Search Results (174)

Background/Objectives: It is of the utmost importance to study environmental bacteria, as these microorganisms remain poorly characterized regarding their diversity, antimicrobial resistance, and impact on the global ecosystem. This knowledge gap is particularly pronounced for marine bacteria. In this study, we aimed to isolate bacteria from different marine samples and to gain insights into the environmental bacterial resistome, an aspect that remains largely neglected. Methods: Bacteria were isolated from several marine sources using two different culture media, and their identification was based on 16S rRNA gene analysis. Whole-genome sequencing was performed for selected isolates belonging to novel taxa. Antimicrobial susceptibility to seven antibiotics was evaluated using the disk diffusion method. Results: A total of 171 bacterial isolates belonging to the phyla Pseudomonadota, Bacteroidota, Planctomycetota, Actinomycetota, and Bacillota were obtained from diverse marine samples. The most abundant group belonged to the class Alphaproteobacteria. Thirty isolates represented novel taxa, comprising 16 new species and one new genus. Despite the challenges associated with determining antibiotic resistance profiles in environmental bacteria, only one isolate (1.8%) was pan-susceptible, whereas 54 (98.2%) showed resistance to at least one of the tested antibiotics. Moreover, 33 isolates exhibited a multidrug-resistant phenotype. Genome analysis of four novel taxa revealed the presence of an incomplete AdeFGH efflux pump. Conclusions: This study highlights the high bacterial diversity in marine environments, the striking prevalence of antibiotic resistance, and the major methodological challenges in studying environmental bacteria. Importantly, it emphasizes the relevance of culturomics-based approaches for uncovering hidden microbial diversity and characterizing environmental resistomes. Full article

The widespread use of antibiotics has led to the persistence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in drinking water systems, posing potential public health risks at the point of use. In this study, a residential secondary water supply system (SWSS) in eastern China was investigated over one year to characterize microbial communities, ARB and ARG occurrence, and their associations with water quality in bulk water and biofilms. Culture-based methods, flow cytometry, quantitative PCR, and high-throughput 16S rRNA and ITS sequencing were applied. Although conventional treatment removed 94.8% of total bacteria, significant microbial regrowth occurred during secondary distribution, with the highest heterotrophic plate counts observed in rooftop storage tanks (up to 4718 CFU/mL). ARG concentrations increased along the distribution line, and the class 1 integron intI1 was enriched in downstream locations, indicating enhanced horizontal gene transfer potential. Sulfonamide resistance genes dominated the resistome, accounting for more than 60% of total ARG abundance in water samples. Seasonally, ARG levels were higher in autumn and winter, coinciding with elevated disinfectant residuals and lower temperatures. Chlorine was negatively associated with total bacterial abundance, while positive correlations were observed with the relative abundance of several ARGs when normalized to bacterial biomass, suggesting selective pressure under oxidative stress. Turbidity and bacterial abundance were positively correlated with ARB, particularly sulfonamide-resistant bacteria. Biofilms exhibited more stable microbial communities and provided microhabitats that facilitated microbial persistence. Notably, fungal abundance showed strong positive correlations with multiple ARGs, implying that microbial interactions may indirectly contribute to ARG persistence in SWSSs. These findings highlight the role of secondary distribution conditions, disinfectant pressure, and microbial interactions in shaping resistance risks in residential water supply systems, and provide insights for improving microbial risk management at the point of consumption. Full article

Background/Objectives: Comparative analysis of antimicrobial resistomes in hospital and community wastewater can provide valuable insights into the diversity and distribution of antimicrobial resistance genes (ARGs), contributing to the advancement of the One Health approach. This study aimed to characterize and compare the resistome profiles of wastewater sources from a hospital and community. Methods: Longitudinal metagenomic analysis was conducted on wastewater samples collected from the National Center for Global Health and Medicine (hospital) and a shopping mall (community) in Tokyo, Japan, between December 2019 and September 2023. ARG abundance was quantified using reads per kilobase per million mapped reads (RPKM) values, and comparative analyses were performed to identify the significantly enriched ARGs in the two sources. Results: A total of 46 monthly wastewater samples from the hospital yielded 825 unique ARGs, with a mean RPKM of 2.5 across all detected genes. In contrast, 333 ARGs were identified in the three shopping mall wastewater samples, with a mean RPKM of 2.1. Among the ARGs significantly enriched in the hospital samples, 23, including genes conferring resistance to aminoglycosides (nine groups) and β-lactam antibiotics (eight groups), exhibited significantly high RPKM values. No ARGs were found to be significantly enriched in the community wastewater samples. Conclusions: This study highlights the higher diversity and abundance of ARGs, particularly those conferring resistance to aminoglycosides and β-lactam antibiotics including carbapenems, in hospital wastewater than in community wastewater. These findings underscore the importance of continuous resistome monitoring of hospital wastewater as part of the integrated One Health surveillance strategy. Full article

Antimicrobial resistance (AMR) poses a global health threat, with urban wastewater systems serving as key reservoirs for resistance dissemination. This study aimed to investigate the relationships among urban environments, bacterial communities, and AMR patterns, and evaluate the specific municipal-scale drivers of resistance gene distribution. Shotgun metagenomic analysis was conducted on 45 wastewater samples collected from 15 municipalities across Latvia to determine the composition of the resistome and its correlation with local factors. The analysis identified 417 distinct antibiotic resistance genes (ARGs) belonging to 108 families, with geographic location serving as the primary driver of ARG distribution, which explained 65.87% of community variation (p = 0.001). Local industrial factors demonstrated significant effects, with food industry wastewater significantly influencing both bacterial taxonomy and ARG profiles (p < 0.05). While the presence of a regional hospital did not shape the overall municipal resistome, hospital-associated wastewater showed 19 overlapping ARGs, including clinically critical carbapenemases. Municipal wastewater systems function as geographically structured reservoirs of AMR that are shaped by localized industrial and healthcare outputs. These findings support wastewater-based AMR surveillance as a valuable tool for tracking specific resistance sources. Full article

Background/Objectives: The mammalian microbiota constitutes a reservoir of antimicrobial resistance genes (ARGs), which can be shaped by environmental and anthropogenic factors. Although bat-associated bacteria have been reported to harbor diverse ARGs globally, the ecological and evolutionary determinants driving this diversity remain unclear. Methods: To characterize ARG diversity in wildlife exposed to contrasting levels of human influence, we analyzed homologs of resistance mechanisms from the Comprehensive Antibiotic Resistance Database in shotgun metagenomes of bat guano. Samples were collected from a colony exposed to continuous anthropogenic activity in Spain (Salamanca) and from a wild, non-impacted bat community in China (Guangdong). Metagenomic analyses revealed marked differences in taxonomic and resistome composition between sites. Results: Salamanca samples contained numerous hospital-associated genera (e.g., Mycobacterium, Staphylococcus, Corynebacterium), while Guangdong was dominated by Lactococcus, Aeromonas, and Stenotrophomonas. β-lactamases and MurA transferase homologs were the most abundant ARGs in both datasets, yet Salamanca exhibited higher richness and functional diversity (median Shannon index = 1.5; Simpson = 0.8) than Guangdong (Shannon = 1.1; Simpson = 0.66). Salamanca also showed enrichment of clinically relevant ARGs, including qacG, emrR, bacA, and acrB, conferring resistance to antibiotics critical for human medicine. In contrast, Guangdong exhibited a more restricted resistome dominated by β-lactamase and MurA homologs. Beta diversity analysis confirmed significant compositional differences between resistomes (PERMANOVA, R² = 0.019, F = 1.33, p = 0.001), indicating ecological rather than stochastic structuring. Conclusions: These findings suggest that anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, potentially increasing their role as reservoirs of antimicrobial resistance. Full article

The widespread use of antibiotics, combined with pervasive exposure to diverse environmental media, has intensified the global challenge of antibiotic resistance. Accumulating evidence reveals that beyond direct antibiotic pressure, residual non-antibiotic chemicals—despite lacking intrinsic antibacterial activity—can significantly promote the enrichment and spread of antibiotic resistance genes (ARGs) in farmland soils through indirect mechanisms such as inducing oxidative stress, altering microbial community structure, and enhancing both vertical and horizontal gene transfer. To address this issue, the present study investigates the influence of representative non-antibiotic contaminants commonly detected in agricultural environments—including pesticides (e.g., Omethoate, imidacloprid, and atrazine), industrial pollutants (e.g., PCB138, BDE47, benzo [a] pyrene, 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD], and benzene), plastic-associated compounds (e.g., Polyethylene trimer, phthalates, and tributyl acetylcitrate), and ingredients from personal care products (e.g., triclosan and bisphenol A)—on ARG transmission dynamics. Leveraging bioinformatics resources such as the CARD database, PDB, AlphaFold, and molecular sequence analysis tools, we identified relevant small-molecule ligands and macromolecular receptors to construct a simulation system modeling ARG transfer pathways. Molecular docking and molecular dynamics (MD) simulations were then implemented, guided by a Plackett–Burman experimental design, to systematically evaluate the impact of individual and co-occurring pollutants. The resulting data were processed using advanced analytical tools, and MD trajectories were interpreted at the molecular level across three scenarios: an unperturbed (blank) system, single-pollutant exposures, and dual-pollutant combinations. By integrating computational simulations with machine learning approaches, this work uncovers the “co-selection” effect exerted by non-antibiotic chemical residues in shaping the environmental resistome, thereby providing a mechanistic and scientific basis for comprehensive risk assessment of agricultural non-point source pollution and the development of effective soil health management and antimicrobial resistance containment strategies. Full article

Microplastics introduced into freshwater environments create novel surfaces that select for specific microbial colonizers and exclude others. In urban rivers, these biofilms can act as reservoirs of antimicrobial resistance and contain potential enzymes for polymer degradation. We studied microbial communities associated with microplastics in the Setun River and examined how their composition changes during laboratory enrichment on plastic substrates. Native river specimen and cultures enriched on low-density polyethylene (LDPE) and polycaprolactone (PCL) were analyzed using mWGS and full-length 16S rRNA nanopore sequencing. Enrichment led to a pronounced shift toward nearly monoculture of Bacillota, more specifically Bacillus cereus, while native plastisphere communities were dominated by Pseudomonadota. Microscopy revealed clear degradation of PCL but not LDPE, and functional screening of native metagenomes uncovered a diverse resistome, including oqxAB efflux operons, mcr-3-like phosphoethanolamine transferases, various $\beta$-lactamases, and class 1 integron genes, demonstrating that the Setun River plastisphere already contained clinically relevant AMR determinants. These findings suggest that certain bacteria such as Bacillus cereus can thrive and dominate on plastic surfaces in urban rivers, while many other taxa cannot persist there, highlighting that microplastics strongly reshape plastisphere communities and emphasize the role of river-borne microplastics as potential vectors of antibiotic resistance. Full article

Background/Objectives: The emergence of hypervirulent Pseudomonas aeruginosa strains resistant to β-lactamase inhibitor antibiotics is a critical health problem as they impede the treatment of infections. The objective of this study was to determine the different molecular arrangements of the virulence genotype related to β-lactamase genotype and the resistance phenotype to a combination of β-lactam antibiotics and β-lactamase inhibitors, and the phylogroups in P. aeruginosa strains isolated from patients with healthcare-associated infections and community-acquired infections. Methods: P. aeruginosa, virulence genes, β-lactamase genes and phylogroups were identified using polymerase chain reaction. Resistance to β-lactam antibiotics and β-lactamase inhibitors was determined using the disk diffusion method. The MIC determination of ticarcillin/clavulanic acid and piperacillin/tazobactam was performed using the MIC test strip for antimicrobial susceptibility testing. Results: In total, 124 P. aeruginosa strains from patients with healthcare-associated (67/124) and community-acquired infections (57/124) were analyzed. Most strains from patients with healthcare-associated infections and community-acquired infections harbored genes for proteases (aprA), phospholipases (pIcH and pIcN), elastases (lasA and lasB), rhamnolipids (rhLA), quorum-sensing system (lasI and rhII), and β-lactamase (bla_oxa-4, bla_oxa-1, and bla_GES). In total, 100% (124/124) and 99.1% (123/124) of the strains isolated from patients with healthcare-associated and community-acquired infections were resistant to the β-lactamase inhibitor antibiotics, amoxicillin/clavulanic acid and ampicillin/sulbactam, respectively, while 54% (67/124) of the strains were resistant to piperacillin/tazobactam. Phylogroup 1 (22/124) was detected more frequently among the strains in relation to phylogroup 2 (8/12). Conclusions: We demonstrated different association profiles of virulence genotype related to the β-lactamase genotype, the β-lactamase inhibitor resistome, phylogroups, and clinical origin of the strains. Therefore, medical treatment regimens against infections caused by P. aeruginosa should be improved. Full article

Growing evidence highlights the role of heavy metals in driving the co-selection of an-tibiotic resistance genes (ARGs), and the human oral cavity is an important reservoir of ARGs. This cross-sectional study investigated the effects of heavy metal exposure on human oral microbiota and ARGs, collecting buccal mucosal and blood samples from residents in a heavy metal-contaminated area (Baiyin City) and a non-contaminated area (Yuzhong County, Lanzhou City). The results showed heavy metal exposure is associated with altered alpha and beta diversity of bacteria and ARGs in human oral cavities, with bacterial compositional shifts being the main factor in ARG variation. Metagenomic analysis revealed heavy metal exposure is linked to modifying the interactions in the bacterial community and between ARGs and metal resistance genes (MRGs), shown by simplified topological structures in bacterial and resistome networks, along with enhanced positive correlations among nodes. Neisseria, Haemophilus, Morococcus, Streptococcus, Staphylococcus, and Mycobacteroides as potential hosts for resistance genes in human oral cavity. Furthermore, blood metal quantification revealed distinct associations with resistance patterns. This study demonstrates significant associations between environmental heavy metal exposure and the oral resistome and emphasizes the role of bacterial community composition. Full article

Antibiotics have revolutionized medicine and animal production, yet their extensive use has accelerated the emergence and spread of antimicrobial resistance (AMR). Beyond clinical contexts, livestock and aquaculture are now recognized as major contributors to the global resistome. This review synthesizes evidence across cattle, poultry, swine, sheep and goats, and aquaculture, highlighting how antimicrobial usage shapes resistance at the human–animal–environment interface. A substantial proportion of administered drugs is excreted unmetabolized, leading to the accumulation of unmetabolized antimicrobial residues, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) in soils, manures, waters, sediments, and air. These reservoirs function as long-term sources and dissemination pathways through runoff, leaching, bioaerosols, effluents, and biological vectors. Despite different production systems, similar ARG families dominate, particularly those conferring resistance to tetracyclines, sulfonamides, and β-lactams. Mobile genetic elements and co-selectors such as heavy metals, disinfectants, and microplastics reinforce their persistence. Aquaculture, where water serves both as habitat and vector, emerges as a critical hotspot, while small ruminant systems remain under-researched despite their importance in many low- and middle-income countries. This synthesis highlights convergent patterns across sectors: antimicrobial use drives ARG enrichment; manures, litters, sediments, and effluents act as persistent reservoirs; and dissemination routes connect farms, ecosystems, and human populations. Within a One Health framework, mitigation requires preventive strategies—vaccination, biosecurity, and optimized waste management—supported by harmonized stewardship policies and integrated environmental surveillance. Full article

The propagation of antibiotic resistance genes (ARGs) in aquatic environments poses a significant threat to global health. This study compared sediment resistome profiles in river crab (Eriocheir sinensis) polyculture systems with and without stone moroko (Pseudorasbora parva). The results showed that, compared to the control group (MC group), the sediment from the polyculture system containing stone moroko (PC group) exhibited significant reductions in the total abundances of ARGs, metal resistance genes (MRGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Crucially, the total abundance and composition of MGEs in pond sediment were substantially correlated with ARGs, MRGs, and BRGs, respectively. Co-occurrence network analysis revealed that there was only one edge between ARGs and MGEs in the PC group, whereas the MC group had eight edges. Additionally, the proportion of mobile ARGs in the PC group was significantly lower than that in the MC group. Alterations in resistome profiles were markedly associated with decreased levels of total carbon (TC) and phosphate in the sediment. All of the findings demonstrated that the introduction of stone moroko in the river crab polyculture system effectively mitigated the sediment resistome primarily by altering environmental factors and suppressing MGEs, thereby disrupting the horizontal transfer network of resistance genes. This study highlights the potential of leveraging aquatic biota as a novel biological strategy for the in situ management of environmental antimicrobial resistance. Full article

Dermatophilosis, caused by the Gram-positive, filamentous bacterium Dermatophilus congolensis, is an important skin disease that adversely affects cattle health and productivity. It also affects other domestic and wild animals and occasionally humans. This review provides a detailed overview of the molecular characteristics and resistome profile of D. congolensis, highlighting recent advances in genomic research. We examine the bacterium’s genome architecture, including its genome size, GC content, gene composition, and phylogenetic placement within the Actinomycetales. Key virulence factors are discussed, including proteolytic enzymes, hyphal invasion, zoospore motility, and the gene products of nasp and agac, emphasizing their roles in tissue invasion, pathogenesis, and diagnostic detection. Furthermore, we analyze resistome, focusing on identified antibiotic resistance genes, diverse resistance mechanisms such as efflux pumps and beta-lactamases, and the contribution of mobile genetic elements to horizontal gene transfer. The implications of these molecular insights for accurate diagnosis, effective treatment, and antibiotic stewardship in cattle production are critically evaluated. Finally, we highlight future research priorities aimed at deepening our understanding of D. congolensis biology and improving strategies for disease control. This review underscores the importance of integrating molecular surveillance with antimicrobial monitoring to safeguard cattle health and promote sustainable livestock management. Full article

This study investigated the effects of supplementing whole milk (WM) with sodium butyrate (SB) on the gastrointestinal microbiota of preweaned calves. Twelve newborn Holstein calves (4 days old, 39.21 ± 1.45 kg) were randomly assigned into one of two dietary treatments: (1) WM without SB (CON) and (2) WM supplemented with SB (8.8 g/d; SB). At 74 days of age, all calves were slaughtered to collect ruminal and cecal digesta. Metagenomic analysis was used to characterize the microbial composition, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs). SB supplementation altered the ruminal microbial composition and increased the abundance of beneficial bacteria, including Actinobacteria, Bifidobacterium, and Olsenella (p < 0.05). Although SB did not significantly affect the overall microbial composition or diversity in the cecum (p > 0.05), it promoted the growth of beneficial genera such as Flavonifractor and Subdoligranulum (p < 0.05). Furthermore, SB supplementation did not significantly alter the composition of VFGs or ARGs in either the rumen or the cecum (p > 0.05). However, significant differences in VFGs and ARGs were observed between the rumen and the cecum, with a greater diversity of both VFGs and ARGs detected in the cecum compared to that in the rumen (p < 0.05). In summary, supplementing whole milk with sodium butyrate modulates gastrointestinal health in preweaned calves by favorably shaping the microbial community without significantly altering the antibiotic resistome or virulome. Full article

Background: Mangrove ecosystems are critical coastal environments providing ecological services and acting as buffers between terrestrial and marine systems. Rising antibiotic use in aquaculture and coastal agriculture has led to the dissemination of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in these habitats. Aim: This narrative review aims to synthesize current knowledge on the prevalence, diversity, and environmental drivers of ARGs in mangrove ecosystems, highlighting their role as reservoirs and the potential for horizontal gene transfer. Methods: Studies published up to September 2024 were identified through PubMed, Scopus, Web of Science, and Google Scholar. Inclusion criteria focused on ARGs and ARB in mangrove sediments, water, and associated biota. Data on ARG prevalence, microbial community composition, detection methods, and environmental factors were extracted and narratively synthesized. Results: Seventeen studies from Asia, South America, and Africa were included. ARGs conferring resistance to tetracyclines, sulfonamides, β-lactams, and multidrug resistance were found to be widespread, particularly near aquaculture and urban-influenced areas. Metagenomic analyses revealed diverse resistomes with frequent mobile genetic elements, indicating high potential for horizontal gene transfer. Environmental factors, including sediment type, organic matter, and salinity, influenced ARG abundance and distribution. Conclusions: Mangrove ecosystems act as both reservoirs and natural buffers for ARGs. Sustainable aquaculture practices, continuous environmental monitoring, and integrated One Health approaches are essential to mitigate ARG dissemination in these sensitive coastal habitats. Full article

Veterinary hospital wastewater (VHW) is a significant environmental concern due to its high nutrient content, organic pollutants, and antibiotic resistance genes (ARGs). This study evaluated the physicochemical properties of VHW, its potential to support Arthrospira platensis cultivation, and its effects on microbial and resistome profiles. VHW contained high levels of ammonia nitrogen, total Kjeldahl nitrogen, biological oxygen demand (BOD), and chemical oxygen demand (COD), indicating substantial contamination. A. platensis was cultivated for 8 days in Zarrouk medium supplemented with 0–100% VHW. Biomass production peaked in 25% VHW (0.78 ± 0.05 g/L), while growth was strongly suppressed at concentrations ≥75%. Pigment levels in 25% VHW increased significantly compared to the control: 1.3-fold for chlorophyll-a (12.0 μg/mL), 1.5-fold for carotenoids (4.4 μg/mL), 1.7-fold for phycocyanin (120 μg/mL), and 2.3-fold for allophycocyanin (54 μg/mL). Shotgun metagenomic analysis revealed that A. platensis cultivation markedly altered the microbial community and reduced the prevalence of ARGs. In 25% VHW, Proteobacteria dominated the community (97.0%), but their abundance declined to 11.6% when co-cultivated with A. platensis. Likewise, Acinetobacter sp. carrying high levels of the aph gene, along with Methylophaga sp. and Pseudomonas_E sp. harboring oqxB, decreased substantially, suggesting that A. platensis effectively suppressed ARG-rich genera. These findings highlight the dual potential of A. platensis for sustainable pigment-rich biomass production and efficient wastewater treatment. Full article