 activation with IXA4 reproduced the effects of BvrR. Findings indicate that BvrR from B. abortus activates IRE1, which subsequently stimulates ATF2 and NF-κB p65, leading to increased expression of IL-6 and TNF-α and the induction of inflammatory responses in HMC3 cells.

On the basis of gut microbiota and short-chain fatty acids (SCFAs), this study aims to identify diagnostic biomarkers for damp-heat diarrhea and cold-damp diarrhea. Rat models of damp-heat diarrhea and cold-damp diarrhea were established. Changes in body weight, body temperature, food intake, water consumption, and the diarrhea index were recorded. ELISA was employed to detect levels of IL-6, IL-1β, TNF-α, and IL-10. Histological evaluations were conducted using H&E staining and AB-PAS staining techniques. Transmission electron microscopy was utilized to observe ultrastructural changes in the colonic epithelium, while Western blot analysis was performed to assess the expression of Occludin, Claudin1, Claudin5, GPR41, GPR43, GPR109A, and NLRP3 in colon tissues. GC–MS analysis was carried out to determine the content of SCFAs in the cecal contents of rats; additionally, 16S rRNA sequencing was performed to analyze the composition of gut microbiota in these animals. Differential analysis methods were applied to evaluate similarities and differences in SCFAs profiles and gut microbiota between damp-heat diarrhea and cold-damp conditions. The body weight and food intake of rats with induced damp-heat diarrhea or cold-damp diarrhea significantly decreased over time as their diarrheal symptoms progressively worsened. However, following treatment with appropriate prescriptions tailored for each condition resulted in an improvement in diarrheal symptoms among the affected rats. In accordance with the “prescription-based syndrome differentiation” theory, the rat experimental animal models of damp-heat diarrhea and cold-dampness diarrhea were successfully established. The models exhibited characteristic diarrheal symptoms alongside increased levels of inflammatory factors indicative of severe histopathological damage; there was also a notable reduction in tight junction protein expression observed across all models studied. Furthermore, the Firmicutes/Bacteroidota ratio showed a significant decrease. Interestingly, differences between damp-heat diarrhea and cold-damp diarrhea manifested as follows: Both modeling groups showed an increase in the relative abundance of Lachnoclostridium and Marvinbryantia. In the damp-heat diarrhea group, the levels of Lachnoclostridium and Marvinbryantia were relatively low; however, these levels gradually increased after successful treatment. In contrast, in the cold-damp diarrhea group, the trends of Lachnoclostridium and Marvinbryantia were opposite. Mucosal color has the potential for clinical diagnosis of damp-heat diarrhea and cold-damp diarrhea. Moreover, Lachnoclostridium and Marvinbryantia are potential biomarkers for distinguishing between damp-heat diarrhea and cold-damp diarrhea. However, the diagnostic basis and accuracy of Lachnoclostridium and Marvinbryantia biomarkers still need to be further validated.

Shewanella algae, a marine-origin opportunistic pathogen, has shown a significant increase in non-coastal infections, yet its environmental adaptability and synergistic pathogenic mechanisms with Epstein-Barr virus (EBV) coinfection remain unclear. This study reports a clinical case of S. algae bloodstream infection complicated by EBV reactivation leading to septic shock in Sichuan Province, China, and elucidates the molecular mechanisms through genomic analysis. Pathogen identification was performed via blood culture, antibiotic susceptibility testing, and genomic annotation. The strain harbored resistance genes (acrB, tolC, tet(35), golS) and virulence factors (bplL/bplF, clpC/clpP, tonB). Phylogenetic analysis indicated the highest genetic affinity to freshwater-derived Shewanella chilikensis, while pan-genome analysis identified 1412 unique genes, including transmembrane transporters and carbohydrate-active enzyme genes, suggesting freshwater adaptive evolution. Metagenomic next-generation sequencing (mNGS) detected a high EBV load. The patient succumbed to multi-organ failure. This study reveals that S. algae may evolve freshwater adaptability to cause inland infections, and EBV coinfection accelerates septic shock through immunosuppression and inflammatory cascades. Genomic analysis provides critical insights for precision diagnosis and treatment of polymicrobial infections.

Coinfection of Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus) is frequently observed. Our previous study demonstrated that S. aureus-derived extracellular vesicles (SaEVs) promote P. aeruginosa pathogenicity by increasing lipopolysaccharide (LPS) production, promoting biofilm formation and decreasing the uptake of P. aeruginosa by macrophages. Proteomic analysis revealed that SaEVs enhance the production of PslE, an exopolysaccharide biosynthetic protein in P. aeruginosa, but the role of Psl exopolysaccharide polymerization on SaEV-mediated P. aeruginosa pathogenicity is unclear. In this study, a pslE-deletion mutant of P. aeruginosa (PaΔpslE) was constructed, and the effect of SaEVs on the pathogenicity of this mutant was evaluated. Our results showed that SaEVs significantly increased the expression of pslA, E, J, K, and L genes in the psl cluster of P. aeruginosa wildtype (PaWT), and this effect was abolished in PaΔpslE. In addition, LPS production and biofilm formation were reduced in PaΔpslE compared to PaWT. SaEVs significantly enhanced LPS production and biofilm formation in PaWT. On the other hand, the effects of SaEVs on the production of lipid A and LPS core and biofilm formation in PaΔpslE were abolished. Invasion of PaWT and PaΔpslE into HaCaT human epithelial cells was not significantly different and the effect of SaEVs on these bacterial cell invasions was not found. However, the uptake of SaEV-treated PaWT by macrophages significantly reduced compared to nontreated PaWT, whereas SaEVs did not alter the uptake of PaΔpslE. These results suggest that PslE is required for SaEV-mediated P. aeruginosa pathogenicity. SaEVs upregulate pslE gene as well as other exopolysaccharide polymerization-related genes, increase LPS production and biofilm formation, and affect the uptake of P. aeruginosa by macrophages.

Crustose coralline algae (CCA) comprise hundreds of different species and are critical to coral reef growth, structural stability and coral recruitment. Despite their integral role in reef functioning, little is known about the diversity and structure of bacterial communities associated with CCA. We address this knowledge gap by characterising the surface microbial communities of 15 Indo-Pacific CCA species across eight different families from the Great Barrier Reef, using 16S rRNA amplicon sequencing. CCA microbial community composition was distinct and found to primarily differentiate by algal host species. When looking at the core bacterial communities, divergence across CCA microbiomes was additionally correlated to host phylogeny. CCA from similar light environments and depths also had more similar microbial communities, suggesting the potential role of environmental parameters in influencing microbial community organisation. The fundamental descriptions of CCA bacterial communities for a wide range of Indo-Pacific species presented here provide essential baseline information to further inform CCA microbial symbiosis research.

Rice blast disease, caused by Pyricularia oryzae Cavara, is the most threatening rice pathogen in Italy. The development of resistant cultivars is a sustainable approach to mitigate yield losses. However, P. oryzae genomic plasticity often allows rapid adaptation to host resistance. Understanding the population structure of plant pathogens is crucial for assessing their genetic diversity and implementing durable management strategies. Despite first attempts from Piotti et al. (2005) to study the Italian P. oryzae population, a gap in current local P. oryzae genetic variability still needs to be addressed. Here, the population structure of a large set of P. oryzae isolates from diseased rice panicles, collected in five different Italian regions between 2011–2012 and 2020–2022, was characterized using SSR genotyping. Mating type was determined to investigate the occurrence of sexual reproduction in Italy. The integration of different cluster analyses of 200 unique multilocus genotypes allowed to identify five distinct genetic clusters. Analysis of molecular variance and of genetic divergence revealed a limited influence of geographic origin and time on population structure. A strong positive correlation was detected between climatic variables and allelic diversity in Piedmont, the most evenly sampled region in this study. The gradual disappearance over time of a genetic cluster could be linked to lower virulence on a susceptible rice cultivar. This study provides new insights into the genetic dynamics of Italian P. oryzae population, supporting the strategic deployment of resistance genes in rice breeding programs.