International Microbiology最新文献

Accurately resolving evolutionary relationships among organisms is a cornerstone of evolutionary biology, with phylogenetic trees serving as critical tools for this purpose. While single-gene phylogenies are widely used, they often fail to capture the full complexity of evolutionary processes, particularly in organisms with complex or variable genomes. Concatenated gene alignments, built from multiple orthologous genes, offer a more robust framework but are challenging to generate, especially in taxa with incomplete or poorly annotated genomes such as fungi. To address this challenge, we present Buscogeny (Busco Phylogeny), an open-source command-line tool that automates the construction of concatenated gene alignments and phylogenetic trees using BUSCO-derived single-copy orthologs. Buscogeny integrates key features including genome quality assessment, ortholog extraction, multiple sequence alignment, gap filtering, and recombination filtering, followed by automated phylogenetic inference. By allowing users to select ortholog datasets of varying resolutions and tailor filtering thresholds, Buscogeny is adaptable to both closely related and more distantly related taxa. We demonstrate the utility of Buscogeny in phylogenetic analyses of both bacterial and fungal genomes, including complex groups such as Alternaria, where annotation and genome completeness vary significantly. The streamlined, reproducible workflow provided by Buscogeny makes BUSCO-based phylogenetic inference accessible to researchers across disciplines, enabling robust evolutionary insights from whole-genome data.

Urinary tract infections (UTIs) represent a significant public health issue. The increasing prevalence of Extended-spectrum β-lactamases (ESBLs) producing Gram-negative bacilli (GNB) significantly limit treatment options. This study investigated the phenotypic and genotypic characteristics of ESBL-producing GNB isolated from urine specimens processed across Ouagadougou, Burkina Faso. A total of 252 non-duplicate Gram-negative bacilli isolates were collected from four clinical laboratories in Ouagadougou, Burkina Faso. Antimicrobial susceptibility was assessed via disk diffusion following European committee on antimicrobial susceptibility testing (EUCAST) guidelines. ESBL production was screened using double-disk synergy testing, and polymerase chain reaction was employed to detect bla_TEM, bla_CTX-M, and bla_SHV genes. Phenotypic ESBL production was detected in 20.6% of the 252 isolates. These ESBL-producing strains exhibited high resistance rates (greater than 85%) to β-lactams, fluoroquinolones, and folate pathway inhibitors, while imipenem and amikacin remained largely effective. The bla_TEM was the most prevalent ESBL gene (48.8%), followed by bla_CTX-M (42.1%) and bla_SHV (11.1%). Cluster analysis identified three genotypic-resistance profiles ranging from low to high multiple antibiotic resistance (MAR) indices. This study underscores the substantial burden of ESBL-associated multidrug resistance among urinary GNB in Burkina Faso. The incorporation of molecular diagnostic tools into routine surveillance programs is critical for early detection, informed therapeutic decision-making, and effective containment of antimicrobial resistance. The data further support the need for expanded genomic research and broader geographic sampling to reinforce national antimicrobial stewardship initiatives.

Marine snails, a diverse and ecologically important group under the class Gastropods, possess unique gut microbial communities that are crucial to their physiology, ecology, and environmental interactions. In this research, we focused on exploring the gut microbiota of two marine snail species Murex forskoehlii (M. forskoehlii) and edible snail Thais savignyi (T. savignyi) to acquire bacterial isolates exhibiting probiotic traits and anticancer activity. The M. forskoehlii gut microbiota was predominant with two main phyla Pseudomonadota (62.8%) and Fusobacteria (34.7%) while T. savignyi gut microbiota was predominant with Pseudomonadota (57.6%), Bacteroidota (29.1%) and Bacillota (9.5%). Two Enterococcus strains identified as Enterococcus faecium (E. faecium) and Enterococcus durans (E. durans) were isolated from M. forskoehlii and T. savignyi gut microbiota, respectively. Investigation of important probiotic characteristics in vitro demonstrated their high tolerance to acidic environment (pH 2.5) up to 6 h and bile salts (0.3 and 0.7%) up to 24 h. Furthermore, investigation into the strains' probiotic properties revealed that the isolated Enterococcus strains exhibited varying antibacterial activity against Gram-positive and Gram-negative bacteria. Microscopic analysis of the Cacao 2 cell lines revealed that cancer cells treated with bacterial cell free supernatant (CFS) exhibited apoptotic morphological alterations. The exopolysaccharide (EPS) production from both isolated strains was estimated. E. faecium and E. durans demonstrated good auto aggregation and hydrophobicity properties for a potential probiotic. This investigation demonstrated the intestinal microbiota biodiversity of marine snails and their use as a niche source for beneficial bacteria as probiotic bacteria.

Aim: This study aimed to characterize the prevalence of fosfomycin resistance in clinical carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) isolates.

Methods: Common drug resistance genes and virulence genes were amplified by polymerase chain reaction (PCR) and verified by whole-genome sequencing. The potential virulence of all the clinical CRKP strains was tested in a Galleria mellonella infection model.

Results: A total of 171 CR-hvKP isolates collected from a Chinese tertiary hospital were analyzed for fosfomycin resistance. 71 strains (41.5%) were sensitive to fosfomycin, and 100 strains (58.5%) were resistant to fosfomycin. All the clinical isolates were found to carry fosfomycin genes fosA and fosA6. Only one fosfomycin-resistant isolate was found to carry the gene fosA3. In addition to the modification of target enzyme murA, the mechanisms of fosfomycin resistance also involve the dysfunction of the transport system including glpt, uhpT, and their regulatory gene CyaA mutation deletion. The Galleria mellonella infection assays confirmed that all the CRKP strains exhibited hypervirulence.

Conclusion: Cumulatively, fosfomycin resistance in CR-hvKP is mediated by diverse mechanisms and is highly prevalent in a tertiary hospital from Jiangxi Province, South China. It is therefore critical to continuously monitor the epidemiology of these fosfomycin-resistant CR-hvKP while simultaneously minimizing potential risks from fosfomycin-resistant CR-hvKP.

Introduction: Silibinin (SB), a bioactive flavonolignan derived from milk thistle seeds (Silybum marianum L.), exhibits well-documented antioxidant, antibacterial, antifungal, antiviral, and hepatoprotective activities. This study aimed to conjugate SB with fourth-generation poly(amidoamine) dendrimer-stabilized gold nanoparticles (DSA) to enhance its solubility and evaluate its antibacterial efficacy against clinical isolates of Staphylococcus aureus (S. aureus).

Methods: The morphology and structural features of silibinin-dendrimer-stabilized gold nanoparticle complex (SB-DSA) were characterized using Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), transmission electron microscopy (TEM) and field-emission scanning electron microscopy (FE-SEM). Antibacterial activity was assessed through biofilm formation assays, checkerboard analysis, and quantitative real-time PCR (qRT-PCR) using clinical S. aureus isolates and a standard reference strain.

Results: Physicochemical analyses confirmed the successful incorporation of SB into the DSA matrix. The average particle size of the SB-DSA nanocomposites was approximately 20 nm. A synergistic interaction between SB-DSA and vancomycin was observed, with SB-DSA significantly enhancing the susceptibility of vancomycin-resistant isolates to vancomycin. Biofilm formation was markedly reduced in resistant isolates treated with the SB-DSA/vancomycin combination compared with vancomycin alone. The time-kill kinetics of SB-DSA in the tested isolates ranged from 4 to 8 h. Combination treatment also resulted in downregulation of icaA, and norA expression in resistant S. aureus isolates.

Conclusion: Silibinin encapsulated within DSA demonstrates potent anti S. aureus activity, likely mediated through downregulation of efflux pump-related genes and improved intracellular retention of vancomycin. Consequently, even low concentrations of vancomycin, when combined with silibinin, effectively inhibited the growth of vancomycin-resistant isolates.

Background: Antibiotic resistance has become a massive public health threat that requires novel and effective antibacterial and antibiofilm alternatives. The use of probiotics is interested to prevent and control certain infections. Acinetobacter baumannii and Enterocoocus faecalis increase their resistance against antibiotic by producing biofilm and the objective of this study was to investigate the antibacterial and antibiofilm property of probiotics and synbiotics against multidrug-resistant A. baumannii and E. faecalis.

Methods: The antimicrobial and the antibiofilm activities of cell- free supernatants of four strains of Lactobacillus against 20 clinical multi-drug resistant (MDR) isolates of Acinetobacter baumannii and Enterocoocus faecalis were determined in the presence of 0.3% of sorbitol, raffinose, citrate, trehalose, inulin, and riboflavin using well diffusion agar and micro-dilution method.

Results: The cell- free supernatant of L. rhamnosus with citrate and trehalose showed the best antibacterial activity against MDR A. baumannii (28.8 ± 2.1 mm, 1.128 µL/mL), and L. rhamnosus with all of prebiotics against MDR E. faecalis (29.8 ± 0 mm, 1.128 µL/mL) compare to probiotic alone. The prebiotics could improve the inhibitory effect of probiotics against the Gram-negative A. baumannii higher than Gram-positive E. faecalis. Biofilm formation was reduced for both pathogens in presence of probiotics and synbiotics. L. plantarum with riboflavin and L. rhamnosus with or without inulin potently inhibits biofilm formation in E. faecalis (50 ± 0.86%) and A. baumannii (75 ± 6.5%), respectively.

Conclusions: The results of current study support the antibiofilm activity of synbiotics, and suggest their use as suitable adjuvants as well as biocontrol agents for treatment.

Clostridium perfringens is a significant foodborne pathogen in the poultry industry, creating a need for novel antimicrobial interventions. This study reports the isolation and comparative biological characterisation of three novel bacteriophages, vB_CpS_CP3C, vB_CpS_CP4C, and vB_CpS_CP5S, identified as dsDNA viruses with siphoviral morphology, belonging to the class Caudoviricetes. The phages exhibited distinct stability profiles: CP3C and CP5S were stable up to 60 °C and across functional pH ranges (pH 5-8 and 4-7, respectively), while CP4C was thermolabile above 25 °C. Lytic dynamics also varied significantly; latent periods were 15 min (CP4C), 20 min (CP3C), and 20 min (CP5S), while average burst sizes were 308 (CP3C), 206 (CP4C), and 73 (CP5S) PFU/cell. Host range analysis against 15 C. perfringens strains revealed all three phages to be highly specific, lysing only the ATCC 13124 strain. In an in vitro challenge on chicken meat at 37 °C, treatments with phages CP3C and CP4C did not produce a significant reduction in bacterial counts, whereas CP5S achieved a significant (p < 0.01) 0.6-log reduction after 48 h compared to the untreated control. Although all isolates share the limitation of a narrow host range, the superior thermal and pH stability combined with its unique biocontrol efficacy on a food matrix identify CP5S as the most promising candidate for future investigation.

Background: This study aimed to determine the prevalence of Hepatitis B Virus (HBV) infection among municipal waste collectors (MWCs) and to identify associated risk factors in Aden, Yemen.

Methods: An analytical cross-sectional study was conducted among 100 MWCs. Blood samples were collected and tested for HBsAg using the Cobas technique.

Results: The overall prevalence of HBV infection was 5.0%, with a higher clustering of 40% observed in the Khormaksar district. A significant association was found between HBV infection and biomedical waste exposure (OR: 20.44, 95% CI: 2.44-171.5; p = 0.019). MWCs in the age group 25-35 years had three times or more risk of HBV infection (OR: 3.8, 95% CI: 0.598-23.88; p = 0.158). Significant risk was also noted among those whose duration of work was >20 years and 10-20 years (OR: 2.09 and 2.3, 95% CI: 0.328-13.27 and 0.359-14.106; p = 0.367 and 0.332), respectively. Exposure to catheterization and needle-stick injuries was significantly associated with HBV positivity (OR: 15.2 and 91; 95% CI: 20.195-117.85 and UD; p = 0.02 and 0.0001), respectively. Clinically, HBV infection was also significantly associated with fever (p = 0.0001), vomiting (p = 0.0001), nausea (p = 0.001), loss of appetite (p = 0.0001), abdominal pain (p = 0.001), and jaundice (p = 0.005).

Conclusion: The prevalence of HBV infection in this study was relatively lower than most global findings. MWCs exposed to biomedical waste had the highest HBV positivity rates. Needle-stick injuries and catheterization may significantly increase the risk of infection. Mandatory screening and vaccination for HBV should be implemented for all municipal waste collectors to reduce the risk of infection.

Microplastics are widely recognized as persistent and pervasive contaminants that endanger human health and ecosystems. Traditional remedial techniques are problematic due to high costs and inefficiency. One sustainable method of dissolving tough polymers into recyclable parts is through microbial and enzymatic engineering. Recent advances in genome-editing technologies, enzyme redesign, and synthetic biology particularly CRISPR-based systems have transformed the way we approach enhancing the efficiency of biodegradation. Recent CRISPR applications, such as base editing and promoter modification, have improved the stability and expression of enzymes, accelerating the catalytic activity of PET hydrolases, including PETase and cutinase. To enable scalable plastic biodegradation, this review combines hybrid CRISPR-based systems with microbial and enzyme engineering techniques. The goals of computational and machine learning-based enzyme design is thermostability and substrate adaptation, while hybrid microbial communities made up of modified bacteria and fungi improve degradation through cooperative processes. Furthermore, combining synthetic biology with hybrid remediation techniques, such as biofilm reactors and enzyme-nanoparticle conjugates, links laboratory research developments with real-world applications. However, issues remain regarding the scalability of polyethylene (PE) and polystyrene (PS) degradation, biosafety standards for genetically modified organisms (GMOs), and environmental hazards associated with degradation byproducts. To effectively manage plastic waste, future research should focus on creating thermostable enzymes, forming synthetic consortia guided by multi-omics, and developing safe hybrid bio-physical systems that support circular bio economy models.