Search Results (1,575)

Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and non-ESBL Escherichia coli across One Health interfaces in Oman. Methods: This prospective cross-sectional study analyzed 295 non-duplicate Escherichia coli isolates derived from 104 clinical, 173 animal [diseased (123) and healthy (50)], 14 sewage and four water sources. Antimicrobial susceptibility testing was performed phenotypically, and a representative subset of 50 ESBL and non-ESBL Escherichia coli from the three interfaces underwent whole genome sequencing to determine MLST, phylogroups, resistance genes, virulence determinants and plasmid replicons. Results: ESBL prevalence was highest in human isolates (73%), followed by sewage (28.6%) and animals (16.3% diseased; 8% healthy). blaCTX-M-15 predominated in humans, whereas blaCTX-M-55 dominated in animals and sewage, suggesting ecological partitioning with partial overlap. Quinolone resistance was lowest in the animal interface. Sewage isolates harbored the most complex resistome, including rmtB and plasmid-mediated quinolone resistance genes. MLST analysis revealed high diversity in human isolates, including globally recognized ExPEC lineages (ST10, ST38, ST73, ST127, ST131), while ST224 dominated in animals with evidence of possible spillover to humans. ST167 was confined to sewage, consistent with environmental maintenance of high-risk clones. Phylogroup structuring showed predominance of A, B2 and D among human isolates and A, B1, and E among animal and sewage isolates. Virulence profiling demonstrated broader virulome diversity in humans, but shared core determinants (fimH, sitA, traT) across all domains. IncFIB(AP001918) was the dominant plasmid replicon, particularly among ESBL isolates, underscoring its role in horizontal gene dissemination. Alarmingly, mutation in pmrB (V161G) was identified in a healthy animal isolate, pointing to a need for greater colistin restriction in animal husbandry. Conclusions: This study highlights plasmid-mediated resistance and shared virulence determinants linking reservoirs; although AMR profile was quite distinct across the three interfaces, human isolates demonstrated greater resistance than animal isolates, suggesting healthcare-driven AMR in Oman. Continued integrated genomic surveillance is essential to monitor gene flow and inform coordinated antimicrobial stewardship strategies. Full article

Background/Objectives: The emergence of antimicrobial-resistant (AMR) pathogens in aquaculture ecosystems poses a significant risk to both food security and human health. Shewanella species are recognized as significant AMR reservoirs, yet their prevalence and resistance mechanisms within a shrimp-related ecosystem remain poorly characterized. This study aimed to perform a genotypic and phenotypic characterization of S. algae VK101, isolated from wild-caught black tiger shrimp (Penaeus monodon) broodstock. Methods: A complete 5.21 Mb genome was generated using a hybrid Illumina and Oxford Nanopore sequencing approach. Antimicrobial susceptibility was evaluated for 21 antibiotics via Minimum Inhibitory Concentration (MIC) testing. Comparative pangenomics and genome-wide association studies (GWAS) across 125 S. algae genomes were conducted to identify novel resistance determinants. Results: MIC analysis revealed that VK101 was resistant to ampicillin (>16 µg/mL) and colistin (8 µg/mL), while showing intermediate susceptibility to imipenem and ciprofloxacin. In silico analysis identified 205 antimicrobial resistance genes (ARGs), including a perfect hit for the fluoroquinolone resistance gene qnrA3. Notably, no mcr genes were detected. Although VK101 exhibited moderate resistance (8 µg/mL), GWAS across the broader S. algae population linked a specific lptA mutation (K140N) to high-level resistance (64 µg/mL). Other GWAS-identified genes (e.g., czcA, ampC, and oprM) likely represent indirect associations driven by genetic linkage or clade-specific markers rather than direct causal factors. Conclusions: These findings highlighted the presence of multidrug-resistant S. algae in wild-caught P. monodon broodstock, reflecting the occurrence of antimicrobial resistance in aquatic environments. Colistin resistance in these isolates was primarily mediated by chromosomal variants rather than mobile mcr elements, indicating the need for integrated genomic surveillance within the aquaculture value chain. Full article

Camel-associated antimicrobial resistance (AMR) is an underrecognized component of the One Health landscape, particularly in the Gulf Cooperation Council (GCC) and North Africa. Available evidence demonstrates the presence of clinically significant resistance mechanisms in camel populations, including extended-spectrum beta-lactamases, carbapenemases, colistin resistance genes, and multidrug-resistant clones. Molecular similarities between camel and human isolates suggest potential cross-species transmission and highlight camels as possible reservoirs within interconnected human–animal–environment systems. Despite documented resistance patterns, camel production systems remain largely excluded from national AMR surveillance and stewardship frameworks. This gap reflects limited camel-specific data on antimicrobial usage and structural challenges related to pastoral mobility, cross-border trade, and emerging commercial intensification. Strengthening diagnostic capacity, implementing tailored antimicrobial stewardship strategies, and integrating camels into national AMR action plans are essential to mitigate potential public health risks. Proactive inclusion of camel systems within regional AMR governance frameworks is necessary to prevent further amplification of resistance. Full article

Atmospheric nitrogen (N) deposition is an important global change driver in forest ecosystems, yet its long-term effects on belowground microbial communities in cold-temperate coniferous forests remain insufficiently understood. In this study, endpoint shotgun metagenomic sequencing was used to evaluate bulk soil microbial communities after 12 years of experimental N addition in a Larix gmelinii-dominated forest in the Greater Khingan Mountains of northeastern China. Four treatments were included: control (0 kg N ha⁻¹ yr⁻¹), low N (25 kg N ha⁻¹ yr⁻¹), medium N (50 kg N ha⁻¹ yr⁻¹), and high N (75 kg N ha⁻¹ yr⁻¹). Microbial alpha diversity did not differ significantly among treatments, although moderate N addition showed a tendency to maintain relatively higher richness and diversity. In contrast, beta-diversity analysis indicated clear shifts in community composition along the N addition gradient. Pseudomonadota, Acidobacteriota, and Actinomycetota dominated the microbial communities, with Pseudomonadota tending to increase under N enrichment, whereas some oligotrophic groups showed reduced relative abundance. Functional annotation showed that metabolism-related genes remained dominant across treatments, and carbohydrate-active enzyme profiles suggested altered microbial potential for complex carbon decomposition under long-term N input. Nitrogen addition also modified the abundance patterns of some antibiotic resistance genes and mobile genetic elements, although overall resistome differentiation among treatments remained limited. These results provide endpoint metagenomic evidence that long-term N addition can reshape bulk soil microbial community composition and selected functional potentials in cold-temperate coniferous forest soils, even when overall alpha diversity remains relatively stable. Full article

Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of invasive disease, yet contemporary genomic data from Canada remain scarce. We investigated 56 cases of invasive SDSE infection identified between 2018 and 2022 in two major tertiary care teaching hospitals in Toronto, Ontario, and characterized 49 corresponding isolates by whole-genome sequencing. Nearly three-quarters of infections were caused by the globally expanding ST20 emm type stG62647 lineage. Patients infected with this lineage were significantly older than those infected with non-ST20 lineages across both bloodstream and non-blood infections. Core-genome phylogenetic analysis revealed a highly clonal ST20 cluster, although two isolates had divergent emm types suggesting recombination at the emm locus. Non-ST20 lineages were numerically smaller and genetically more heterogeneous, including distinct sublineages within ST3 and ST34. All isolates were susceptible to β-lactams and vancomycin. Resistance to tetracycline, erythromycin, and clindamycin was detected in a subset of isolates and was associated with genes tetM, tetO, ermA, ermB, and msrD. Several antimicrobial resistance determinants were located on mobile genetic elements, including integrative and conjugative elements. Our findings provide a contemporary genomic view of invasive SDSE in Toronto, highlighting the dominance of the ST20 stG62647 lineage in agreement with recent global observations. Full article

Campylobacter jejuni is a major zoonotic pathogen that circulates among birds, livestock, humans, and environmental reservoirs, yet the genomic mechanisms that enable persistence and transmission across divergent hosts remain incompletely understood. Here, we sequenced 61 C. jejuni isolates recovered from multiple host-associated sources in Shenzhen, China, from 2016 to 2023, and analyzed them together with 312 dereplicated publicly available high-quality reference genomes. Phylogenomic analyses resolved three major clades, including one avian-restricted clade and two clades showing frequent cross-host occurrence. Human-associated isolates displayed lower coding density than mammal-associated isolates and significantly higher proteome-level carbon and nitrogen demands than avian-associated isolates. Comparative genomic analyses further revealed strong host-associated divergence in chromosome-encoded, plasmid-encoded, and horizontally acquired gene repertoires. In human-derived isolates, 11 dataset-specific human-unique KEGG genes and 48 human-unique virulence-associated genes were identified, and human-associated strains showed the strongest multidrug-resistance signal across both chromosome-encoded and mobile-gene compartments. Resistance-associated functions enriched in human-associated genomes included antibiotic inactivation, efflux-mediated resistance, target protection/replacement/alteration, reduced permeability, and nutrient-acquisition-associated resistance. By contrast, core host-interaction loci remained under strong purifying selection, indicating that major human-associated traits were linked more closely to mobile gene acquisition than to extensive mutation-driven diversification. Together, these findings support a proposed genome-partition framework of host adaptation in C. jejuni, in which relatively stable chromosomal backgrounds are complemented by rapid plasmid- and horizontal-transfer-mediated acquisition of high-impact accessory genes. Full article

Cadmium (Cd) is a major environmental pollutant due to its high mobility and persistence in soils, facilitating entry into the food chain and threatening ecosystems and human health. However, the mechanisms that enable Salix species, well adapted for Cd remediation, to both tolerate and accumulate Cd remain elusive. Here, two Salix genotypes with contrasting Cd tolerance were examined under control and Cd stress using integrated physiological, transcriptomic, and metabolomic analyses of roots and leaves. The Cd-tolerant genotype (Salix suchowensis P294) maintained biomass under Cd stress, whereas the Cd-sensitive genotype (Salix sinopurpurea × Salix integra P646) showed a ~17% reduction. P294 accumulated more Cd in its stems (132.76 mg kg⁻¹) and leaves (122.25 mg kg⁻¹) than P646 (93.54 and 56.24 mg kg⁻¹). Transcriptomics responses were stronger in roots, with 896 DEGs in P294 and 462 in P646, enriched in nitrogen metabolism, phenylpropanoid biosynthesis, and metal transport, whereas only 167 and 176 DEGs were detected in leaves for P294 and P646, respectively. Metabolomics revealed more altered metabolites in roots (125 in P294, 89 in P646), mainly organic acids, amino acids, and flavonoids, compared with leaves (46 and 66). RT-qPCR validated the root-specific upregulation of key detoxification and transport genes (ABCA7, PRX72, GSTU1, GSTU4, ZIP1). These results reveal a root-centered regulatory network underlying Cd accumulation and tolerance, integrating detoxification, redox homeostasis, and structural reinforcement, as well as providing valuable targets for genetic improvement of phytoremediation efficiency. Full article

To characterize the ecological and genomic architecture of temperate bacteriophages in Escherichia coli isolated from Brazilian broiler chickens, we analyzed 63 femur-derived genomes, most fulfilling molecular avian pathogenic E. coli (APEC) criteria, and tested whether temperate phage regions are enriched for antimicrobial resistance genes (ARGs), virulence factors, plasmid markers, and other mobilome components. Diversity was summarized using incidence-based richness estimators and bootstrap confidence intervals, and positional enrichment was assessed using permutation-based statistical analysis. We detected 1164 phage-like elements, including 188 medium- and high-quality phages, of which 93.6% were temperate. Median temperate diversity per genome was three phage genera and three temperate regions. At the population level, 19 temperate genera were observed, with a Chao2 estimate of 21.2, indicating near-saturated genus-level diversity. Positional mobilome analysis showed significant enrichment of insertion sequences within temperate regions (p < 0.05), while ARGs, virulence factors, and plasmid markers were not significantly enriched inside temperate phage coordinates (p > 0.05). The surrounding genomic neighborhood (±20 kb) accumulated mobile elements but showed no significant enrichment. CRISPR spacer matches further supported ongoing host–phage interactions. Overall, temperate phages are widespread and ecologically structured in Brazilian broiler-associated E. coli, but they are not preferential hotspots for ARG, virulence, or plasmid gene enrichment; instead, they are chiefly associated with insertion-sequence enrichment. Full article

Background: Enterobacter hormaechei, a member of the Enterobacter cloacae complex (ECC), is increasingly recognized as a multidrug-resistant (MDR) nosocomial pathogen. However, subspecies-level genomic data from Ecuador remain limited. Methods: Four clinical E. hormaechei isolates from a hospital in northern Ecuador were analyzed using antimicrobial susceptibility testing and whole-genome sequencing (WGS). Genomic characterization included multilocus sequence typing (MLST), resistome profiling, plasmid replicon detection, integron screening, genomic island analysis, and phylogenetic comparison with publicly available Ecuadorian genomes. Results: WGS identified three isolates as subsp. xiangfangensis (ST136 and ST337) and one as subsp. hoffmannii (ST145). Two ST136 isolates exhibited extensive MDR phenotypes associated with bla_CTX-M-15, bla_OXA-1, bla_ACT-16, and additional aminoglycoside and fluoroquinolone resistance genes. ST145 showed moderate resistance, whereas ST337 remained largely susceptible despite harboring bla_ACT-16. Multiple genomic islands and plasmid replicons (IncF/IncR or IncHI2) were detected. Phylogenetic analysis demonstrated clustering with previously reported Ecuadorian lineages. Conclusions: This study provides subspecies-level genomic characterization of clinical E. hormaechei in Ecuador and describes heterogeneous resistance profiles and associated mobile genetic elements, contributing baseline data for regional surveillance. Full article

Streptococcus parauberis is a major pathogen responsible for streptococcosis in both marine and freshwater fish species, causing substantial economic losses in aquaculture. The increasing prevalence of multidrug resistance has highlighted the urgent need for alternative disease control strategies. Interference with bacterial quorum sensing (QS) systems represents a promising approach. This study aimed to identify and biochemically characterize an Rgg-family transcriptional regulator and evaluate its potential as a target for quorum sensing-related regulatory interference in vitro. We hypothesized that this Rgg regulator may function as a quorum sensing-associated transcription factor capable of promoter binding and modulation by small molecules. Bioinformatic analyses were used to identify the rgg gene encoding an Rgg-family transcriptional regulator and predict its structural features. The gene was cloned, heterologously expressed, and purified. Promoter binding activity was examined using electrophoretic mobility shift assay (EMSA), and key amino acid residues were identified through site-directed mutagenesis. The inhibitory effect of the cyclic peptide cyclosporin A (CsA) on Rgg-promoter binding was further assessed. The rgg gene (864 bp) encoding a 287-amino-acid protein (34.1 kDa) was successfully identified and expressed. Purified Rgg specifically bound to its own promoter region in a concentration-dependent manner. Mutations at conserved arginine residues R12 and R15 within the helix-turn-helix DNA-binding domain abolished promoter binding activity. Furthermore, CsA disturbed Rgg-promoter binding in a dose-dependent manner. This study provides the first in vitro characterization of an Rgg-family transcriptional regulator in fish-derived S. parauberis. The findings expand current understanding of Rgg-family regulators potentially associated with quorum sensing in aquatic streptococci and provide a preliminary basis for further investigation of quorum sensing-related regulatory interference strategies for controlling streptococcal diseases in aquaculture. Full article

Background/Objectives: Multidrug-resistant Salmonella enterica serovar Enteritidis, especially those isolated from humans, remains a public concern. In the present study, S. Enteritidis strain 31404 was obtained clinically from a fecal sample of a fifteen-year-old girl, who was positive for bla_NDM-13. Methods: Antibiotic susceptibility testing and whole genome sequencing were performed. Core genome MLST and hierarchical clustering (HierCC) were performed using EnteroBase. Population structure analysis of 57 S. Enteritidis isolates collected between 2023 and 2025 in Jiaxing city was conducted. A comparative structure analysis of bla_NDM-13-positive plasmids was also performed. Results: S. Enteritidis strain 31404 was resistant to 13 antimicrobial agents. We found that strain 31404 belonged to ST11 and carried resistance genes, such as bla_NDM-13, bla_CTX-M-14, ble_MBL, fosA3, qnrS, and tet (A). bla_NDM-13 was located on an IncI1-I (α) plasmid designated as p31404-NDM13. S. Enteritidis isolate 31404 was closely related to PNUSAS514422, which was isolated from the United States in 2025. Comparative genetic environment related to bla_NDM-13-positive plasmids available in the NCBI database indicates that ΔTn125-mediated contexts were commonly associated with bla_NDM-13. IS1294 (IS91 family), which replaces ISAba125, is likely to mobilize bla_NDM-13. Conclusions: The findings in this study provide insights into the molecular characterization and diversification of bla_NDM-13. The identification of bla_NDM-13-containing transferable plasmids in different serotypes of Salmonella isolates (such as S. Rissen, S. Typhimurium, and S. Enteritidis) in different cities in China highlights the risk of the spread of carbapenem-resistant genes among Salmonella isolates. Full article

In the post-antibiotic era, the Bacillus-based direct-fed beneficial microorganisms are emerging as a cornerstone for sustainable animal farming. This study aimed to screen and evaluate Bacillus strains with probiotic potential for use as feed additives. A total of 394 Bacillus strains were initially screened based on their extracellular enzyme production (cellulase, protease, and amylase) and antibacterial activities against Escherichia coli, Staphylococcus aureus, and Salmonella enterica. Two strains, Bacillus velezensis FJAT-10508 and FJAT-13563, were selected and subsequently subjected to in vitro probiotic characterization, safety assessment, and whole-genome analysis. The results demonstrated that both strains exhibited α-hemolysis, acceptable antibiotic susceptibility profiles, absence of invasion and cytotoxicity effect on the Caco-2 cells, and no mobile virulence or antibiotic resistance genes, indicating their safety as probiotic candidates. High endospore-forming efficiencies (72.4–90.8%), strong auto-aggregation (74–85%) and co-aggregation abilities (52–82%) were observed. In addition, both strains showed considerable tolerance to simulated gastrointestinal conditions, with vegetative cell and endospore survival rates of 28.33–38.33% and 85–89.67% at pH 2.0, and 38.33–43.33% and 90.33–96.33% in 0.3% bile salts, respectively. Overall, B. velezensis FJAT-10508 and FJAT-13563 demonstrated robust in vitro probiotic properties, supporting their potential application as reliable Bacillus-based feed additives. Full article

Bone formation requires a substantial energy supply to sustain extracellular matrix production and mineralization, yet the temporal contribution of lipid metabolism during osteoblast maturation remains incompletely characterized. This study investigated the molecular and transcriptional remodeling of lipid metabolism. Intracellular lipid distribution was analyzed by confocal microscopy using Nile Red staining. Transcriptional modulation of lipid synthesis, storage, lipolysis, genes associated with mitochondrial fatty acid oxidation, and osteogenic markers were assessed by quantitative real-time PCR, and the biochemical composition was evaluated by Raman spectroscopy. Early stages of spheroid development showed higher expression of genes involved in lipid synthesis and storage (FASN, DGAT2, and PLIN2) together with intracellular lipid accumulation, whereas later stages displayed increased expression of lipolytic and β-oxidation markers (PNPLA2/ATGL, CPT1A, and HADHA), accompanied by the redistribution of lipid droplets. The Raman analysis revealed a time-dependent variation of lipid-associated CH₂/CH₃ bands and modulation of protein-related Amide I–III signals, consistent with biochemical remodeling during maturation. Overall, the data indicate a coordinated transcriptional shift from lipid accumulation-associated pathways toward lipid mobilization during osteogenic progression in a 3D culture. This model provides a controlled experimental platform for investigating metabolic regulation during bone formation and for studying metabolic alterations associated with skeletal disorders. Full article

Antibiotic resistance genes (ARGs) are increasingly recognized as emerging contaminants in wastewater treatment systems; however, their responses to dissolved oxygen (DO)-limited conditions caused by insufficient aeration, particularly in the presence of microplastics, remain poorly understood. In this study, three sequencing batch reactors (SBRs) were operated for 31 days under progressively oxygen-limited conditions with different concentrations of polyethylene terephthalate (PET) microplastics to investigate their combined effects on treatment performance, microbial communities, ARGs, mobile genetic elements (MGEs), and PET degradation-related genes using metagenomic analysis. Prolonged oxygen limitation maintained relatively stable organic matter removal but progressively deteriorated ammonium removal and sludge settleability, while PET addition significantly aggravated these effects. PET exposure markedly increased the absolute abundance of ARGs without substantially altering resistome composition or dominant resistance mechanisms, suggesting an amplification rather than restructuring of the resistome. Correlation analyses indicated that ARGs enrichment was primarily host-associated and driven by the proliferation of a limited number of microbial taxa. Several potential ARG hosts were also strongly associated with PET degradation-related genes, indicating shared microbial populations linking PET-associated functions and antibiotic resistance. In addition, strong positive correlations between ARGs and MGEs suggested an important role of gene mobility in resistome dynamics under oxygen-limited conditions. Overall, these results demonstrate that oxygen limitation combined with PET microplastics promotes host-associated ARG enrichment in wastewater systems, highlighting potential environmental and public health risks and emphasizing the importance of maintaining operational stability to mitigate antibiotic resistance dissemination. Full article

Cadmium (Cd) is widely dispersed in the environment and has emerged as a major environmental contaminant. Although Salix viminalis shows potential for phytoremediation of Cd pollution, the defence mechanism of its roots against heavy metals remains unclear. This study explores the adaptive response of S. viminalis roots to Cd stress from physiological, transcriptomic, and metabolomic perspectives. The results suggest that Cd stress exerts inhibitory effects on root growth and development. Compared with the control (Cd-free), the root volume and dry weight of S. viminalis exposed to Cd decreased by 26% and 29%, respectively. After exposure to Cd stress for 14 and 21 days, the Cd content in the roots increased by 117-fold and 134-fold, the hydrogen peroxide content increased by 89% and 110%, and the malondialdehyde content increased by 82% and 88%, respectively. This phenomenon can be attributed to the fact that the continuous accumulation of Cd in the roots may have aggravated the degree of lipid peroxidation. A total of 9171 differentially expressed genes (DEGs) and 169 differential metabolites (DIMs) were identified through transcriptomic and metabolomic analyses. Further combined analyses revealed the potential roles of several pathways in the defensive response of S. viminalis roots against Cd stress, including plant hormone signal transduction, thiamine metabolism, glycolysis, glycerophospholipid metabolism, and other pathways. Notably, the feedback regulatory effects formed by thiamine metabolism and hormone signal transduction related to auxin, jasmonic acid, and salicylic acid play a crucial role in the early stage when roots are exposed to Cd stress. These effects mobilized osmotic adjustment in roots by enhancing saccharide metabolism and activated the Cd detoxification process by altering lipid metabolism, thereby contributing positively to the defence of willow roots against Cd stress. These findings provide insights into the adaptive mechanism of S. viminalis roots in response to Cd and the application of fast-growing woody plants in heavy metal phytoremediation. Full article