Search Results (90)

Clostridioides difficile Infection (CDI) continues to be a major cause of antibiotic-associated diarrhea and pseudomembranous colitis, fueled in large measure by virulence factors TcdA and TcdB. These giant glucosyltransferase toxins interfere with host cytoskeletal integrity and inflammatory signaling by inhibiting Rho GTPase; however, the detailed structural dynamics, receptor selectivity, and subcellular trafficking mechanisms remain in part unspecified. This review integrates recent insights from cryo-electron microscopy (cryo-EM) and X-ray crystallography to describe the quaternary architecture of TcdA/B, emphasizing conformational changes key to pore formation and endosomal escape. We also examine the genomic heterogeneity of hypervirulent C. difficile strains (e.g., ribotype 027), correlating toxin gene polymorphisms (e.g., tcdC mutations) with increased toxin production and virulence. Mechanistic explanations of toxin-driven inflammasome activation and epithelial barrier dysfunction are situated within host immune evasion mechanisms, including microbiota-derived bile acid regulation of toxin stability. Subsequent innovative therapeutic strategies, encompassing the utilization of engineered neutralizing antibodies that specifically target the autoprocessing domain alongside structure-guided small-molecule inhibitors, are subjected to a rigorous evaluation. By integrating structural biology, systems-level omics, and clinical epidemiology, this review establishes a comprehensive framework for understanding C. difficile toxin pathogenesis and guiding next-generation precision antimicrobials. Full article

Minimally processed foods (MPFs), often considered ready-to-eat, do not undergo cooking and therefore require proper handling and preparation to ensure safety. If not handled correctly, these foods can serve as a pathway for diseases caused by pathogenic bacteria, including Escherichia coli and Salmonella spp. The antibacterial activity of essential oils (EOs) has been increasingly studied as a tool for controlling microorganisms in the food sector. Therefore, we aimed to verify the contamination of MPF by E. coli and Salmonella and to test the sensitivity of these strains to Copaifera langsdorffii, Schinus terebinthifolius, Citrus reticulata, Eucalyptus citriodora, Elettaria cardamomum, Ocimum basilicum, and Eugenia caryophyllus EOs using the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) methods. From 25 MPF samples, one E. coli strain and one Salmonella spp. were isolated. C. langsdorffii and C. reticulata EOs did not show antibacterial activity, while S. terebinthifolius and E. citriodora inhibited the growth of both strains. The E. cardamomum, O. basilicum, and E. caryophyllus EOs presented inhibitory and bactericidal responses at concentrations 0.78, 0.39, and 0.19% (v/v), respectively, compared to the two isolated strains. The present study reinforces the antibacterial potential of EOs and suggests their application in the MPF production chain. Full article

Pathogenic Escherichia coli can cause a variety of intestinal and extra-intestinal infections in humans and animals. The availability and subsequent misuse of antimicrobials, especially in poultry production systems, has contributed immensely to the emergence and spread of multidrug-resistant E. coli. This study investigated the genotypic characterization of colistin-resistant E. coli and selected antimicrobial-resistance encoding genes along with their phenotypic resistant pattern and the multiple antimicrobial resistant (MAR) index from village chickens in Kelantan. Sixty E. coli isolates obtained from a previous study’s stock culture were enriched and analyzed using routine microbiological methods: Kirby–Bauer disc diffusion method, minimum inhibitory concentration (MIC), and PCR amplification of E. coli species-specific and multidrug-resistance mcr-positive E. coli. All the isolates were confirmed as E. coli and 16.6% (10/60) were positive for mcr. Five isolates were positive for mcr-1, three for mcr-4, and two for mcr-9. The mcr-positive isolates showed varying degrees of resistance to different antimicrobials. The isolates were resistant to gentamicin (100%), chloramphenicol (100%), and tetracycline (89.4%) and susceptible to ceftaxidime (2.26%) and imipenem (18%). Furthermore, 100%, 94.7%, and 89.4% of isolates from village chickens belonged to phylogroup C, B2, and E, while 21.0% and 42.1% of the isolates belonged to phylogroup A and B1, respectively. Sequence types (STs) of selected E. coli isolates were further analyzed using multi-locus sequence typing, and 10 different STs were identified. This study showed the emerging threats of multidrug-resistant mcr-positive E. coli gene in village chickens that are believed to be raised with minimal or no antibiotics. Full article

Background: Shigella species are the leading cause of human shigellosis. In Zambia, more than 30% of children experiencing diarrhea are infected with Shigella species. The increasing resistance of Shigella species to the recommended therapy is of great concern. Therefore, this study investigated the antibiotic resistance profiles and phenotypic and genotypic characteristics of Shigella isolates at the largest referral hospital in Zambia. Methodology: Of the forty-eight archived presumptive Shigella isolates, thirty-two were serologically confirmed and subjected to antimicrobial susceptibility testing using the Kirby Bauer disk diffusion method. Thereafter, polymerase chain reaction was performed to detect the bla genes. Results: Most isolates were Shigella flexneri (16/32, 50%) and Shigella sonnei (14/32, 44%), while Shigella boydii and Shigella dysenteriae were rare. High resistance rates were noted for sulfamethoxazole/trimethoprim (78%) and tetracycline (75%), while 15.6% of the isolates showed resistance to ciprofloxacin and/or azithromycin. The bla_TEM gene encoding beta-lactamase was detected in 7/32 (22%) of isolates. Conclusions: In this study, a significant number of multidrug-resistant isolates were identified. Additionally, Shigella species resistant to the World Health Organization-recommended drugs call for strengthened laboratory diagnosis and close monitoring of these pathogens to guide the clinical management of shigellosis. Full article

Concerns about the health consequences of seafood-born human pathogens are ongoing given their occurrence, prevalence, and ability to cause infections, and sometimes death in humans as well as seafood-associated morbidity and mortality worldwide. An applied time-series (2000–2017) analysis of six reefs examined pathogen-specific annual trends and seasonal patterns in the eastern oyster, Crassostrea virginica, in Galveston Bay (Texas), a subtropical estuary in the Gulf of Mexico. Pearson correlation coefficients showed that temperature had a strong positive correlation with Vibrio vulnificus and V. parahaemolyticus (r = 0.66 and 0.51), but not the pathogenic thermostable direct hemolysin (tdh+) V. parahaemolyticus (r = 0.12). The correlations between Vibrio spp. and salinity showed the opposite trend. A cross-correlation factor analysis revealed the strongest positive correlations (r = 0.41 and r = 0.36, respectively) for high densities of V. vulnificus during high Perkinsus marinus infections with short lags (up to 1 month); this was not the case for total or tdh+ V. parahaemolyticus. These results reveal some of the complexity of interannual and long-term patterns of pathogens in oysters. Given climate change impacts and a growing aquaculture industry, examinations of oyster microbiomes in response to environmental and water quality variables are needed. 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

Textile dyes pose a major environmental threat due to their toxicity, persistence in water bodies, and resistance to conventional wastewater treatment. To address this, researchers have explored biological and physicochemical degradation methods, focusing on microbial, photolytic, and nanoparticle-mediated approaches, among others. Microbial degradation depends on fungi, bacteria, yeasts, and algae, utilizing enzymatic pathways involving oxidoreductases like laccases, peroxidases, and azoreductases to breakdown or modify complex dye molecules. Photolytic degradation employs hydroxyl radical generation and electron-hole pair formation, while nanoparticle-mediated degradation utilizes titanium dioxide (TiO₂), zinc oxide (ZnO), and silver (Ag) nanoparticles to enhance dye removal. To improve efficiency, microbial consortia have been developed to enhance decolorization and mineralization, offering a cost-effective and eco-friendly alternative to physicochemical methods. Photocatalytic degradation, particularly using TiO₂, harnesses light energy for dye breakdown. Research advancements focus on shifting TiO₂ activation from UV to visible light through doping and composite materials, while optimizing surface area and mesoporosity for better adsorption. Nanoparticle-mediated approaches benefit from a high surface area and rapid adsorption, with ongoing improvements in synthesis, functionalization, and reusability, particularly through magnetic nanoparticle integration. These emerging technologies provide sustainable solutions for dye degradation. The primary aim of this review is to comprehensively evaluate and synthesize current research and advancements in the degradation of azo dyes through microbial methods, photolytic processes, and nanotechnology-based approaches. The review also provides detailed information on salient mechanistic aspects of these methods, efficiencies, advantages, challenges, and potential applications in industrial and environmental contexts. Full article

This study aimed to characterize the fermentation of commercial xylooligosaccharide (XOS) using Lactiplantibacillus plantarum S61. XOS was utilized as the main carbon source in a modified MRS medium (MRSm) at concentrations of 1%, 2%, 4%, and 6% (w/v). The growth of L. plantarum S61 was tracked daily over a week and compared to a control MRS medium using glucose as the main carbon source. The pH, total free acidity, and biomass were analyzed during fermentation, and the resulting fermentation product was analyzed for its content of fatty acids, total polyphenols, and the production of antioxidant and antimicrobial metabolites. The findings revealed that L. plantarum S61 thrived in MRSm, particularly at a 6% XOS concentration, which was identified as the best condition among the four tested concentrations (1%, 2%, 4%, and 6%). The fermentation of XOS by L. plantarum S61 significantly increased the total phenolic content and antioxidant activity compared to glucose, with the highest phenolic content observed at 6% XOS (6.70 ± 0.01 mg GAE/g). The strains produced various organic acids including lactic, malic, and oxalic acids from glucose and XOS. Notably, the strains yielded a broader range of organic acids with higher contents in the presence of XOS, leading to enhanced antifungal and antibacterial activities compared to glucose. Significant antibacterial activity was observed against Gram-negative bacteria, particularly Salmonella enterica, with inhibition zones of 20.25 mm and 11.75 mm for XOS (5% and 6%) and glucose, respectively. For Gram-positive bacteria, S. aureus and M. luteus exhibited inhibition zones of 20.01 mm for XOS 6% and 10.25 mm for glucose. In terms of antifungal activity, the strongest inhibition was observed against Rhodotorula glutinis, with inhibition zones of 26.00 mm for XOS 6% and 20.04 mm for glucose. The fermentation product of XOS by L. plantarum S61 showed significant inhibitory effects against pathogenic bacteria and yeasts, suggesting its potential application in the manufacturing of preservatives with antifungal properties and pharmaceutical products targeting pathogenic and spoilage yeasts. Full article

The continuous use of antibiotics is associated with many complications in the poultry industry. Probiotics have emerged as a viable alternative over the past few decades to counter the adverse effects of antibiotics. No candidate probiotic microorganisms have been fully evaluated in the poultry industry for their effectiveness as potential probiotics in guinea fowls (GFs) compared to chickens. Recently, a metagenome evaluation of GFs in our laboratory revealed a predominance of Lactobacillus reuteri (L. reuteri) and actinobacteria class of bacteria in their gastrointestinal tract. The aim of this study is to evaluate a well-known lactic acid probiotic bacterium (L. reuteri) and a unique probiotic (S. coelicolor) that has not been assessed in any guinea fowl species. In the current study, L. reuteri and Streptomyces coelicolor (S. coelicolor) were selected as probiotic bacteria, encapsulated, and added into French guinea fowl (FGF) feed individually at a concentration of 10⁸ cfu/g or both microorganisms combined each at 10⁴ cfu/g. In an 8-week study, 216-day-old guinea keets were randomly assigned to four dietary treatments as indicated: (1) L. reuteri (10⁸ cfu/g); (2) S. coelicolor (10⁸ cfu/g); (3) mixture of L. reuteri (10⁴ cfu/g) and S. coelicolor (10⁴ cfu/g); and (4) control treatment (no probiotics included). The L. reuteri, S. coelicolor, and L. reuteri + S. coelicolor were added into the feed using wheat middlings as a carrier at a final concentration of 10⁸ cfu/g. The FGFs that were fed diets containing L. reuteri showed improved feed consumption at 3–8 weeks of age (WOA). The guineas fed L. reuteri and S. coelicolor showed a lower feed conversion ratio (FCR), which was significant at 2 and 8 WOA, and a numerically lower 8-week average FCR when compared with other dietary treatments. Differences in body weight gain among all dietary treatments were not significant. This research suggests that L. reuteri and S. coelicolor may have the potential for use as probiotics in FGFs when used in combination or separately. Full article

In the recent past, microbiome manipulation has emerged as a promising approach to improve plant growth performance by exploring the deep insight of plant–microbe interactions. The exploration of a plant microbiome either present on an ectosphere or endosphere can provide a far better understanding about the potential application of plant-associated microbes for the improvement of plant growth, protection from pathogen invasion, and tolerance to environmental stresses of a diverse nature. In this context, next-generation sequencing methods, omics approaches, and synthetic biology have made significant progress in plant microbiome research and are being frequently used to explore the intriguing role of plant-associated microorganisms. Despite the successfulness of conventional approaches, the incorporation of CRISPR/Cas9, RNA interference technology, rhizosphere engineering, microbiome engineering, and other manipulation techniques appear to be a promising approach to enhancing plant performance, and tolerance against biotic and abiotic stress factors. The present review presents the significance of plant microbe interaction, vital functional aspects, collaborative action, potential constraints, and finally the latest developments in bioengineering approaches destined for microbiome modulation with an objective to improve the performance of a host plant challenged with environmental stressors. Full article

The microbiome plays a crucial role in cancer development, influencing fundamental processes such as cell proliferation, apoptosis, immune system regulation, and host metabolism. Recent studies have highlighted a possible relationship between esophageal cancer and the oral microbiota, making oral microflora a possible risk factor. The bacteria Prevotella intermedia, Tannerella forsythia, Streptococcus sanguinis, and Streptococcus mutans, implicated in various oral pathologies, were of interest in this study, which was initiated to examine their potential role in the etiology of esophageal squamous cell carcinoma (ESCC). To achieve this, a case-control design was used, with whole saliva samples collected from 24 healthy controls and 24 patients with esophageal squamous cell carcinoma. DNA was then extracted, and real-time PCR was performed to quantify the presence of the targeted bacteria in both groups. The results showed that all the bacteria studied were present in the saliva of both patients with ESCC and healthy controls. However, expression levels were significantly higher in patients with ESCC. Specifically, a marked increase in the presence of P. intermedia, T. forsythia, S. sanguinis, and S. mutans was observed in the patients with cancer compared to the healthy controls. In short, this study highlights a significant imbalance in the microbial flora, with an increased abundance of selected bacteria in patients with ESCC. The monitoring of these bacteria could thus be exploited to track patients who are at risk. Their integration into diagnostic and therapeutic strategies would offer new prospects for the early diagnosis and improved prognosis of patients at risk of ESCC. Full article

This study explores the prevalence and antibiotic resistance of urinary tract infections (UTIs) in pregnant women in central Portugal. A retrospective observational study was conducted on 201 positive urine cultures from pregnant women at a hospital center between January 2018 and December 2022. The data collected included age, hospital admission source, history of antibiotic therapy, catheterization status, identity of bacterial isolates, and their antibiotic profile. The most common bacterial strains were Escherichia coli (52.4%) and Streptococcus agalactiae (16.9%). In terms of antibiotic resistance, Escherichia coli demonstrated complete sensitivity to ertapenem, while Streptococcus agalactiae showed sensitivity to four antibiotics, including trimethoprim/sulfamethoxazole. Notably, most infections occurred in the third trimester, underscoring the need for continuous monitoring throughout pregnancy. This study emphasizes the importance of tailored treatment strategies to manage UTIs in pregnancy effectively, reducing the potential maternal and fetal complications. These findings contribute to regional data on UTI management in pregnant populations and aim to support improved healthcare practices. These regional data provide a solid foundation for optimizing healthcare practices in pregnant women, suggesting targeted approaches to combat antibiotic resistance and improve maternal–fetal safety during UTI treatment. Full article

Background: Purple urine discoloration, known as purple urine bag syndrome (PUBS), has various etiologies ranging from benign to serious conditions. We present a case of cefiderocol-induced PUBS and review the literature. Methods: A 56-year-old bedridden patient developed purplish urine discoloration three days after initiating cefiderocol treatment for severe sepsis caused by carbapenem-resistant Acinetobacter baumannii/nosocomialis isolated from an infected sacral pressure ulcer. A comprehensive literature review of PubMed and Google Scholar was performed, with articles screened by two independent reviewers. Results: Our patient’s urine color cleared one day after cefiderocol discontinuation. Eight additional cases of cefiderocol-induced PUBS were identified in the literature. In all reported cases, urine discoloration resolved spontaneously within 1 to 3 days of cefiderocol cessation. Conclusions: Cefiderocol-induced PUBS is being increasingly recognized. While generally benign and self-limiting, it is crucial to exclude other potentially life-threatening diagnoses before attributing PUBS to cefiderocol. Full article

Members of the Dolichocephalovirinae subfamily are giant viruses with an elongated head and a flexible tail that is used to infect Caulobacter strains. In this paper, we describe the isolation and characterization of nine newly isolated phages and present evidence that seven of these phages represent a new Dolichocephalovirinae genus that has significant differences from the four previously described Dolichocephalovirinae genera. In addition, since these new phages were isolated from a single sampling site over the course of three years, a comparison of their genome sequences reveals a low level of within-population diversity resulting from both single-nucleotide polymorphisms and insertions or deletions. A comparison of the host ranges of these phages suggests that differences in host susceptibility may be an important factor in maintaining this diversity. Full article

Background: Aeromonas hydrophila is a key pathogen affecting freshwater fish, including Labeo rohita (rohu), causing significant aquaculture losses. This study explores the role of intimin and invasin, known virulence factors, in A. hydrophila pathogenesis using in silico methods. Methods: We analyzed the distribution of invasin and intimin across 53 A. hydrophila genomes and examined their physicochemical properties, secondary structures, and 3D models. Since crystal structures were unavailable, homology-based modeling was employed to study the structure of rohu β-integrins. In silico docking was performed to explore the interactions between intimin/invasin and β-integrins. Results: Our findings revealed that intimin and invasin were present in only 6 out of the 53 A. hydrophila strains examined, which were designated as hypervirulent strains. The transmembrane regions of intimin and invasin were modeled as β-barrels, a common feature of porins. The in silico docking experiments indicated the significant binding affinity of invasin and intimin with all the β-integrins of rohu fish, suggesting a critical role in host attachment and cellular internalization. Conclusions: This in silico study highlights the pivotal role of invasin and intimin in host tissue’s binding efficacy, offering valuable insights into the binding potential of A. hydrophila across various organs in rohu fish. Full article