Search Results (4,500)

Plateau waters in Northern Sichuan, China, act as critical headwaters of the Yellow River. Microbial communities in water bodies and soil matrices within this region are increasingly pressured by intensive animal rearing; yet few studies have characterized microbial shifts across entire riverine niches. In this study, we employed next-generation sequencing based metagenomics to investigate microbial features, community structure and diversity, metabolic potentials, and antibiotic resistance genes (ARGs) in the Baihe River, a tributary in the source region of the Yellow River. Sampling locations covered the main stem and three tributaries of the Baihe River, spanning from its source, through upstream and downstream segments, to the convergence site with the main stem of the Yellow River. Results revealed that Pseudomonadota and Bacteroidota were the most abundant phyla. The relative abundance of most taxa at multiple taxonomic levels exhibited an increasing trend along the river continuum driven by rising total nitrogen (TN) and total phosphorus (TP) concentrations; however, a notable exception occurred at BH1 (the Baihe source), where the abundance of numerous taxa was markedly higher than in downstream samples. We detected abundant ARGs predominantly associated with antibiotic resistance. Furthermore, prevalent viruses affiliated with the phyla Uroviricota and Nucleocytoviricota, together with pathogenic bacteria, were identified as etiological agents of diverse infectious diseases. This study provides novel perspectives for managing aquatic contamination in plateau river ecosystems by linking environmental variables, microbial succession, and resistome distribution. Full article

Tropical coastal waters are increasingly recognized as critical reservoirs for virulent, antibiotic-resistant enteric pathogens, yet seasonal dynamics governing their spatial distribution remain poorly characterized. We hypothesized that hydrological shifts and anthropogenic nutrient enrichment drive the seasonal distribution, virulence profiles, and antimicrobial resistance (AMR) of Escherichia coli, Salmonella spp., and Shigella spp. in the Jaffna Peninsula, Sri Lanka. Across 25 coastal sites during dry and transitional seasons, we integrated physicochemical water quality assessment, culture-based enumeration, PCR-based virulence gene profiling, Minimum Inhibitory Concentration (MIC) assays, GIS mapping, and statistical analyses. Key water quality parameters, including ammonium, nitrite, and total phosphorus, showed significant seasonal variation (p < 0.05), reflecting distinct hydrological regimes across seasons. A total of 220 E. coli, 200 Salmonella spp., and 100 Shigella spp. isolates were examined for virulence gene profiles and antibiotic tolerance. E. coli was detected at 80–88% of sites, Salmonella spp. at 72–88%, and Shigella spp. at 32–48%. Among E. coli isolates, stx1 was detected at 20–28% of sites and eae at 16% across both seasons. The stn gene was detected in Salmonella spp. at 12–28% of sites seasonally. Virulence profiling confirmed STEC harbouring stx1, stx2, and eae; Salmonella spp. carried stn; and Shigella spp. possessed invasion-associated genes. Trimethoprim–sulfamethoxazole resistance was recorded in 63.2% of E. coli, 33.0% of Salmonella spp., and 31.0% of Shigella spp. isolates at the lowest tested concentration of 4 µg/mL., while ciprofloxacin and piperacillin–tazobactam retained greater efficacy. Correlation analyses revealed significant associations among faecal contamination, nutrient enrichment, and virulence gene prevalence, implicating untreated sewage discharge and eutrophication as likely ecological factors associated with pathogen occurrence. These findings designate the Jaffna coastal zone as a significant reservoir of virulent AMR enteric pathogens, underscoring the urgent need for integrated One Health surveillance and seasonally adaptive coastal water quality management. Full article

The management of livestock manure is associated with substantial ammonia (NH₃) emissions and the accumulation of emerging contaminants, including antibiotics, antibiotic resistance genes (ARGs), and microplastics, posing risks to environmental quality and public health. Biochar has emerged as a promising strategy for mitigating gaseous emissions and reducing contaminant mobility during manure storage and composting processes. This review synthesizes recent research on the application of biochar in livestock manure management systems, focusing on NH₃ emissions, antibiotic degradation, ARG reduction, and microplastic removal. Particular attention is given to the effectiveness of biochar in mitigating pollutants during manure storage, housing operations, and composting processes. Across the literature, reported NH₃ mitigation efficiencies vary widely, from negligible effects to reductions exceeding 90–97%, depending on feedstock type, pyrolysis conditions, particle size, and application strategy. Biochar also promotes antibiotic degradation and ARG mitigation, with reductions of up to 98% reported in composting systems. Emerging evidence further suggests that biochar can reduce microplastics by approximately 15–64% in sludge composting. Plant-derived and chemically modified biochars generally outperform manure-derived biochars due to higher surface area, cation exchange capacity, and greater abundance of functional groups. The review highlights that activation treatments, co-composting strategies, and microbial interactions are key factors controlling pollutant mitigation efficiency. Despite promising outcomes, large-scale application remains limited by economic constraints, variability in biochar properties, and the lack of long-term field-scale validation. Future research should prioritize standardized production protocols, field implementation studies, and integrated environmental and economic assessments to support the practical adoption of biochar in sustainable livestock waste management systems. Full article

Background/Objectives: Antimicrobial resistance in pediatric infections presents a worsening global public health challenge, with antimicrobial resistance (AMR) accounting for more than one million deaths annually and disproportionately affecting children younger than 5 years of age. Neonates and critically ill children face heightened risk owing to immature immunity, frequent healthcare exposures, and limited therapeutic options. This review synthesizes evidence on the epidemiology, mechanisms of resistance, clinical outcomes, and management of AMR across the full pediatric age range. Methods: PubMed/MEDLINE and Google Scholar were searched for literature from 2014 to 2026 using terms covering antibiotic resistance, pediatric populations, and key pathogens. Approximately 1840 records were screened; 69 sources met all inclusion criteria. A narrative synthesis approach was used, given heterogeneity across study designs and outcomes. Results: Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, carbapenem-resistant pathogens, and methicillin-resistant Staphylococcus aureus drive substantial morbidity and mortality in children. Approximately one in five pediatric Gram-negative bloodstream isolates are resistant to third-generation cephalosporins, a phenotype independently associated with a roughly three-fold increase in adjusted mortality. Carbapenem-resistant Klebsiella pneumoniae bacteremia carries a 30-day mortality approaching 40%, and isolates in low- and middle-income countries (LMICs) frequently harbor multiple resistance genes. Pneumococcal conjugate vaccine implementation was associated with absolute reductions of 7–11% in the proportion of pediatric pneumococcal isolates that were penicillin-non-susceptible or penicillin-resistant, largely by preventing infections caused by resistant serotypes and by reducing antibiotic selection pressure, rather than through a direct effect on resistance mechanisms; global AMR mortality in children younger than 5 years of age fell by more than 50% between 1990 and 2021. Conclusions: Pediatric AMR reflects intersecting microbiological, clinical, and health-system challenges. Priority actions include scaling antimicrobial stewardship programs, expanding access to rapid molecular diagnostics, integrating whole-genome sequencing into surveillance, conducting pediatric-inclusive randomized trials, and deploying vaccines as primary prevention tools, with particular emphasis on LMICs where the burden is greatest. Full article

Fiber-degrading microorganisms are widely recognized for their potential to convert renewable lignocellulosic biomass into animal feed. However, translating this potential into practical application faces five critical yet underappreciated challenges. First, current screening methods, primarily including plate dilution and Congo red staining, are low-throughput, poorly reproducible and fail to capture the synergistic actions of natural microbial consortia. Second, the lack of standardized assays for quantifying cellulolytic activity compromises the reliability of cross-study comparisons. Third, safety assessments for fiber-degrading microorganisms remain superficial, with most studies neglecting mycotoxin production, antibiotic resistance gene transfer and long-term colonization risks. Fourth, fundamental differences between fungal and bacterial degradative systems, such as enzyme multiplicity, oxygen requirements and cellulosome assembly, are rarely considered in strain selection, leading to suboptimal application outcomes. Finally, the vast majority of positive in vitro degradation results fail to translate into improved animal performance in vivo, owing to poor microbial survival in the gastrointestinal tract, mismatched enzyme activity with gut pH and temperature, coupled with the absence of dose–response validation. This review critically evaluates these five bottlenecks across fiber-degrading microorganism types, screening platforms and practical livestock production applications. Overall, future progress should depend less on discovering “novel” strains and more on establishing standardized screening pipelines, rigorous safety frameworks and mechanistic understanding of in vivo efficacy, including direct head-to-head comparisons between fungal enzymes and bacterial probiotics under identical conditions. Full article

Back-mixing has been widely applied during practical composting to initiate the process and improve compost product quality. However, for antibiotic mycelial residue (AMR), a fermentation by-product containing residual antibiotics, the ecological safety of this treatment remains unclear. In this study, pleuromutilin mycelial residue (PMR) was subjected to a 35-day aerobic composting experiment with a back-mixing treatment (T group) and the conventional composting group (CK group) to evaluate composting performance and antibiotic resistance risk. The results demonstrated that the T group exhibited more rapid heating and a higher degree of humification. Additionally, the T group not only exhibited faster pleuromutilin degradation, reaching below the detection limit 3 days earlier than in the CK group, but also achieved up to a 3.1-fold reduction in antibiotic resistance genes (ARGs) and a 93.2% overall reduction in mobile genetic elements (MGEs). Redundancy analysis (RDA), variance partitioning analysis (VPA), and co-occurrence network analysis indicated that microbial community structure appeared to be more strongly associated with ARG variation than MGEs under the tested conditions. Overall, back-mixing accelerated pleuromutilin degradation and enhanced PMR composting performance, while no substantial enrichment of the detected ARGs was observed under the tested composting conditions. This study provides a scientific basis for the safe resource utilization of AMR. Full article

(1) Background: The increasing antibiotic resistance of pathogens is necessitating new therapies that target virulence factors. Virulence factors include biofilm formation, which is a key pathogenic factor involved in bacterial pathogenicity and resistance. (2) Methods: Initially, biofilm formation assays were performed to screen the biofilm formation inhibition effects of gastrodin. A bacterial growth assay was performed to examine the synergistic effects and qRT-PCR was performed to identify the underlying molecular regulatory mechanisms. (3) Results: Gastrodin inhibits biofilm formation by bacteria such as E. faecalis (IC₅₀ = 1.56 μg/mL), E. faecium (IC₅₀ = 0.19 μg/mL), S. aureus (IC₅₀ = 6.25 μg/mL), C. acnes (IC₅₀ = 0.78 μg/mL), S. sobrinus (IC₅₀ = 12.5 μg/mL), P. aeruginosa (IC₅₀ = 25.00 μg/mL), and E. coli (IC₅₀ = 25. 10 μg/mL) without directly affecting bacterial growth, as shown by bacterial growth assay. Gastrodin also reduced the expression of cytolysin genes (cylLS, cylR2, and cylM), quorum sensing genes (fsrB, fsrC, gelE, ebpA, ebpB, acm, scm, and bps) and biofilm virulence genes (esp) as shown by qRT-PCR analysis and exhibited dramatic synergistic antibacterial effects in the growth assay. (4) Conclusions: These results suggest that gastrodin may be a promising novel antibacterial adjuvant for biofilm-related bacterial infections, but further experiments, including in vivo assays, are still needed. Full article

The global dissemination of carbapenem resistance is predominantly facilitated by plasmid-mediated carbapenemase genes, notably blaOXA-48-like genes. A comprehensive understanding of their evolutionary relationships and structural conservation is essential for monitoring their spread and informing therapeutic strategies. This study aimed to investigate the phylogenetic relationships and structural conservation of blaOXA-48-like carbapenemase genes in multiple Gram-negative bacterial species. We analysed blaOXA-48-like carbapenemase sequences obtained from a hospital in Pakistan and compared them with globally reported variants retrieved from GenBank. Carbapenemase gene sequences (blaOXA-48-like, blaNDM, and blaVIM) were analyzed using maximum-likelihood phylogenetics (MEGA11, Tamura–Nei model, 1000 bootstrap replicates). Comparative global sequences were retrieved from GenBank. Structural modeling of blaOXA-48-like genes was performed using SWISS-MODEL Workspace with the template PDB 3HBR, followed by validation using GMQE, QMEANDisCo, and Ramachandran plot analyses. Phylogenetic analysis revealed a tight clustering of blaOXA-48-like genes across A. baumannii, K. pneumoniae, and E. meningoseptica, showing high similarity to globally distributed plasmid-associated sequences. Structural modeling demonstrated strong conservation of the enzyme, with preserved catalytic residues (Ser70, Lys73, Ser118, Trp157, and Tyr211) and minimal structural deviation (RMSD < 0.3 Å). blaOXA-48-like carbapenemases exhibit strong phylogenetic conservation and structural stability across species and regions, consistent with the horizontal dissemination of blaOXA-48-like genes across bacterial hosts. These findings indicate that blaOXA-48-like carbapenemases have high evolutionary stability. Full article

Inflammation plays a pivotal role in the pathogenesis of acne vulgaris, with Cutibacterium acnes recognised as a key etiological agent. The global increase in acne prevalence, coupled with the rising incidence of antibiotic-resistant strains, underscores the necessity for alternative therapeutic strategies. Vaccination has emerged as a promising approach, with various candidates targeting live-attenuated strains and specific virulence factors. Nevertheless, the expanding availability of C. acnes genomic data presents an opportunity to identify previously uncharacterized antigens that hold potential as novel targets for the development of next-generation acne vaccines. Therefore, this study aimed to identify core proteins among C. acnes genomes and evaluate their immunogenicity as potential multi-epitope peptide constructs. In addition, IA1-specific proteins of C. acnes were examined to develop the peptide constructs targeting acne-associated isolates. Pan-core analysis of 609 genomes identified 972 core genes. These genes were subsequently analysed for epitope prediction and antigenicity, and the highly antigenic epitopes were selected and combined for further analysis. Multi-epitope peptides were constructed based on predicted MHC-I, MHC-II, and linear B-cell epitopes, yielding four promising candidates derived from C. acnes core proteins and IA1-specific proteins. Molecular docking analysis indicated that both groups showed binding affinity for TLR2 and TLR4 receptors, suggesting possible molecular compatibility with these receptors. Furthermore, in silico immune simulations indicated that both types of multi-epitope peptides were associated with simulated humoral and cellular immune response profiles, although these responses require experimental validation. This computational workflow may help narrow the selection of potential acne vaccine candidates and prioritise multi-epitope peptide constructs for subsequent vaccine design steps and experimental validation. Full article

To improve clinical decision-making about Carbapenem-resistant Gram-negative bacteria (CR-GNB) infections and halt the spread of resistant microbes, quicker and less expensive diagnostic techniques are required. Thus, the purpose of this study was to thoroughly evaluate the diagnostic efficiency (sensitivity, specificity, and concordance) of direct-from-specimen multiplex lateral flow immunoassay (LFIA) across diverse raw clinical specimens and pathogen types from critically sick patients. A total of 300 non-duplicate samples were tested to detect CR-GNB. Five major Carbapenemase genes were detected directly from the specimen using carbapenem-resistant K.N.I.V.O. detection K-Set and from culture using culture-enhanced multiplex PCR. Turnaround time (TAT) of each method was calculated. The direct LFIA revealed 100% specificity for NDM, KPC, and IMP enzymes in all tested clinical matrices (blood, urine, and respiratory samples). The study demonstrated 100% sensitivity and specificity with perfect categorical agreement (κ = 1.000) for the blaKPC in the Klebsiella pneumoniae and for blaOXA-48 and blaIMP in the Acinetobacter baumannii; however, sensitivity of blaVIM was significantly diminished across all isolates and samples. TAT decreased significantly (p < 0.001) from 30 to 70 h to about 50 min. The tested direct LFIA facilitates the prompt enhancement of lifesaving tailored antibiotic treatment for severe illnesses. Full article

Background/Objectives: Antimicrobial resistance (AMR) in Staphylococcus spp. associated with poultry production is an emerging concern with implications for animal and public health. This study aimed to characterize antimicrobial susceptibility patterns and detect targeted methicillin resistance determinants in Staphylococcus isolates recovered from broiler chickens affected by bacterial chondronecrosis with osteomyelitis (BCO). Methods: A total of 200 bacterial isolates were evaluated, of which 167 were confirmed as Staphylococcus spp. Species identification was performed using presumptive phenotypic characterization followed by 16S rRNA gene sequencing. Antimicrobial susceptibility was assessed using disk diffusion, while presumptive methicillin-resistant phenotypes were evaluated using oxacillin screening and CHROMagar MRSA. Targeted molecular detection of mecA and mecC was performed by PCR. Results: The isolates demonstrated substantial species diversity, with S. aureus as the predominant species. Antimicrobial resistance was mainly observed against β-lactam antibiotics, particularly penicillin (33.5%), whereas high susceptibility was retained for non-β-lactam agents, including ciprofloxacin, tetracycline, trimethoprim–sulfamethoxazole, and azithromycin. A targeted PCR detected mecA in 7.2% of isolates, while mecC was not detected. The detection of mecA in oxacillin-susceptible isolates suggested genotype–phenotype discordance. Conclusions: BCO-associated Staphylococcus spp. from broiler chickens showed diverse species distribution, penicillin-dominant resistance, and targeted mecA detection across multiple species, supporting the use of combined phenotypic and molecular approaches for methicillin resistance surveillance. Full article

Subclinical bovine mastitis (SBM) is an inflammatory condition of the udder that remains a major concern for the dairy industry due to its high incidence and the direct and indirect associated costs. Antibiotics are widely used for prophylaxis and therapy in livestock, especially for SBM. However, overuse and misuse have contributed to the emergence of antimicrobial resistance (AMR), enabling resistant bacteria to enter the food chain and potentially spread to humans. This study aimed to detect antibiotic-resistant Staphylococcus and Streptococcus associated with SBM in dairy cows from Pioter, north-central Ecuador. For this, a commercial screening test, morphological and biochemical assays, standard culture techniques, mass spectrometry, and PCR (polymerase chain reaction) were applied. Among 99 isolates, 77 were Staphylococcus and 22 were Streptococcus. Among the identified Staphylococcus isolates, S. aureus was the predominant species (36.4%). Resistance in Staphylococcus exceeded 70% for fosfomycin and was under 30% for the other antibiotics tested. In Streptococcus, S. uberis predominated (54.5%), with resistance primarily to penicillin and tetracycline (>50%). PCR identified mecA, nuc, and lukSF-PV genes in 7.8%, 29.9%, and 6.5% of Staphylococcus isolates, respectively. In Streptococcus, the ermB and blaZ genes were found in 18.2% and 50% of isolates, respectively. These data provide a baseline on SBM-associated AMR in the study area and highlight the need for ongoing surveillance and improved milking practices to mitigate risks to the dairy sector and public health. Full article

Introduction: Stenotrophomonas maltophilia (S. maltophilia) has emerged as an important opportunistic pathogen. It is resistant to most available antibiotics due to its intrinsic resistance, leaving only some antibacterial agents as possible therapeutic options, which is further complicated by acquired mechanisms of antimicrobial resistance. This study aimed to provide a comprehensive genomic characterization of clinical S. maltophilia complex (Smc) isolates, focusing on molecular characterization of its resistance and virulence, since studies tackling this are scarce in Oman. Methods: This study is a prospective cross-sectional study, in which a total of 21 clinical isolates of Smc were collected from different clinical samples and further characterized using Whole Genome Sequencing. Results: Besides S. maltophilia, the isolates included S. hibiscicola, S. pavanii, and S. muris for the first time in Oman. All isolates were found to be susceptible to cefiderocol, levofloxacin, and minocycline. Sequence types (STs) were diverse among the isolates, with more than half of the isolates showing new STs with novel alleles. Additionally, blaOXA-2, sul1, and the recently described aac(6′)-Iap and aph(9)-Ic were detected among the isolates. Moreover, virulence-associated genes (smf-1, pilT, pilQ, gpmA, rmlA, spgM, stmPr1, plcN, clpP, and katE) were highly conserved across all isolates. Mobile genetic elements were detected in most of the isolates (76.20%). Conclusions: The collected isolates showed high ST diversity and showed no specific pattern in terms of antibiotic susceptibility and resistance genes. More studies are needed to establish relationships between the different members of the Smc and the different molecular resistome and virulome. Full article

Lactic acid bacteria (LAB) have been widely utilized in the production of fermented foods worldwide due to their well-established health-promoting benefits for both humans and animals. In addition to their nutritional value, LAB exhibit antagonistic activity against foodborne pathogens, particularly Salmonella spp., which are commonly associated with livestock and animal production systems. LAB exert a range of biological effects that can inhibit the growth of Salmonella and modulate its virulence. In the present study, the antagonistic potential of Weissella confusa WM36 was evaluated based on its ability to inhibit S. Typhimurium growth, disrupt biofilm formation, and suppress the expression of virulence-associated genes. A preliminary safety assessment of W. confusa WM36 was conducted through hemolytic activity and antibiotic susceptibility profiling. In addition, the biofunctional properties of its cell-free supernatant (CFS), herein referred to as postbiotic metabolites, were investigated with a particular focus on antioxidant activity. Experimental results demonstrated that W. confusa WM36 and its CFS at 40% (v/v) achieved a complete reduction (100%) of S. Typhimurium cell counts within 6 to 12 h of treatment. Furthermore, CFS at 20% and 40% (v/v) significantly impaired biofilm formation, while treatment with 20% (v/v) CFS markedly downregulated the expression of key virulence genes. The strain WM36 exhibited α-hemolytic activity and showed susceptibility to most of the antibiotics tested, although resistance to ceftriaxone and trimethoprim–sulfamethoxazole was observed. These findings provide preliminary information regarding its safety characteristics; however, further molecular and in vivo investigations are required to comprehensively evaluate its safety for practical applications. Additionally, the CFS exhibited notable antioxidant activity, with DPPH radical scavenging capacity of 8.90 ± 0.06 mM Trolox equivalents and ABTS radical scavenging power of 13.10 ± 1.42 mM Trolox equivalents. Collectively, these findings highlight the potential of W. confusa WM36 and its postbiotic metabolites as promising biocontrol and functional agents against S. Typhimurium, while further safety validation remains necessary. Full article

This study aimed to investigate the molecular basis of high-level tetracycline resistance to tetracycline antibiotics in Aeromonas hydrophila isolated from fish farming. Comparative genomic analysis of the tetracycline-sensitive strain NJ-35 and the tetracycline-resistant strain AH823 revealed that the tetracycline repressor gene tetR in AH823 had undergone base mutations, resulting in premature translational termination. The tetR gene in NJ-35 was inhibited using a plasmid-based antisense RNA strategy, and the knockdown efficiency was confirmed by RT-qPCR. The resulting tetR antisense RNA-expressing strain, AHtetR-as, exhibited significantly increased resistance to tetracycline antibiotics (minocycline, tetracycline, and doxycycline), but did not affect biofilm formation or hemolysis. Moreover, tetR knockdown in NJ-35 was associated with increased efflux activity and reduced intracellular doxycycline accumulation. Transcriptomic analysis revealed that genes encoding the 30S ribosomal subunit proteins showed a differential expression pattern, with rpsO upregulated and rpsD and rpsP downregulated. These findings suggest that tetR contributes to tetracycline resistance in A. hydrophila and is associated with broad transcriptional changes related to cellular transport and ribosomal function. Full article