Search Results (4,592)

Kindergarten environments combine high microbial exposure with increased immunological vulnerability, yet antibiotic resistance genes (ARGs) in kindergarten dust remain poorly characterized. This systematic review synthesized evidence on the occurrence and potential health relevance of ARGs in kindergarten dust. Following PRISMA 2020 guidelines, PubMed, Scopus, and Web of Science were searched. Four studies from China, Hong Kong, and Norway (2018–2024) met the inclusion criteria. ARGs were detected in all kindergarten dust samples, indicating that dust is a consistent reservoir of antibiotic resistance determinants. A consensus resistome (classes detected in ≥2 studies) encompassed sulfonamide, macrolide–lincosamide–streptogramin B (MLSB), tetracycline, beta-lactam, aminoglycoside, and multidrug resistance genes; beta-lactam resistance genes were the only class reported in all four studies. Clinically important ARGs associated with last-resort antibiotics, including mecA, vanA, bla_NDM, and mcr-5, were reported in three studies. Class 1 integron-integrase genes (intI1) frequently co-occurred with ARGs, suggesting potential horizontal gene transfer. Limited evidence indicated higher ARG abundance in urban and winter samples. One study reported antibiotic-resistant bacteria carrying resistance markers concordant with those in kindergarten dust in the urine of children attending the same facilities; however, this cross-sectional, single-site evidence is consistent with, but not sufficient to establish, a dust-to-child exposure pathway. The available evidence supports the plausibility that kindergarten dust may contribute to children’s exposure to ARGs and ARG-carrying bacteria, but current studies do not establish causal transmission from dust to child colonization or infection. Standardized monitoring and longitudinal studies are needed to assess health risks and guide mitigation strategies in early childhood educational settings. Full article

The continuous slowdown in the research and development of new antibiotics and antibiotic overuse have turned the problem of antibacterial resistance into a global public health crisis. As a very promising alternative to multi-drug-resistant bacterial infection, phage therapy is receiving renewed attention. However, the inherent biological limitations of natural phages restrict their extensive clinical application. This review examines how synthetic biology can be harnessed to transform phages and to build the next generation of antibacterial therapies. We outline the main advantages of natural phages, including high host specificity, self-amplification, bactericidal activity and the ability to degrade biofilms. We also point out the bottlenecks of clinical applications of bacteriophages, such as narrow host range, rapid removal in the body and potential genetic safety risks. Moreover, we elaborate on the core synthetic biological tools used to overcome the above limitations, including CRISPR-Cas gene editing, receptor-binding protein reprogramming, functional load delivery and immunogenic regulation, and summarize the recent clinical progress and personalized treatment process. The increasing clinical evidence shows that synthetic biology can effectively overcome the inherent defects of natural bacteriophages, confirming the safety and initial efficacy of bacteriophage therapy. Engineered phages provide a practical strategy to meet the antimicrobial resistance challenge. Clinical applications of such phages will mainly depend on progress in production standardization, regulatory framework construction and scientific and reasonable joint treatment program development. Full article

Understanding the functional potential of the gut microbiota for carbapenem-resistant Enterobacterales (CRE) decolonisation is essential for developing novel non-antibiotic strategies to promote their clearance. In a previous study, we identified distinct taxonomic signatures associated with spontaneous CRE decolonisation (DeCol). Here, we aimed to determine whether these taxonomic differences were accompanied by differences in the predicted functional potential of the gut microbiota. Patients were identified from a database of individuals colonised with CRE. We performed Illumina shotgun metagenomic sequencing on 14 persistent CRE carriage (Col) and 23 DeCol patients with OXA-48-producing isolates. Bioinformatic analysis was performed using SqueezeMeta and differential abundance of functional and metabolic genes was assessed using DESeq2. Several antimicrobial resistance genes, including blaOXA-48, were underrepresented in DeCol patients. In contrast, DeCol patients showed an overrepresentation of genes associated with motility, regulated adhesion, short-chain fatty acid (SCFA)-related pathways and alternative carbohydrate metabolism. These orthologue enrichment patterns are consistent with functions previously linked to intestinal homeostasis in the literature. Conversely, Col patients exhibited an overrepresentation of genes associated with redox defence, biofilm formation and amino acid metabolism, suggesting distinct predicted functional profiles between persistent carriage and spontaneous decolonisation. Spontaneous CRE decolonisation was associated with distinct KEGG-based functional signatures and a lower abundance of antimicrobial resistance determinants. These functional profiles were consistent with the taxonomic differences previously identified in the same cohort and generate hypotheses regarding microbiome functions that may contribute to colonisation clearance. Because these findings are based on gene-content analysis, they reflect predicted functional potential rather than direct evidence of metabolic activity. Further multi-omics and experimental studies are required to validate these observations. Full article

Post-weaning diarrhea caused by pathogenic Escherichia coli is a significant economic challenge in global swine production. Rising antimicrobial resistance linked to traditional antibiotics necessitates safe, sustainable alternatives. This study isolated and characterized host-associated Bacillus species from the gastrointestinal tracts of healthy pigs to evaluate their probiotic potential. Fifty-nine Bacillus isolates were screened for safety, gastrointestinal tract survivability, mucosal adhesion, and antimicrobial efficacy. Several isolates demonstrated robust tolerance to simulated gastrointestinal stress (acidic pH and bile salts), non-hemolytic profiles, and strong mucosal adhesion. Multiple isolates displayed inhibitory activity against pathogenic Escherichia coli in vitro. The most promising candidate, Bacillus subtilis 1BP1Co1, underwent Nanopore whole-genome sequencing. Genomic profiling confirmed its safety, revealing a complete absence of known virulence factors and high-risk antimicrobial resistance genes. Furthermore, genome annotation identified multiple biosynthetic gene clusters responsible for the production of antimicrobial secondary metabolites, including surfactin, fengycin, bacillaene, and subtilosin A, which mechanistically supports its pathogen-inhibitory properties. Collectively, these findings highlight indigenous Bacillus strains, particularly Bacillus subtilis 1BP1Co1, as promising probiotic candidates with the potential to be developed to mitigate Escherichia coli-associated enteric disorders in swine production systems. Full article

The ban on antibiotic growth promoters in livestock production has created an urgent demand for safe and effective probiotic alternatives derived from indigenous animal microbiota. Here, we isolated Enterococcus hirae HI3 from Hu sheep jejunum and confirmed its species assignment via whole-genome sequencing, with ANI analysis showing 98.92% identity to the E. hirae reference genome. HI3 showed moderate acid tolerance, with survival rates of 19.31% (95% CI: 15.83–22.78%) at pH 2 and 18.40% (95% CI: 17.87–18.94%) at pH 3 after 4 h, and maintained > 50% survival in 2% bile salts. It was susceptible to penicillin, ampicillin, erythromycin, and chloramphenicol. No hemolytic activity was observed, and major enterococcal virulence genes (gelE, cyl, esp, hyl) were absent from the HI3 genome. The HI3 genome (3.06 Mb) consists of one circular chromosome and three circular plasmids. Functional annotation identified 229 carbohydrate metabolism genes (including 65 glycoside hydrolases) and 43 probiotic-related genes involved in acid tolerance (atpA–G, nhaC), bile salt tolerance (cbh), stress responses (clp family, groEL, dnaK, cspA, sod2), and adhesion (ltaS, srtA, eno, epsA). Multiple bacteriocin biosynthetic gene clusters (enterolysin A, class II lanthipeptide, etc.) were identified. Plasmid-borne tetracycline resistance genes tet(M) and tet(L) were detected; however, their functional transferability requires experimental validation. No other known transferable resistance determinants were identified in the genomic analysis. These in vitro and genomic findings represent an initial characterization of E. hirae HI3 and support its potential as a ruminant probiotic candidate. However, in vivo studies are required to validate its colonization capacity, safety, and efficacy in the target ruminant species. Full article

The present study was performed to determine the antibiotic resistance genes (ARGs), virulence determinants, and mobile genetic elements in multidrug-resistant Escherichia coli CUK-76 isolated from wastewater in Himachal Pradesh, India. Whole genome sequencing was performed using the Illumina Miseq system, and the draft genome sequence was assembled by Unicycler v0.5.1 and annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP v6.10). The bioinformatics-based prediction analysis was performed using ResFinder v4.7.2 and CARD v4.0.1 (antibiotic resistance genes), VirulenceFinder v2.0, VFDB and MGEFinder v1.0.3 (virulence determinants), PlasmidFinder v2.0.1 (plasmid sequences), MLST v2.0 (sequence type), ISFinder and TnCentral v2.0 (insertion sequences and transposons), PathogenFinder2 v0.6.0 (pathogenicity), RAST (subsystems category) and Phigaro (prophage sequences). The draft genome of E. coli CUK-76 strain comprised 4,607,136 bp with a GC content of 51%. Genome annotation revealed 4498 genes of which 4289 were protein-coding genes, 78 RNA genes, and 131 pseudogenes. It was related to sequence type ST949 and its predicted resistome consisted of bla_CTX-M-15, bla_TEM-1B (class A β-lactamase genes), bla_EC-14 (class C β-lactamase gene), aph(6)-Id, aph(3″)-Ib, qnrS1, sul2, tet(A), and dfrA14 genes. Additionally, multiple virulence genes, two plasmid sequences viz. IncFIB(K) and IncFIB(AP001918), insertion sequences, transposons and prophage sequences were detected. The genomic dataset of this strain will be a valuable resource for comparative genomic studies on E. coli. Full article

Antimicrobial resistance (AMR) is a major public health concern, and wastewater monitoring can complement clinical surveillance by capturing resistance signals at the population level. This exploratory study assessed selected antibiotic-resistant bacteria and antimicrobial resistance genes (ARGs) in untreated influent wastewater from the municipal wastewater treatment plant of Patras, Greece. Escherichia coli, Pseudomonas aeruginosa, and Enterococcus spp. were isolated using culture-based methods, tested for antimicrobial susceptibility by disk diffusion and Etest according to EUCAST epidemiological cut-off values, and screened by real-time PCR for intI1, sul1, qnrS1, blaTEM, blaVIM, vanA, and ermB. Among 16 E. coli isolates, non-wild-type (non-WT) profiles were detected on 14/16 for meropenem and 15/16 for ciprofloxacin, whereas only 1/16 was non-WT for ampicillin. All 13 P. aeruginosa isolates were wild type (WT) for meropenem but non-WT for ciprofloxacin, while all 17 Enterococcus spp. isolates were WT for vancomycin and ampicillin. Molecular screening showed that blaTEM was the most frequently detected gene in E. coli, while intI1 and sul1 were detected in subsets of P. aeruginosa isolates. No targeted ARGs were detected in Enterococcus spp. These findings provide preliminary, site-specific baseline information on selected AMR phenotypes and genetic determinants in wastewater-derived bacterial isolates from Patras. Full article

This study evaluated the potential of synergistically degraded low-molecular-weight chitosan (LMW-CS) as a functional feed additive to promote growth, antioxidant capacity, innate immunity, and disease resistance in Pacific white shrimp (Litopenaeus vannamei). High-molecular-weight chitosan (HMW-CS, approximately 85 kDa) was degraded using γ-irradiation in combination with H₂O₂ to produce LMW-CS with improved functional properties. Shrimp were fed five experimental diets for 4 weeks: a control diet, HMW-CS0.4 (0.4% w/w), LMW-CS0.1 (0.1% w/w), LMW-CS0.2 (0.2% w/w), and LMW-CS0.4 (0.4% w/w). Growth performance, oxidative stress markers, antioxidant enzyme activities, lysozyme activity, immune-related gene expression, bacterial load, and survival after Vibrio parahaemolyticus challenge were evaluated. The results indicate that dietary LMW-CS supplementation improved growth performance and feed utilization, with LMW-CS0.2 showing significantly higher final weight, total weight gain, and average daily gain than the control group (p < 0.05). Antioxidant assays showed that LMW-CS reduced malondialdehyde levels and increased reduced glutathione, nitric oxide, glutathione reductase, catalase, superoxide dismutase, glutathione peroxidase, and glutathione-S-transferase activities in both plasma and hepatopancreas (p < 0.05). Lysozyme activity was significantly enhanced, particularly in the LMW-CS0.4 and HMW-CS0.4 groups (p < 0.05). Gene expression analysis revealed upregulation of genes associated with growth regulation, antimicrobial defense, pathogen recognition, and prophenoloxidase activation, including igf2, cstn, lgbp, lyz, and propo2. Gut microbiota profiling showed that chitosan supplementation altered bacterial community composition, reduced the relative abundance of some Vibrio-associated taxa, and descriptively lowered predicted pathogenic and stress-tolerant bacterial phenotypes. Following the Vibrio parahaemolyticus challenge, shrimp fed LMW-CS0.4 showed the lowest bacterial load and highest survival rate, indicating improved disease resistance (p < 0.05). Overall, synergistically degraded LMW-CS enhanced growth, redox balance, innate immune competence, gut microbial structure, and resistance to V. parahaemolyticus, supporting its potential as an antibiotic-free functional feed additive for sustainable shrimp aquaculture. Full article

Shiga toxin-producing Escherichia coli (STEC) contamination and proliferation in aquaculture and aquatic systems is worrisome for global food safety, as well as veterinary and public health. Traditionally linked with terrestrial ruminant reservoirs, aquaculture matrices, including farmed finfish, shellfish, culture water, and benthic organisms, are increasingly acknowledged as potential conduits for the dissemination of STEC. Herein, the review documented data concerning the prevalence, genomic composition, and ecological dynamics of STEC across various aquaculture environments across different regions of the globe. As a result, the persistence of virulence-associated genes (VAGs) and antibiotic-resistant genes (ARGs) in STEC within the aquaculture supply chain presents a considerable risk to global food security and public health, highlighting the urgent necessity for comprehensive “One Health” surveillance frameworks aimed at alleviating aquatic biosecurity challenges. Full article

Recent research has demonstrated the important role of hydrogen sulfide (H₂S) and its derivatives, reactive sulfur species (RSS), as modulators of various redox-regulated physiological processes in bacteria. Bacterial cells are equipped with enzymes that synthesize and catabolize H₂S and RSS, and sensors that control the expression of genes whose products ensure the maintenance of safe levels of these compounds in cells and the survival of bacteria in the host environment. With the rapid growth of resistant pathogens, the impact of H₂S and RSS on bacterial virulence and antibiotic sensitivity is attracting increasing attention. The possibility of enhancing the efficacy of widely used antibiotics by artificially modulating H₂S levels is being explored. This review summarizes current data on the sources and conditions of endogenous H₂S and RSS production, the molecular mechanisms of action of various concentrations of exogenous and endogenous H₂S, and the regulatory factors that control the expression of virulence and antibiotic resistance genes. Possible reasons for the conflicting results obtained by different research groups regarding the possibility of modulating bacterial sensitivity to antibiotics by altering the production of endogenous H₂S are discussed. Full article

Background: The spread of extended-spectrum β-lactamase-producing Klebsiella is an emerging public health concern presenting severe clinical impacts. This problem is particularly severe in developing countries where irrational use of antibiotics makes the treatment of such infections more challenging. Methods: In this cross-sectional study, we investigated antibiotic resistance among clinical Klebsiella pneumoniae isolates from 256 patient specimens from Al-Diwaniyah hospitals, using standard microbiological methods followed by PCR. Antimicrobial susceptibility testing identified resistance rates and proportions of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Carbapenemase genes were detected by multiplex PCR and sequencing. Mutations were characterized, and their functional significance was predicted using in silico prediction tools. Results: Fifty Klebsiella pneumoniae isolates were recovered, exhibiting high resistance rates (42–100%) to penicillins, cephalosporins, fluoroquinolones and carbapenems, with 62% classified as MDR and 38% as XDR. Carbapenemase genes were highly prevalent (blaOXA-48 56%, blaIMP 44%, blaVIM 30%, blaKPC 28%, blaNDM 26%), with 60% of isolates co-harbouring ≥ two genes. Most mutations were predicted to be structurally tolerated, while active-site-proximal substitutions (H120L in NDM-52 and V120L in OXA-48) were predicted to affect enzyme activity. However, docking analysis suggested no significant alteration in carbapenem binding affinity. Conclusions: Our results highlight a very high prevalence of MDR/XDR Klebsiella pneumoniae, associated with diverse carbapenemase genes and resistance-related polymorphisms that may indicate potential functional impacts. To the best of our knowledge, this is the first study in Iraq to combine carbapenemase gene mutation analysis with structural modelling and molecular docking. This study emphasizes the urgent need for effective antimicrobial resistance surveillance in Iraq. Full article

The use of invertebrates for sewage sludge bioconversion offers a sustainable strategy for waste valorization, yet species-specific effects on microbial communities and biosafety remain unclear. Here, we compared the impacts of the earthworm Eisenia andrei (Ea) and the mealworm Tenebrio molitor (Tm) on the bacteriomes and mycobiomes of sewage sludge (ss) using 16S rRNA and ITS amplicon sequencing. Gut passage in both Ea and Tm markedly altered bacterial and fungal composition relative to ss, but produced distinct community profiles with differential shifts across multiple taxa. Both invertebrates reduced bacterial richness by ~40%, while fungal responses diverged: Ea largely preserved mycobiome richness despite reduced evenness, whereas Tm caused a near-complete collapse (~83% Amplicon Sequence Variant loss). Beta diversity analyses revealed clear, non-overlapping separation among ss, Ea, and Tm for both microbial domains. Tm frass showed strong enrichment of clinically relevant bacterial pathogens, while Ea casts exhibited no such enrichment. For fungi, Ea reshaped pathogen composition, whereas Tm largely eliminated fungal pathogens through broad community collapse. Both treatments reduced predicted antibiotic resistance gene abundance, but functional profiles differed, with Ea showing greater functional stability. These findings demonstrate that microbiome restructuring during bioconversion is species-dependent, with contrasting ecological and biosafety implications for downstream environmental use. Full article

Multidrug-resistant (MDR) Salmonella Typhimurium, largely spread through poultry products, increasingly resists antibiotic treatment. We evaluated dietary pomegranate peel extract-loaded nano-emulsions (PomNEs) on performance, immunity, antioxidant capacity, and S. Typhimurium resistance in laying hens. A total of 250 15-week-old Hy-Line Brown hens received a basal diet or diets supplemented with PomNEs at 0.3, 0.6, or 1.2 g/kg, and then were challenged with S. Typhimurium at 34 weeks. Hens fed PomNEs, especially PomNEs1.2, showed improved egg production and feed efficiency before challenge and restored normal output afterward. Supplementation reduced Salmonella colonization in the ovaries, liver, and eggs, with considerable reduction in eggs and ovaries at the highest dose by ten weeks, and down-regulated bacterial virulence genes (hilA, invA). Immune function improved through higher phagocytic activity, intracellular killing, and lysozyme levels, lower nitric oxide, up-regulated IgA and β-defensins (AvBD6, AvBD12), and suppressed pro-inflammatory cytokines and chemokines. Intestinal and ovarian redox balance improved via reduced COX2 and elevated GPX-1, HO-1, NQO1, SOD-1, and CAT expression. These benefits support PomNEs as promising natural feed additives to enhance laying performance, antioxidant defense, and immunity against salmonellosis, offering a sustainable strategy for supporting disease control in poultry production. Full article

Colistin (polymyxin E), a last-resort antibiotic for the treatment of multidrug-resistant Gram-negative bacterial infections, is becoming increasingly compromised by the rapid emergence and dissemination of resistance. The extensive use of colistin in agriculture and veterinary medicine has accelerated the spread of plasmid-mediated mobile colistin resistance (mcr) genes, facilitating transmission across human, animal, and environmental reservoirs. This review provides a comprehensive overview of the epidemiology, molecular mechanisms, and geographical distribution of colistin resistance in the Middle East and North Africa (MENA) region. Analysis of the available literature indicates that Tunisia reports the highest prevalence of colistin-resistant Gram-negative bacteria in North Africa (58.09%), followed by Egypt (24.76%), Algeria (14.29%), and Libya (2.86%). Across the region, mcr-1 is the predominant plasmid-mediated resistance determinant, whereas chromosomal alterations involving the mgrB, pmrA/pmrB, and phoP/phoQ regulatory systems are the principal non-plasmid-mediated mechanisms. Resistance has been documented in major clinical pathogens, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa, as well as in livestock, poultry, aquaculture, wildlife, food products, and environmental samples, highlighting the interconnected nature of resistance transmission under a One Health framework. The evidence demonstrates substantial geographical variability and significant gaps in surveillance across several MENA countries, limiting accurate regional burden estimates. Strengthening antimicrobial stewardship, harmonized surveillance programs, molecular monitoring of resistance determinants, and the implementation of One Health strategies are essential to limit the continued emergence and dissemination of colistin resistance throughout the region. Full article

The increased occurrence of tetracycline resistance (conferred by the tet(X3)/tet(X4) resistance genes) poses a major challenge to the clinical treatment of infections using tetracyclines, including tigecycline, which is the “last-resort” therapeutic agent. Thus, there is an urgent need to develop inhibitors targeting Tet(X3)/Tet(X4) to address the crisis of tetracycline resistance. This study revealed that quercetin is an inhibitor of Tet(X3)/Tet(X4), which, when combined with different tetracyclines, can exert synergistic growth-inhibitory effects against Tet(X3)/Tet(X4)-positive bacteria (fractional inhibitory concentration < 0.5). Quercetin + tigecycline significantly decreased the biofilm-forming ability of bacteria. Mechanistic investigations revealed that quercetin inhibits the catalytic activity of Tet(X4) against tetracycline antibiotics by binding to the catalytic active site. In the Galleria mellonella larval infection model of Tet(X4)-positive E. coli J53p47EC or Tet(X4)-negative E. coli J53, tigecycline + quercetin enhanced the survival rate, decreased melanization, and suppressed bacterial load. Thus, the findings of this study will enable the development of novel Tet(X3)/Tet(X4)-targeted therapeutic strategies for clinical infections caused by drug-resistant Enterobacteriaceae and Acinetobacter baumannii, especially Tet(X3)/Tet(X4)-positive pathogens. Full article