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679300.9905Interplays between cyanobacterial blooms and antibiotic resistance genes. Cyanobacterial harmful algal blooms (cyanoHABs), which are a form of microbial dysbiosis in freshwater environments, are an emerging environmental and public health concern. Additionally, the freshwater environment serves as a reservoir of antibiotic resistance genes (ARGs), which pose a risk of transmission during microbial dysbiosis, such as cyanoHABs. However, the interactions between potential synergistic pollutants, cyanoHABs, and ARGs remain poorly understood. During cyanoHABs, Microcystis and high microcystin levels were dominant in all the nine regions of the river sampled. The resistome, mobilome, and microbiome were interrelated and linked to the physicochemical properties of freshwater. Planktothrix and Pseudanabaena competed with Actinobacteriota and Proteobacteria during cyanoHABs. Forty two ARG carriers were identified, most of which belonged to Actinobacteriota and Proteobacteria. ARG carriers showed a strong correlation with ARGs density, which decreased with the severity of cyanoHAB. Although ARGs decreased due to a reduction of ARG carriers during cyanoHABs, mobile gene elements (MGEs) and virulence factors (VFs) genes increased. We explored the relationship between cyanoHABs and ARGs for potential synergistic interaction. Our findings demonstrated that cyanobacteria compete with freshwater commensal bacteria such as Actinobacteriota and Proteobacteria, which carry ARGs in freshwater, resulting in a reduction of ARGs levels. Moreover, cyanoHABs generate biotic and abiotic stress in the freshwater microbiome, which may lead to an increase in MGEs and VFs. Exploration of the intricate interplays between microbiome, resistome, mobilome, and pathobiome during cyanoHABs not only revealed that the mechanisms underlying the dynamics of microbial dysbiosis but also emphasizes the need to prioritize the prevention of microbial dysbiosis in the risk management of ARGs.202337897871
638110.9905Occurrence and distribution of antibiotic resistance genes in Elymus nutans silage from different altitudes on the Qinghai-Tibetan Plateau. INTRODUCTION: Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) have attracted more attentions in fermented feed recently. However, little information is available on the occurrence and distribution of ARGs in ensiled forages in the alpine region of the Qinghai-Tibetan plateau (QTP) with an extremely harsh environment. METHODS: The study investigated the distribution and spread mechanism of ARB and ARGs in Elymus nutans silage along 2600 m (low), 3600 m (medium) and 4600 m (high) altitude in the QTP. RESULTS: The major ARG types in Elymus nutans silage were multidrug, aminoglycoside, bacitracin, beta-lactam and polymyxin, while tnpA and IS91 were the dominant mobile genetic elements (MGEs) subtypes in the Elymus nutans silage. The dominant ARGs were mainly carried by Pantoea, Enterobacter, Serratia, and Lelliottia. Although altitudinal gradient had no influence on the diversity or abundance of other ARGs and MGEs in the Elymus nutans silage (p > 0.05), the network co-occurrence patterns among ARGs, MGEs, and bacteria in high-altitude silage were more complex than that in low- and medium-altitude silages. The dominant clinical ARGs in the alpine silage were bacA and acrF, and the abundance of clinical ARGs decreased with prolonged fermentation time. DISCUSSION: This study provides important data on the status of ARGs in ensiled forage from the alpine region of the QTP.202540458713
700420.9899Sheep and rapeseed cake manure promote antibiotic resistome in agricultural soil. The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Both rapeseed cake manure and sheep manure increased the abundance and diversity of ARGs, with sheep manure particularly enhancing the abundance of ARGs conferring resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB). Mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that rapeseed cake manure and sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.202540633350
638330.9898Metagenomic analysis of microbiological risk in bioaerosols during biowaste valorization using Musca domestica. Bioconversion using insects has gradually become a promising technology for biowaste management and protein production. However, knowledge about microbiological risk of insect related bioaerosols is sparse and conventional methods failed to provide higher resolved information of environmental microbe. In this study, a metagenomic analysis including microorganisms, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile gene elements (MGEs), and endotoxin distribution in bioaerosols during biowaste conversion via Musca domestica revealed that bioaerosols in Fly rearing room possess the highest ARGs abundances and MGEs diversity. Through a metagenome-assembled genomes (MAGs)-based pipeline, compelling evidence of ARGs/VFGs host assignment and ARG-VFG co-occurrence pattern were provided from metagenomic perspective. Bioaerosols in Bioconversion and Maggot separation zone were identified to own high density of MAGs carrying both ARGs and VFGs. Bacteria in Proteobacteria, Actinobacteriota, and Firmicutes phyla were predominate hosts of ARGs and VFGs. Multidrug-Motility, Multidrug-Adherence, and Beta lactam-Motility pairs were the most common ARG-VFG co-occurrence pattern in this study. Results obtained are of great significance for microbiological risk assessment during housefly biowaste conversion process.202336681377
682140.9895Mangrove plastisphere as a hotspot for high-risk antibiotic resistance genes and pathogens. Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.202540043931
700750.9895Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils. Organic manure has been implicated as an important source of antibiotic resistance genes (ARGs) in agricultural soils. However, the profiles of biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence genes (VGs) and their bacterial hosts in manure-amended soils remain largely unknown. Herein, a systematic metagenome-based survey was conducted to comprehensively explore the changes in resistomes, VGs and their bacterial hosts, mobile genetic elements (MGEs), and pathogenic bacteria in manure-amended greenhouse soils. Many manure-borne ARGs, BRGs, MRGs, VGs, and bacterial pathogens could be transferred into soils by applying manures, and their abundance and diversity were markedly positively correlated with greenhouse planting years (manure amendment years). The main ARGs transferred from manures to soils conferred resistance to tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin. Both statistical analysis and gene arrangements showed a good positive co-occurrence pattern of ARGs/BRGs/MRGs/VGs and MGEs. Furthermore, bacterial hosts of resistomes and VGs were significantly changed in the greenhouse soils in comparison with the field soils. Our findings confirmed the migration and dissemination of resistomes, VGs, and bacterial pathogens, and their accumulation and persistence were correlated with the continuous application of manures.202032298867
693960.9894Field ponding water exacerbates the dissemination of manure-derived antibiotic resistance genes from paddy soil to surrounding waterbodies. Farmlands fertilized with livestock manure-derived amendments have become a hot topic in the dissemination of antibiotic resistance genes (ARGs). Field ponding water connects rice paddies with surrounding water bodies, such as reservoirs, rivers, and lakes. However, there is a knowledge gap in understanding whether and how manure-borne ARGs can be transferred from paddy soil into field ponding water. Our studies suggest that the manure-derived ARGs aadA1, bla1, catA1, cmlA1-01, cmx(A), ermB, mepA and tetPB-01 can easily be transferred into field ponding water from paddy soil. The bacterial phyla Crenarchaeota, Verrucomicrobia, Cyanobacteria, Choloroflexi, Acidobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are potential hosts of ARGs. Opportunistic pathogens detected in both paddy soil and field ponding water showed robust correlations with ARGs. Network co-occurrence analysis showed that mobile genetic elements (MGEs) were strongly correlated with ARGs. Our findings highlight that manure-borne ARGs and antibiotic-resistant bacteria in paddy fields can conveniently disseminate to the surrounding waterbodies through field ponding water, posing a threat to public health. This study provides a new perspective for comprehensively assessing the risk posed by ARGs in paddy ecosystems.202337007487
682370.9891Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient. The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.202235716556
700580.9891The mobility, host, and co-occurrence of antibiotic resistance genes in multi-type pig manure-soil systems: Metagenome assembly analysis. Antibiotic resistance genes (ARGs) pose significant threats to public health and environmental safety, yet the mobility and hosts of ARGs in animal manure-soil systems remain poorly understood. Here, we evaluated the environmental risks of tilmicosin (TIL) and investigated ARG profiles, mobility, and drivers in pig manure-soil systems using metagenomic assembly. TIL was effectively degraded during aerobic composting and fertilization via hydroxylation, demethylation, and deglycosylation. Notably, the total abundance of ARGs significantly decreased during aerobic composting and fertilization, and manure types affected the distribution and composition of ARGs in fertilized soils. There was a special correlation between the genetic location and type of ARGs. In addition, the results showed co-localization of some specific ARGs and mobile genetic elements (MGEs) (tetA-tetR- transposase; tetR-floR- Tn3 family). A significant correlation was found between Escherichia coli and multiple ARG types, especially multidrug ARGs. Microbial community was the dominant factor driving the variations of ARGs in pig manure-soil systems, followed by MGEs, environmental factors, and antibiotic concentration. This study advances the understanding on the environmental risk assessment of TIL and elucidates the key drivers of ARG dissemination in pig manure-soil systems, providing critical insights and actionable strategies for sustainable livestock management and environmental risk control.202540865323
693790.9891Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river. Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.202540712359
7006100.9890Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting. Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.202337409977
6829110.9890Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater. The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.202540614847
7167120.9889Occurrence and distribution of antibiotic pollution and antibiotic resistance genes in seagrass meadow sediments based on metagenomics. Seagrass meadows are one of the most important coastal ecosystems that provide essential ecological and economic services. The contamination levels of antibiotic and antibiotic resistance genes (ARGs) in coastal ecosystems are severely elevated owing to anthropogenic disturbances, such as terrestrial input, aquaculture effluent, and sewage discharge. However, few studies have focused on the occurrence and distribution of antibiotics and their corresponding ARGs in this habitat. Thus, we investigated the antibiotic and ARGs profiles, microbial communities, and ARG-carrying host bacteria in typical seagrass meadow sediments collected from Swan Lake, Caofeidian shoal harbor, Qingdao Bay, and Sishili Bay in the Bohai Sea and northern Yellow Sea. The total concentrations of 30 detected antibiotics ranged from 99.35 to 478.02 μg/kg, tetracyclines were more prevalent than other antibiotics. Metagenomic analyses showed that 342 ARG subtypes associated with 22 ARG types were identified in the seagrass meadow sediments. Multidrug resistance genes and RanA were the most dominant ARG types and subtypes, respectively. Co-occurrence network analysis revealed that Halioglobus, Zeaxanthinibacter, and Aureitalea may be potential hosts at the genus level, and the relative abundances of these bacteria were higher in Sishili Bay than those in other areas. This study provided important insights into the pollution status of antibiotics and ARGs in typical seagrass meadow sediments. Effective management should be performed to control the potential ecological health risks in seagrass meadow ecosystems.202438782270
7164130.9889Anthropogenic pressures amplify high-risk antibiotic resistome via co-selection among biocide resistance, virulence, and antibiotic resistance genes in the Ganjiang River basin: Drivers diverge in densely versus sparsely populated reaches. As the largest river in the Poyang Lake system, the Ganjiang River faces escalating anthropogenic pressures that amplify resistance gene dissemination. This study integrated antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) to reveal their co-selection mechanisms and divergent environmental drivers between densely (DES) and sparsely populated (SPAR) regions of the Ganjiang River basin. The microbial and viral communities and structures differed significantly between the DES and SPAR regions (PERMANOVA, p < 0.001). Midstream DES areas were hotspots for ARGs/BRGs/VFGs enrichment, with peak enrichment multiples reaching 10.2, 5.7, and 5.9-fold respectively. Procrustes analysis revealed limited dependence of ARGs transmission on mobile genetic elements (MGEs) (p > 0.05). Separately, 74 % of dominant ARGs (top 1 %) showed strong correlations with BRGs (r(2) = 0.973, p < 0.01) and VFGs (r(2) = 0.966, p < 0.01) via co-selection. Pathogenic Pseudomonas spp. carrying multidrug-resistant ARGs, BRGs, and adhesion-VFGs were identified as high-risk vectors. In SPAR areas, anthropogenic pressure directly dominated ARGs risk (RC = 54.2 %, β = 0.39, p < 0.05), with biological factors as secondary contributors (RC = 45.8 %, β = 0.33, p < 0.05). In contrast, DES regions showed anthropogenic pressure exerting broader, enduring influences across microorganisms, physicochemical parameters, and biological factors, escalating ARGs risks through diverse pathways, with BRGs/VFGs acting as direct drivers. This study proposes establishing a risk prevention system using BRGs and pathogenic microorganisms as early-warning indicators.202540858019
7168140.9889Insights into microbial contamination in multi-type manure-amended soils: The profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes. Concerns regarding biological risk in environment have garnered increasing attention. Manure has been believed to be a significant source of antibiotic resistance genes (ARGs) in agricultural soil. Nevertheless, the profile of microbial contamination including ARGs, virulence factor genes (VFGs) and human bacterial pathogens (HBPs) in different manure-amended soils remain largely unknown. Here, we conducted the systematic metagenome-based study to explore changes in resistome, VFGs and HBPs in soils treated by frequently-used manures. The results revealed that many manure-borne ARGs, VFGs, and HBPs could be spreaded into soils, and their diversity and abundance were significantly different among chemical fertilizer, pig manure, chicken manure, cow dung and silkworm excrement application. A total of 157 potential HBPs accounting about 1.33% of total bacteria were detected. The main ARGs transferred from manures to soil conferred resistance to vancomycin and macrolide-lincosamide-streptogramin. The series analysis revealed positive co-occurrence patterns of ARGs-HBPs, VFGs-HBPs and ARGs-VFGs. Microbial contamination were more serious in pig manure and silkworm excrement sample than in the other samples, implying the usage of these two manures increased the risk of HBPs and dissemination of ARGs. This study confirmed the prevalence and discrepancy of resistome, VFGs and HBPs in different manure-amended soils.202235728317
6790150.9888Overlooked dissemination risks of antimicrobial resistance through green tide proliferation. Green tides, particularly those induced by Enteromorpha, pose significant environmental challenges, exacerbated by climate change, coastal eutrophication, and other anthropogenic impacts. More concerningly, these blooms may influence the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) within ecosystems. However, the manner in which Enteromorpha blooms affect the distribution and spread of antimicrobial resistance (AMR) remains uncertain. This study investigated ARG profiles, dynamic composition, and associated health risks within the Enteromorpha phycosphere and surrounding seawater in typical bays (Jiaozhou, Aoshan, and Lingshan) in the South Yellow Sea. The Enteromorpha phycosphere exhibited significantly higher ARG abundance (p < 0.05) but lower diversity compared to the surrounding seawater. Source-tracking and metagenomic analyses revealed that the phycosphere was the main contributor to the resistome of surrounding seawater. Moreover, resistant pathogens, especially ESKAPE pathogens, with horizontal gene transfer (HGT) potential, were more abundant in the phycosphere than in the surrounding seawater. The phycosphere released high-risk ARGs to the surrounding seawater during Enteromorpha blooms, posing serious health and ecological AMR risks in marine environments. This study highlights the significant role of Enteromorpha blooms in ARG spread and associated risks, urging a reassessment of AMR burden from a public health perspective.202539488061
7169160.9888Distributions of pathogenic bacteria, antibiotic resistance genes, and virulence factors in pig farms in China. The abundance of antibiotic resistance genes (ARGs) in pig feces can lead to their dissemination in the pig farm environment, posing a serious risk to human health through potential exposure and transmission. However, the extent of microbial contamination in pig farms, including ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and human bacterial pathogens (HBPs), is still largely unknown. In this study, metagenomics was employed to identify the composition and characteristics of microorganism communities, ARGs, VFGs, MGEs and HBPs in pig farm environments from seven different regions of China. The results showed that there were significant differences in the composition of microorganisms and Firmicutes, Bacteroides, Proteobacteriahe Spirochaetes were the dominant phyla in the pig farm environment. The abundance and composition of ARGs, VFGs, MGEs and HBPs varied significantly in pig farm environments in different regions, with the abundance in Fujian being significantly higher than that in other regions. In total, 216 ARGs, 479 VFGs, 143 MGEs and 78 HBPs were identified across all pig feces, soil, and wastewater samples. The most prominent ARGs were those related to tetracycline, aminoglycoside, and MLS resistance. Escherichia coli, Arcobacter cryaerophilus, Corynebacterium xerosis, Aerococcus viridans, and Collinsella aerofaciens were the most commonly found HBPs in the pig farm environment. Procrustes analysis and Mantel test results showed a strong correlation between ARGs and HBPs, VFGs and HBPs, and ARGs and VFGs. ARGs were mainly harbored by E. coli, Klebsiella pneumoniae, and Enterococcus faecalis in the pig farm environments. The random forest model indicated that the presence of MGEs (intI1, IS91, and tnpA) was significantly correlated with the total abundance of resistance genes, which can be utilized as an important indicator for measuring resistance genes. The study establishes a foundational understanding of the prevalence and diversity of ARGs, VFGs, and HBPs in pig farm environments, aiding in the development of effective management strategies to mitigate ecological and public health risks.202540609272
6830170.9888Heavy metal could drive co-selection of antibiotic resistance in terrestrial subsurface soils. Terrestrial surface ecosystems are important sinks for antibiotic resistance genes (ARGs) due to the continuous discharge of contaminants from human-impacted ecosystems. However, the abundance and resistance types of ARGs and their influencing factors in terrestrial subsurface soils are not well known. In this study, we investigated the abundance and diversity of ARGs, and their correlations with metal resistance genes (MRGs), mobile genetic elements (MGEs), bacteria, and heavy metals in subsurface soils using high throughput quantitative PCR and metagenomic sequencing approaches. Abundant and diverse ARGs were detected with high spatial heterogeneity among sampling sites. Vertically, there was no significant difference in ARG profiles between the aquifer and non-aquifer soils. Heavy metals were key factors shaping ARG profiles in soils with high heavy metal contents, while they showed no significant effect in low contents. Moreover, heavy metals could trigger the proliferation of antibiotic resistance by increasing MGE abundance or influencing bacterial communities. Metagenomic analysis also revealed the widespread co-occurrence of ARGs and MRGs, with heavy metals possibly enhancing the co-selection of ARGs and MRGs in soils with high heavy metal contents. This study highlighted the heavy metal-driven co-selection of ARGs and revealed the occurrence of ARG pollution in terrestrial subsurface soils.202133858075
6804180.9887Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics. Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.202438636860
8111190.9887Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system. Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.202539970645