Archives of Microbiology最新文献

Typhoid fever, predominantly caused by Salmonella Typhi, remains a significant global health concern and hence requires early-stage diagnosis to control the outbreaks of this pathogen. The currently used methods for detecting Salmonella Typhi require more turnaround time, up to 2–3 days, to yield results due to the requirement of bacterial culture and identification. This study represents the robust and specific detection of Salmonella Typhi using quantitative polymerase chain reaction (qPCR) in clinical and biological samples. Here, we describe the development and validation of a qPCR-based approach that enables the direct detection of Salmonella Typhi within 15 h from the time of blood sample collection. Notably, this method eliminates the requirement for genomic DNA isolation and bacterial culture, thus significantly expediting the diagnostic process. The primer set is specific to the gene CdtB of Salmonella Typhi that amplifies a 154-base pair DNA. Through testing over 100 patient samples, we identified five positive cases of Salmonella Typhi infection, with results corroborated by clinical laboratory records. To ensure the specificity and reliability of the qPCR run, all the experiments were performed in triplicate. Remarkably, the developed primer set can distinctly distinguish between the positive and negative samples. This invention holds a promising alternative to the current diagnostic modalities with a specific diagnosis of typhoid fever.

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Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical nosocomial pathogen with limited therapeutic options. This study aimed to describe clonal relationships among CRAB isolates and genomic insights from representative clusters. A total of 128 non-duplicate CRAB isolates were included in the study. Pulsed-field gel electrophoresis (PFGE) was used to assess clonal relationships and as a preliminary clustering tool for isolate selection. Twelve representative isolates from distinct PFGE clusters were selected for whole-genome sequencing using Oxford Nanopore. Genome assembly, annotation, and comparative analyses were performed using Flye, Prokka, and Roary, respectively. Antimicrobial resistance (AMR) genes, plasmids, insertion sequences, integrons and prophages were identified using the CARD, MOB-suite, ISEscan, IntegronFinder, and PHASTEST tools, respectively. Multilocus sequence typing (MLST) and pangenome analyses were conducted to determine genetic diversity and relatedness among the CRAB isolates. Antibiotic susceptibility testing revealed an extensively drug-resistant phenotype, colistin resistance rate was 23.4%. Mutations in lpxC, lpxD, pmrB, and lpxA were identified in colistin-resistant isolates, suggesting a possible role. Most isolates belonged to the globally disseminated clone ST2_Pasteur, while others were classified as ST636 and ST78. Genomic comparisons identified diverse resistance genes, mobile genetic elements, plasmids, integrons, and virulence factors. Pangenome analysis uncovered a considerable genomic diversity, with 2700 core genes (42.5%) and 3649 accessory genes (57.5%), including 1864 strain-specific (cloud) genes (29.4%) among the isolates. Overall, our findings demonstrate the complex genomic architecture of CRAB and highlight the potential role of genomic surveillance in local infection control.

The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6–24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6–11 months (n = 17) and 12–24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6–84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5–70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.

The classical methods of disinfection such as UV, ozonation, and chlorination have some limitations, including low efficiency of pathogen destruction, high energy requirements, and the creation of disinfection by-products (DBPs). The availability of clean drinking water is one of the great challenges still faced by the world. The discovery of silver nanoparticles, also known as AgNPs, has proven them to be effective antibacterial agents for the long-term disinfection of water. This paper presents the primary mechanisms by which AgNPs inactive pathogens, including membrane disruption, induction of oxidative stress, and disruption of DNA and protein synthesis. AgNPs facilitate rapid and effective microbial inactivation when incorporated into a variety of scaffold systems, including carbon-based materials, hydrogels, foams, and ceramics. particle size, shape, particle concentration, substrate material, water chemistry, flow conditions, and other relevant variables that influence AgNPs efficacy are examined in greater detail. Various important limitations are highlighted, for example, cost, long-term stability, nanoparticle leaching, and potential environmental risks. Finally, recommendations are offered regarding priorities for future research, with attention directed to hybrid disinfection platforms, scalable point-of use technologies, improved immobilization strategies, reduced silver release, and biocompatible designs. In conclusion, silver-based nanoparticles offer a viable path for the development of energy-efficient, safe, and sustainable water disinfection solutions that align with sustainability and global health goals.

The bacterial pathogen Acinetobacter baumannii is an opportunistic and nosocomial causative agent of multidrug resistant infections worldwide. The present study conducted comparative genomic analyses to identify relevant pathogenicity traits in A. baumannii strains from diverse clinical samples and geographical regions in Mexico. Pangenome analysis clustered the strains into four phylogenomic clades, comprising various international clones. Clades I and II strains, predominantly from blood and respiratory infections in the Central region, were significantly associated with the Latin American IC5 clone (P = 0.0002), whereas clade III strains, primarily from diverse samples in the Northwestern region, were significantly associated with the European IC2 clone (P = 0.0030). Virulence determinants implicated in adhesion (ompA, omp38), biofilm formation (pgaA-D, csuA/BABCDE), motility (pil, fim), regulatory systems (bfmRS, barAB, abaR/abaI), iron acquisition (bas, bau), and efflux pump-delivery systems (adeFGH) were identified among the A. baumannii strains, representing all clades and geographical regions. Analysis of intrinsic and acquired antimicrobial resistance revealed that clades I and II strains were significantly correlated with resistance to β-lactamases (blaADC-6, blaOXA-239, blaOXA-65), sulfonamides (sul2), and chloramphenicol (cmlB1) (P = 0.0001). Interestingly, clade III strains, predominantly from the agricultural Northwestern region, exhibited a significant association of broader resistance genes against aminoglycosides (aac(6’)-Ib’, aph(3’)-Ia, armA, aadA), β-lactamases (blaTEM-4, blaADC-25, blaOXA-66), sulfonamides (sul1), tetracyclines (tetA), and macrolides (mphD, msrE) (P = 0.0001). Subsequent characterization of mobile genetic elements indicated genetic plasticity and potential transfer of antimicrobial resistance. Collectively, this fundamental information would enable the improvement of epidemiological surveillance and intervention strategies for A. baumannii.

Antimicrobial resistance (AMR) in Acinetobacter baumannii represents a critical global health challenge, particularly in intensive care settings where the pathogen causes severe, refractory infections. As a leading member of the ESKAPE group, A. baumannii has accumulated extensive resistance to multiple antibiotic classes, including carbapenems, resulting in the widespread emergence of multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan-drug-resistant (PDR) strains. This review provides a chronological overview of the evolution of antimicrobial therapies used against A. baumannii, spanning the early era of penicillins and tetracyclines to contemporary agents such as eravacycline and ceftazidime–avibactam. We delineate the molecular mechanisms underlying resistance development, including carbapenemase production, robust RND efflux systems, horizontal gene transfer, biofilm formation, and the global dissemination of high-risk international clones (IC1–IC9). The compounding impact of the COVID-19 pandemic on the spread of carbapenem-resistant A. baumannii (CRAB) is also examined. A special emphasis is placed on Zosurabalpin, a first-in-class macrocyclic peptide antibiotic with a unique mechanism of action that targets the LptB₂FG complex essential for lipooligosaccharide (LOS) transport and outer membrane assembly. Preclinical data and emerging clinical findings highlight its potent activity against highly resistant CRAB strains and its ability to circumvent conventional resistance pathways, marking it as a promising candidate in the antimicrobial pipeline. Finally, we evaluate the limitations of current treatment modalities and explore emerging strategies, including phage therapy, novel target discovery, and non-traditional therapeutics, offering a forward-looking perspective on restoring and sustaining effective anti-Acinetobacter interventions.

Probiotics are live microorganisms that confer health benefits when administered in adequate amounts, enhance immune function, promote gut health, and are increasingly recognized as effective alternatives to antibiotics for improving animal health and productivity. This study investigated the probiotic potential of lactic acid bacteria (LAB) from Mystus cavasius through morphological, physiological, and molecular characterization for aquaculture feed applications. Out of twenty-two presumptive LAB isolates, eleven were sequenced after biochemical screening, and molecular analysis confirmed eight as LAB (Weisella confusa ML1, ML2, ML3, ML6, ML7; Enterococcus faecalis ML8, ML9; Lactococcus garvieae ML10). The study also found a potential non-LAB probiotic bacterium Bacillus subtilis ML4. Moreover, the study identified Paraburkholderia phytofirmans, a potential plant probiotic bacterium, for the first time in fish. Among the identified LAB isolates, L. garvieae ML10 was excluded from probiotic potential assessments because of its reported disease-causing potential and associated health risks. All the tested LAB isolates were found to tolerate acidic pH (2–5) and bile salts (2.5–7.5%), indicating their probiotic potential for aquaculture applications. Additionally, the isolates showed no hemolytic activity and demonstrated strong probiotic potential, characterized by high cell surface hydrophobicity, ranging from 41.98 ± 16.68% to 62.19 ± 4.09% in xylene and 51.58 ± 1.67% to 64.83 ± 4.91% in toluene, robust autoaggregation (55.51 ± 3.63% to 64.33 ± 2.87%) and substantial coaggregation with Staphylococcus haemolyticus (46.27 ± 2.96% to 53.54 ± 0.72%) and Bacillus cereus (34.34 ± 3.16% to 51.76 ± 4.08%). Furthermore, they exhibited potent in vitro inhibitory effects against the fish pathogens Aeromonas veronii and L. garvieae and revealed susceptibility to several commonly used antibiotics. Therefore, the results revealed that the selected LAB isolates might be ideal probiotic candidates to be used in sustainable aquaculture practices.

Resorcine-based macrocycles have received significant attention in drug delivery applications owing to their tunable functional groups, well-defined cavities, and inherent self-assembly behavior, considering essential for encapsulation and controlled release of loaded drug candidates. However, existing resorcinarene derivatives face certain limitations in drug loading, physiologic stability, and compatibility with structurally complex natural therapeutics, necessitating the development of novel macrocyclic architectures with improved stability and compatibility for hydrophobic drugs. To address this gap, the current research synthesized a novel resorcinarene-based macrocycle, referred to as Indole Macrocycle (IM), to improve the therapeutic potential of quercetin (QTN). The synthesized IM was characterized utilizing Mass, ¹H- and ¹³C-NMR, and FT-IR spectroscopy. Biocompatibility studies indicated high cell viability of NIH-3T3 cells at 30 µM (95.72 ± 0.4% at 24 h and 94.10 ± 0.3% at 48 h) and low hemolytic activity (9.32% ± 1.65% at 1000 µg/mL). The critical micelle concentration (CMC) of IM was determined to be 0.022 mM. QTN-loaded IM vesicles exhibited a spherical morphology with a size of 248.7 ± 7.17 nm, zeta potential of − 15.8 ± 0.8 mV, PDI of 0.258 ± 0.05, and encapsulation efficiency of 74 ± 2.57%, while demonstrating a controlled drug release profile, with maximum release of 69% ± 1.8% over 48 h. Antibacterial evaluation against multidrug-resistant S. aureus strains (NCTC 13143 and NCTC 13277) revealed a significantly reduced MIC of 170 ± 8.23 µg/mL compared to 488 ± 9.53 µg/mL for free QTN. The results were further confirmed through AFM analysis, demonstrating significant bacterial membrane disruption following treatment. These findings revealed that QTN-loaded IM vesicles are a promising system for improving drug delivery and combating MDR bacterial infections.

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Alcanivorax borkumensis is a key marine hydrocarbon-degrading bacterium with the potential to clean up oil spills from the sea and protect marine ecosystems. The accidental release of crude oil and other oil products is a major concern for the environment, as it has detrimental effects on marine life. Several strains of A. borkumensis have been isolated from a variety of different marine habitats, such as temperature, deep-sea and polar regions, with pathways of alkane degradation, as well as strain-specific genetic adaptations in the areas of hydrocarbon use, nutrient uptake, and resistance to adverse environmental conditions. Among these, A. borkumensis SK2 strain has been widely characterised as the model organism, giving extensive information on the genomic, metabolic, and physiological foundations of efficient alkane degradation. The genetic features of SK2 help explain its efficiency towards biodegradation and its overall contribution towards environmental recovery following hydrocarbon contamination. This article is a review of the current knowledge on the ecological importance, genetic structure, and biodegradation of the alkane hydroxylase-containing A. borkumensis, focusing on alkane hydroxylase systems, biosurfactant synthesis, biofilms and nutrient scavenging probability. These findings highlight the potential of increasing Alcanivorax catabolic activities in the wake of an oil spill to mitigate the environmental disaster effects. Further functional analysis of the genes and proteins of A. borkumensis is essential for achieving its biotechnological and ecological potential in marine hydrocarbon remediation.

Vancomycin is a critical glycopeptide antibiotic for treating severe infections caused by Gram-positive bacteria, particularly MRSA and Clostridioides difficile, by inhibiting cell wall synthesis through binding to D-Ala–D-Ala termini of peptidoglycan precursors. Resistance has emerged in Enterococcus spp (VRE) and Staphylococcus spp, (VISA/VRSA) through acquisition of van operons, precursor modification (D-Ala-D-Lac/D-Ser), cell wall thickening, biofilm formation, and regulatory mutations, leading to treatment failures and increased morbidity. Global genomic surveillance reveals ongoing clonal expansion and horizontal spread of resistance determinants. This review comprehensively examines vancomycin’s mechanism of action, the evolutionary emergence and genetic basis of resistance, adaptive survival strategies of pathogens, clinical/epidemiological consequences, current alternative therapies, and precision stewardship approaches including area under the concentration–time curve/minimum inhibitory concentration (AUC/MIC)-guided therapeutic drug monitoring (TDM). Most importantly, it highlights the transformative and still under-appreciated role of artificial intelligence in overcoming vancomycin resistance: machine learning accelerates discovery of novel antimicrobial peptides and repurposed drugs, AI-driven surveillance enables real-time resistance detection and outbreak forecasting, and hybrid AI-molecular modeling rationally designs superior vancomycin derivatives with enhanced activity against VRE and VRSA. These rapidly evolving AI-integrated strategies, when combined with strengthened infection control and stewardship, offer the most promising path forward to preserve and extend the clinical utility of vancomycin and related antibiotics.