Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan. - Related Documents




#
Rank
Similarity
Title + Abs.
Year
PMID
012345
683501.0000Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan. Antibiotic resistance genes (ARGs) present in urban rivers have the potential to disseminate antibiotic-resistant bacteria into other environments, posing significant threats to both ecological and public health. Although metagenomic analyses have been widely employed to detect ARGs in rivers, our understanding of their dynamics across different seasons in diverse watersheds remains limited. In this study, we performed a comprehensive genomic analysis of the Kanda River in Japan at 11 sites from upstream to estuary throughout the year to assess the spread of ARGs and their associations with bacterial communities. Analysis of 110 water samples using the 16S rRNA gene revealed variations in bacterial composition corresponding to seasonal changes in environmental parameters along the river. Shotgun metagenomics-based profiling of ARGs in 44 water samples indicated higher ARG abundance downstream, particularly during the summer. Weighted gene co-expression network analysis (WGCNA) linking bacterial lineages and ARGs revealed that 12 ARG subtypes co-occurred with 128 amplicon sequence variants (ASVs). WGCNA suggested potential hosts for ErmB, ErmF, ErmG, tetQ, tet (W/N/W), aadA2, and adeF, including gut-associated bacteria (e.g., Prevotella, Bacteroides, Arcobacter) and indigenous aquatic microbes (e.g., Limnohabitans and C39). In addition, Pseudarcobacter (a later synonym of Arcobater) was identified as a host for adeF, which was also confirmed by single cell genomics. This study shows that ARG distribution in urban rivers is affected by seasonal and geographical factors and demonstrates the importance of monitoring rivers using multiple types of genome sequencing, including 16S rRNA gene sequencing, metagenomics, and single cell genomics.202539488451
317610.9998Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil. The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs' abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.202337742410
321720.9998Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems. Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.202539689477
686230.9998Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China. Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.202337263036
686640.9998Deciphering the antibiotic resistome in stratified source water reservoirs in China: Distribution, risk, and ecological drive. The proliferation and dissemination of antibiotic resistance genes (ARGs) in source water reservoirs may pose a threat to human health. This study investigated the antibiotic resistance in stratified reservoirs in China across different seasons and spatial locations. In total, 120 ARG subtypes belonging to 15 ARG types were detected with an abundance ranging from 171.06 to 793.71 × /Gb. Multidrug, tetracycline, aminoglycoside, and bacitracin resistance genes were dominant in the reservoirs. The abundance and transfer potential of ARGs were notably higher, especially during the stratified period, with markedly elevated levels in the bottom layer compared to the surface layer. Metagenomic assembly yielded 1357 ARG-carrying contigs, belonging to 83 resistant bacterial species, of which 13 were identified as human pathogen bacteria (HPB). HPB hosts (Sphingomonas sp., Burkholderiales sp., and Ralstonia sp., etc.) were super carriers of ARGs. Genes including ompR, bacA, golS, and ugd carried on HPB plasmids exhibited higher abundance in the water, warranting attention to the risk of resistance transmission. Environmental pressures have caused a shift in the assembly mechanism of ARGs, transitioning from a random process in surface water to a deterministic process in bottom water. The results of this study will deepen people's understanding of the ARG risk in stratified reservoirs.202539673943
683650.9998Microbiome and antibiotic resistome in household dust from Beijing, China. We spend ever-increasing time indoors along with urbanization; however, the geographical distribution patterns of microbiome and antibiotic resistome, and their driving forces in household environment remains poorly characterized. Here, we surveyed the bacterial and fungal communities, and the resistome in settled dust gathered from 82 homes located across Beijing, China, employing Illumina sequencing and high-throughput quantitative PCR techniques. There was no clear geographical distribution pattern in dust-related bacterial communities although a slight but significant (P < 0.05) distance-decay relationship occurred in its community similarity; by contrast, a relatively distinct geographical clustering and a stronger distance-decay relationship were observed in fungal communities at the local scale. The cross-domain (bacteria versus fungi) relationships in the microbiome of the dust samples were mostly observed as robust co-occurrence correlations. The bacterial communities were dominated by Proteobacteria and Actinobacteria phyla, with human skin, soil and plants being potential major sources. The fungal communities largely comprised potential allergens (a median 61% of the fungal sequences), with Alternaria genus within Ascomycota phylum being the most predominant taxa. The profile of dust-related bacterial communities was mainly affected by housing factors related to occupants and houseplants, while that of fungal communities was determined by georeferenced environmental factors, particularly vascular plant diversity. Additionally, a great diversity (1.96 on average for Shannon index) and normalized abundance (2.22 copies per bacterial cell on average) of antibiotic resistance genes were detected across the dust samples, with the dominance of genes resistant to vancomycin and Macrolide-Lincosamide-Streptogramin B. The resistome profile exhibited no distinct geographical pattern, and was primarily driven by certain bacterial phyla and occupancy-related factors. Overall, we underline the significance of anthropogenic impacts and house location in structuring bacterial and fungal communities inside homes, respectively, and suggest that household dust is an overlooked reservoir for antibiotic resistance.202032248025
728560.9998Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.201829765365
686870.9998Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River. As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6')-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.202438039820
686380.9998Prevalence, source and risk of antibiotic resistance genes in the sediments of Lake Tai (China) deciphered by metagenomic assembly: A comparison with other global lakes. Lakes are one of the natural reservoirs of antibiotic resistance genes (ARGs) in environments. Long retention times in lakes potentially allow ARGs to persist and may create increased opportunities for the emergence of resistant pathogens. In this study, we investigated the prevalence, source and dissemination risk of ARGs in the sediments of a typical urban lake, Lake Tai (China) which has been a drastic example of water pollution with eutrophication in the world due to its proliferated cyanobacterial blooms. High-throughput profilings of ARGs in the sediments of Lake Tai were characterized with metagenomic assembly, and were compared with those in other global lakes from Australia, Canada, Indonesia, Rwanda and the United States of America. The hosts of ARGs in the sediments of Lake Tai were explored based on the taxonomic annotation of ARG-carrying contigs and network analysis, and a novel recently-discovered crAssphage was employed for source tracking of resistance bacteria. Meanwhile, the potential resistome risk was identified by projecting the co-occurrence of acquired ARGs, mobile genetic elements (MGEs) and human bacterial pathogens into a three-dimensional exposure space. Results showed 321 ARG subtypes belonging to 21 ARG types were detected in the sediments of Lake Tai, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone, mupirocin and trimethoprim resistance genes. Relatively, the ARG levels in the sediments of Lake Tai were significantly higher than those in other global lakes. Source tracking showed the coverages of detected crAssphage in the sediments of Lake Tai were positively correlated with the total ARG coverage, suggesting the contribution of human fecal contamination to the prevalence of ARGs in this lake. It should be noted that the co-occurrence ratio of ARGs, MGEs and human pathogens in the sediments of Lake Tai was higher than that in other global lakes, likely indicating a higher risk for the resistance dissemination in the China's third largest freshwater lake.201930928850
686790.9998Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches. Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.202438452676
6850100.9998Fate of high-risk antibiotic resistance genes in large-scale aquaculture sediments: Geographical differentiation and corresponding drivers. Antibiotic resistance genes (ARGs), emerging environmental contaminants, have become challenges of public health security. However, the distribution and drivers of ARGs, especially high-risk ARGs, in large-scale aquaculture sediments remain unknown. Here, we collected sediment samples from 40 crayfish ponds in seven main crayfish culture provinces in China and then investigated the distribution and risk of ARGs based on high-throughput sequencing and quantitative PCR techniques. Our results suggested that aquaculture sediment was potential reservoir of ARGs and the abundance of aadA-02 was the highest. High-risk ARG (floR) was also prevalent in the sediment and was the most abundant in Jiangsu Province, where opportunistic pathogens were also enriched. The abundance of floR was positively correlated with different environmental factors, such as total phosphorus in water and total carbon in sediment. In addition, Mycobacterium sp., opportunistic pathogenic bacteria, might be potential host for floR. Furthermore, the potential propagation pathway of ARGs was from sediment to crayfish gut, and Bacteroidetes and Proteobacteria might be the main bacterial groups responsible for the proliferation of ARGs. Generally, our results illustrate that pond sediment may be an ARG reservoir of aquatic animals. Meanwhile, our study helps develop valuable strategies for accessing risks and managing ARGs.202337714353
7371110.9998Plastisphere and the occurrence of antibiotic resistance in a 40-year-old abandoned coastal landfill site in Chile. Plastispheres are microbial communities that inhabit plastic surfaces and have been extensively studied in aquatic environments. However, little is known about their occurrence in landfills. We investigated plastisphere communities in a 40-year-old coastal abandoned landfill in Rocuant-Andalién, Chile, and aimed to characterize landfill plastisphere communities and assess their potential role as reservoirs of antibiotic resistance genes (ARGs). High-density polyethylene was the predominant plastic type (56 %). Microscopy revealed diverse bacterial morphotypes, including bacilli, cocci, and filamentous forms, forming clusters on plastic surfaces. 16S rRNA gene sequencing revealed that Actinobacteria, Firmicutes, and Proteobacteria dominated most samples, with high overall diversity and richness. Beta diversity analysis indicated significant variation in bacterial communities among sites but not among polymer types. Notably, the intI1 gene, associated with the spread of antibiotic resistance, was detected at 67 % of the sampled sites. These findings reveal that landfills act as reservoirs for a wide range of bacteria, some of which may have clinical significance, highlighting their ecological and public health impact. Furthermore, plastics are likely to transport resistance genes originating from human activities, spreading them into nearby ecosystems, such as wetlands and oceans, where they interact with wildlife.202541109620
3213120.9998Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas. Groundwater is an essential public and drinking water supply and its protection is a goal for global policies. Here, we investigated the presence and prevalence of antibiotic residues, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial contamination in groundwater environments at various distances from urban areas. Antibiotic concentrations ranged from below detection limit to 917 ng/L, being trimethoprim, macrolide, and sulfonamide the most abundant antibiotic classes. A total of eleven ARGs (aminoglycoside, β-lactam, chloramphenicol, Macrolide-Lincosamide-Streptogramin B - MLSB, sulfonamide, and tetracycline), one antiseptic resistance gene, and two MGEs were detected by qPCR with relative abundances ranging from 6.61 × 10(-7) to 2.30 × 10(-1) copies/16S rRNA gene copies. ARGs and MGEs were widespread in the investigated groundwater environments, with increased abundances not only in urban, but also in remote areas. Distinct bacterial community profiles were observed, with a higher prevalence of Betaproteobacteria and Bacteroidetes in the less-impacted areas, and that of Firmicutes in the contaminated groundwater. The combined characteristics of increased species diversity, distinct phylogenetic composition, and the possible presence of fecal and/or pathogenic bacteria could indicate different types of contamination. Significant correlations between ARGs, MGEs and specific taxa within the groundwater bacterial community were identified, revealing the potential hosts of resistance types. Although no universal marker gene could be determined, a co-selection of int1, qacEΔ1 and sulI genes, a proxy group for anthropogenic pollution, with the tetC, tetO, tetW resistance genes was identified. As the tet group was observed to follow the pattern of environmental contamination for the groundwater samples investigated in this study, our results strongly support the proposal of this group of genes as an environmental tracer of human impact. Overall, the present study investigated several emerging contaminants in groundwater habitats that may be included in monitoring programs to enable further regulatory and protection measures.201829454283
7286130.9998Influence of Seasonality and Pollution on the Presence of Antibiotic Resistance Genes and Potentially Pathogenic Bacteria in a Tropical Urban River. BACKGROUND/OBJECTIVES: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. METHODS: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. RESULTS: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. CONCLUSIONS: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems.202540867992
6864140.9998Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes. Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.202134380279
6852150.9998Distribution and co-occurrence patterns of antibiotic resistance genes in black soils in Northeast China. Black soils (Mollisols) are among the most important soil resources for crop production and food security. In China, they are mainly distributed in the northeastern region. To investigate soil antibiotic resistance distribution patterns and monitor soil quality, we randomly chose nine corn fields in Northeast China and analyzed the antibiotic resistance gene (ARG) distribution and co-occurrence patterns on the basis of high-throughput approaches and network analyses. High genetic diversity (136 unique genes) and low ARG abundances (10(-5)-10(-2) copies/16S rRNA gene copy) were detected, with relatively few interactions among ARGs. Type I integron genes were prevalent in the soil and were positively correlated with ARGs, which may increase the risk of ARG transmission. Most ARGs were strongly associated with microorganisms. Moreover, several ARGs were significantly correlated with antibiotics, nutrients, and metal elements. The generation and dissemination of ARGs, which were most likely mediated by mobile genetic elements (MGEs) and bacteria, were affected by environmental conditions. These results provide insights into the widespread co-occurrence patterns in soil resistomes.202235809539
6886160.9997Bacterial community and antibiotic resistance genes assembly processes were shaped by different mechanisms in the deep-sea basins of the Western Pacific Ocean. As the intrinsic property of microorganisms, antibiotic resistance genes (ARGs) are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, human activities often obscure the natural distribution of ARGs through deterministic selective pressures. The deep-sea basin of the western Pacific Ocean is one of the least disturbed areas globally by human activities, providing a natural laboratory to investigate the intrinsic mechanisms governing ARGs in natural environments. In this study, we analyzed bacterial community and ARG diversity in 15 surface sediment samples from three deep-sea basins in the western Pacific Ocean. The relative abundance of ARGs in the surface sediments ranged from 3.10 × 10(-3) to 5.37 × 10(-2) copies/16S rRNA copies, with multidrug and β-lactam resistance genes dominated in all samples (49.06%-100%). The bacteria were mainly dominated by the Proteobacteria. The principal coordinate analysis (PCoA) showed significant spatial heterogeneity of ARGs and bacteria among the three basins. Null model, neutral community models (NCM), and normalized stochasticity ratio (NST) indicated that bacterial community was dominated by stochastic assembly, driven by geographic barriers leading to independent evolution. Conversely, the NST revealed that the ARGs profile was mainly shaped by deterministic processes. Environmental factors are more crucial than geographical factors and bacterial community for ARG occurrence among the selected factors. Meanwhile, we found that the spread of ARGs was mainly through vertical gene transfer in the pre-antibiotic era. The disparity between the assembly processes of bacterial community and ARGs may be attributed to the fact that ARG hosts were not the dominant bacteria in the community. This study first reported the distribution and assembly processes of ARGs and bacterial community in surface sediments of the western Pacific.202439481517
3177170.9997Metagenomic investigation of antibiotic resistance genes and resistant bacteria contamination in pharmaceutical plant sites in China. Pharmaceutical plant sites play a significant role in the dissemination of antibiotic resistance genes (ARGs) into the environment. It is imperative to comprehensively monitor of ARGs across various environmental media at these sites. This study focused on three pharmaceutical plants, two located in North China and one in South China. Through metagenomic approaches, we examined the composition, mobility potential, and bacterial hosts of ARGs in diverse media such as process water, groundwater, topsoil, soil cores, and pharmaceutical fermentation residues across diverse environmental matrices, including topsoil, soil cores, process water, groundwater, and pharmaceutical fermentation residues. We identified a wide array of ARGs, comprising 21 types and 740 subtypes, with process water exhibiting the highest abundance and diversity. Treatment processes varied in their efficacy in eliminating ARGs, and the clinically relevant ARGs should also be considered when evaluating wastewater treatment plant efficiency. Geographical distinctions in groundwater ARG distribution between northern and southern regions were observed. Soil samples from the three sites showed minimal impact from pharmaceutical activity, with vancomycin-resistance genes being the most prevalent. High levels of ARGs in pharmaceutical fermentation residues underscore the necessity for improved waste management practices. Metagenomic assembly revealed that plasmid-mediated ARGs were more abundant than chromosome-mediated ARGs. Metagenome-assembled genomes (MAGs) analysis identified 166 MAGs, with 62 harboring multiple ARGs. Certain bacteria tended to carry specific types of ARGs, revealing distinct host-resistance associations. This study enhances our understanding of ARG dissemination across different environmental media within pharmaceutical plants and underscores the importance of implementing strict regulations for effluent and residue discharge to control ARG spread.202438960118
6845180.9997A Comparative Analysis of Aquatic and Polyethylene-Associated Antibiotic-Resistant Microbiota in the Mediterranean Sea. In this study, we evaluated the microbiome and the resistome profile of water and fragments of polyethylene (PE) waste collected at the same time from a stream and the seawater in a coastal area of Northwestern Sicily. Although a core microbiome was determined by sequencing of the V3-V4 region of the bacterial 16S rDNA gene, quantitative differences were found among the microbial communities on PE waste and the corresponding water samples. Our findings indicated that PE waste contains a more abundant and increased core microbiome diversity than the corresponding water samples. Moreover, PCR analysis of specific antibiotic resistance genes (ARGs) showed that PE waste harbors more ARGs than the water samples. Thus, PE waste could act as a carrier of antibiotic-resistant microbiota, representing an increased danger for the marine environment and living organisms, as well.202133800749
3215190.9997Prevalence of antibiotic resistance genes its association with microbiota in raw milk of northwest Xinjiang. The issue of antibiotic resistance caused by antibiotic resistance genes (ARGs) has become a significant concern in environmental research in recent years, while raw milk is an important link in the food chain and has become one of the carriers and reservoirs of ARGs, which has not been taken seriously. This research employed high-throughput quantitative PCR and Illumina sequencing techniques targeting the 16S rRNA gene. These methods were used to examine the bacterial community composition and genes associated with antibiotic resistance in raw milk samples collected from the northwestern area of Xinjiang. An aggregate of 31 distinct resistance alleles were identified, with their abundance reaching as high as 3.70 × 10(5) copies per gram in the analyzed raw milk samples. Microorganisms harboring ARGs that confer resistance to beta-lactams, tetracyclines, aminoglycosides, and chloramphenicol derivatives were prevalent in raw milk. Procrustes analysis revealed a certain degree of correlation between the microbial community and the antibiotic resistance gene (ARG) profiles. Furthermore, network analysis demonstrated that Actinobacteria and Firmicutes were the predominant phyla exhibiting co-occurrence relationships with specific ARGs. Combining the findings from Variance Partitioning Analysis (VPA), the distribution of ARGs was mainly driven by three factors: the combined effect of physicochemical properties and mobile genetic elements (MGEs) (33.5%), the interplay between physicochemical parameters and microbial communities (31.8%), and the independent contribution of physicochemical factors (20.7%). The study demonstrates that the overall abundance of ARGs correlates with physicochemical parameters, bacterial community composition, and the presence of MGEs. Furthermore, understanding these associations facilitates the evaluation of antibiotic resistance risks, thereby contributing to enhanced farm management practices and the assurance of food safety.202540718809