Spread Of Antibiotic Resistance Genes Research Articles

Deciphering the Driving Mechanism and Regulatory Strategies of Antibiotic Resistance Genes Transmission in Lead-Contaminated Soil Microbial Communities by Multiple Remediation Methods

Pb-contaminated soil poses inherent risks for the spread of antibiotic resistance genes (ARGs). However, few reports have investigated the distribution of lead resistance genes (LRGs), particularly their role in ARGs dynamics during Pb-contaminated soil remediation. This study explored the mechanisms driving ARGs variation under different remediation strategies. The results indicated that an increase in the total abundance of ARGs after applying montmorillonite (Imvite), the composite remediation agents of MgO and Ca(H2PO4)2 (MgO-Ca(H2PO4)2), and the composite remediation agents of montmorillonite, MgO, and Ca(H2PO4)2 (Imvite-MgO-Ca(H2PO4)2). Bioelectrochemical systems (BES) effectively reduced ARGs abundance, and when combined with Imvite-MgO-Ca(H2PO4)2, lowered the risk of ARGs proliferation linked to antibiotic deactivation. Changes in Pb concentration and pH reshaped microbial communities, impacting both LRGs and ARGs. To reduce the risk of ARGs proliferation and transmission during, various control strategies, such as modifying Pb stress, adjusting pH, and manipulating microbial community structure, have been proposed. The study provided theoretical foundation and practical strategies for controlling ARGs dissemination during the remediation of heavy metal-contaminated soil.

Optimum Thermal Treatment for Removing Antibiotic Resistance Genes and Retaining Nutrients in Poultry Broiler Manure

Poultry broiler manure is a reservoir of antibiotic resistance genes (ARGs), antibiotics, organic carbon, and plant nutrients. However, its direct application leads to spread of ARGs in agricultural fields, causing public concerns. It is thus crucial to identify optimum heating conditions that remove ARGs while retaining nutrients. This study examined the effects of heating temperatures (100-500oC) and durations (30, 120 and 240min) on the removals of ARGs and antibiotics from poultry broiler manure and nutrient retention. The results showed that the poultry broiler manure contained a total of 211 ARG subtypes, which were susceptible to temperature. The contents of ARGs and antibiotics decreased with increasing temperature. The temperature had a significant effect on the loss of available phosphorus (r = -0.893, P <0.01), while other nutrients had no significant loss. The results show that the heat treatment at 110°C for 240min maximized the removals of ARGs while the loss of nutrients was minimized. Under these optimum conditions, all ARGs and antibiotics (e.g., oxytetracycline, tetracycline, doxycycline, tilmicosin, tylosin, sulfamethazine, and sulfadiazine) were removed while 91.98% of total carbon, 99.89% of total nitrogen, 92.38% of total phosphorus, 50.10% of available phosphorus, 99.96% of total potassium, and 95.02% available potassium were preserved. These findings suggest that heat treatment at 110oC for 240min could be an effective and affordable approach to safe use of poultry broiler manure.

Potential for synergism of sequential UV-NaClO disinfection on ARGs removal in municipal sewage: Effectiveness, kinetics, and mechanisms

Conventional disinfection technologies have limitations in effectively addressing the challenges posed by the emerging pollutant of antibiotic resistance genes (ARGs). To reduce the risk of antibiotic resistance in wastewater treatment plant (WWTP) effluent, this study investigated the effectiveness of ultraviolet (UV) irradiation followed by Sodium hypochlorite (NaClO) (sequential UV-NaClO) disinfection in removing six classes and 18 subtypes of ARGs in the secondary effluent of a municipal WWTP. The study showed that UV disinfection could reduce tetracycline ARGs (TCs-ARGs) subtype tetQ by 0.98 log, while it was ineffective in removing sulfonamide ARGs (SAs-ARGs). NaClO disinfection was very effective in removing ARGs. Increasing the disinfectant dosage is more effective than extending the disinfection time. The highest removal was observed for the SAs-ARGs subtype sul1 with 4.15 log and the β-lactams-ARGs(β-LACs-ARGs) subtype blaCTX-M1 with 3.87 log. Sequential UV-NaClO disinfection has the potential for synergistic effects in disinfection. Sequential UV-NaClO disinfection with a UV dosage of 15 mJ/cm2 and a NaClO dosage of 10 mg/L can effectively remove 1.46 log of the total 18 subtypes of ARGs, which is 0.73 log higher than the removal achieved by standalone UV irradiation at a fluence of 100 mJ/cm2, and equivalent to the results obtained with NaClO disinfection alone at a dose of 30 mg/L. Additionally, sequential UV-NaClO disinfection can reduce the repair efficiency of ARGs. The proposed modified Hom model can be used to analyze the kinetics of sequential UV-NaClO disinfection synergy. Analysis of microbial community structure and co-occurrence of ARGs showed synchronized and consistent removal of ARGs and their potential bacterial hosts. Sequential UV-NaClO disinfection could achieve 99 % removal of more than half of the genera. Overall, our results indicate that sequential disinfection is a promising disinfection technology for disinfecting municipal wastewater and reducing the spread and transfer of ARGs.

The source and dissemination of ARGs in pristine environments: Elucidating the role of migratory birds in the Arctic

Antibiotic resistance genes (ARGs) are a class of emerging contaminants that significantly threaten public health. In this work, the profiles of ARGs and microbial communities in the soil, sediment, migratory bird, and local deer fecal samples collected from the Arctic were characterized using a metagenomic approach. The results retrieved the baseline profiles of ARGs and identified the role of migratory birds in disseminating ARGs in the Arctic. A total of 26 ARG types and 718 subtypes were determined, and 131 core ARGs were identified. All the samples were dominated by multidrug resistance genes, and some genes resistant to antibiotics commonly used in anthropogenic were also detected. Characterization of ARGs in bird fecal samples was significantly distinct from other media, with higher abundance, richness, and unique ARGs detected. Proteobacteria was the most predominant phylum in soil and fecal samples, while Thaumarchaeota was prevalent in sediment samples. Firmicutes harbored the majority of ARGs in all samples. The results of FEAST indicated that migratory birds were crucial allochthonous ARG sources in the Arctic. These significant findings shed light on the global spread of ARGs and should facilitate efforts to map baseline levels of ARGs before the era of antibiotics.

Global quantification and distribution of antibiotic resistance genes in oceans and seas: Anthropogenic impacts and regional variability

The global spread of antibiotic resistance genes (ARGs) in the marine environment poses a significant threat to public health and natural ecosystems. This study quantified and analysed the distribution and co-occurrence patterns of ARGs in a wide range of oceans and high seas, including the Atlantic, Arctic and Indian Ocean, the Mediterranean Sea and the Persian Gulf. Focusing on beta-lactamases (blaOXA-48, blaCTX-M-1 group, and blaTEM), sulfonamides (sul1) and tetracycline (tetA), our results showed that sul1 was ubiquitous, indicating widespread dissemination. Notably, the Mediterranean Sea exhibited higher levels of multiple ARGs in single samples, suggesting significant anthropogenic impact. Interestingly, the Arctic Ocean, particularly around the Svalbard Islands, also showed the presence of multiple ARGs, highlighting the pervasive occurrence of antibiotic resistance in remote areas. We employed two clustering approaches to explore ARG patterns, primarily focusing on identifying geographic trends and differences in ARG abundance. Additionally, we investigated potential sources of contamination, including proximity to wastewater treatment plants, ports, marine traffic, and currents.These findings clearly demonstrate that antibiotic resistance gene contamination is widespread across diverse marine environments, with significant regional variations. This underscores the urgent need for tailored intervention strategies and global collaboration to mitigate the spread of ARGs and manage their complex dynamics in marine ecosystems.

Antibiotic resistance genes are transferred from manure-contaminated water bodies to the gut microbiota of animals through the food chain

Fecal-contaminated water may enter the food chain and become an important route for the transmission of antibiotic resistance genes (ARGs) to the human microbiome. However, little is known about the spread of ARGs from fecal contamination in water bodies along the aquatic food chain. In this study, laboratory-raised Daphnia magna and Aristichthys nobilis were used to investigate the effects of the addition of manure on target ARGs in water and their intestinal contents to determine the potential transmission route of ARGs in the aquatic food chain system. The abundance of target ARGs in water as well as D. magna and A. nobilis intestinal contents significantly increased when fecal contamination was present. ARGs bioaccumulated along the food chain, with four ARGs (tetM-01, tetX, qnrS, and sul2) detected regularly. Mn and Cr were key environmental factors that promoted the transfer of ARGs along the food chain. Fecal addition significantly changed the structure of microbial communities in water, D. magna gut, and A. nobilis gut. The ARG spectrum was significantly correlated with the composition and structure of the bacterial community. Proteobacteria, Bacteroidetes, and Firmicutes were identified as the main host bacteria and were likely to act as carriers of ARGs to promote the spread of antibiotic resistance in the food chain. The composition and structure of bacterial communities, along with mobile genetic elements, were two key drivers of ARG transfer. These findings provide new insights into the distribution and spread of ARGs along the freshwater food chain.

Metagenomic approach reveals the role of bioagents in the environmental dissemination risk of rhizosphere soil antibiotic resistance genes pollution

Antibiotic resistance genes (ARGs) have been identified as emerging contaminants, raising concerns around the world. As environmentally friendly bioagents (BA), plant growth-promoting rhizobacteria (PGPR) have been used in agricultural systems. The introduction of BA will lead to the turnover of the microbial communities structure. Nevertheless, it is still unclear how the colonization of the invaded microorganisms could affects the rhizosphere resistome. Consequently, 190 ARGs and 25 integrative and conjugative elements (ICEs) were annotated using the metagenomic approach in 18 samples from the Solanaceae crop rhizosphere soil under BA and conventional treatment (CK) groups. Our study found that, after 90 days of treatment, ARG abundance was lower in the CK group than in the BA group. The results showed that aminoglycoside antibiotic resistance (OprZ), phenicol antibiotic resistance (OprN), aminoglycoside antibiotic resistance (ceoA/B), aminocoumarin antibiotic resistance (mdtB) and phenicol antibiotic resistance (MexW) syntenic with ICEs. Moreover, in 11 sequences, OprN (phenicol antibiotic resistance) was observed to have synteny with ICEPaeLESB58-1, indicating that the ICEs could contribute to the spread of ARGs. Additionally, the binning result showed that the potential bacterial hosts of the ARGs were beneficial bacteria which could promote the nutrition cycle, such as Haliangium, Nitrospira, Sideroxydans, Burkholderia, etc, suggesting that bacterial hosts have a great influence on ARG profiles. According to the findings, considering the dissemination of ARGs, BA should be applied with caution, especially the use of beneficial bacteria in BA. In a nutshell, this study offers valuable insights into ARGs pollution control from the perspective of the development and application of BA, to make effective strategies for blocking pollution risk migration in the ecological environment.

Bacterial 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.

Oxygen-limited niches enhance activated sludge resilience to shock loads and mitigate antibiotic resistance

Conventional activated sludge (CAS) used in wastewater treatment plants that receive industrial wastewater are frequently challenged by toxic pollutants, which may impede the stable and efficient removal of pollutants. Additionally, these toxic pollutants may also exacerbate the spread of antibiotic resistance genes (ARGs). This study introduces a novel approach by incorporating oxygen-limited niches (i.e., anaerobic/anoxic zones) into CAS systems, demonstrating a significant improvement in resilience against toxic shock loads and ARG mitigation. Pilot-scale experiments revealed that oxygen-limited niches can positively impact the removal of conventional pollutants under toxic shock conditions and enhance the degradation of pharmaceuticals. 16S rRNA gene and metagenomic sequencing highlighted significant differences in microbial communities between the anaerobic/anoxic and aerobic zones. Furthermore, metagenomic analysis revealed that the oxygen-limited niches lead to lower abundance of ARGs, and the proportion of high-risk ARGs in anaerobic/anoxic zone was significantly lower than that in CAS. 14 genera potentially involved in ARG propagation were identified, and their abundance was obviously lower in anaerobic/anoxic zone. Our findings highlight the introduction of oxygen-limited niches as a modification to CAS systems, offering a new and promising strategy for managing toxic shocks, enhancing pollutant degradation, and reducing the health risks associated with ARGs in wastewater treatment processes.

Anthropogenic activities significantly interfered distribution and co-occurrence patterns of antibiotic resistance genes in a small rural watershed in Southwest China

The prevalence and spread of antibiotic resistance genes (ARGs) have been a significant concern for global public health in recent years. Small rural watersheds are the smallest units of factor mobility for agricultural production in China, and their ARG profiles are the best scale of the contamination status, but the mapping and the distribution and diffusion of ARGs in the water and soil of small rural watersheds are inadequate. In this study, based on microbial metagenomics, we invested prevalence maps of 209 ARGs corresponding to typical commonly used antibiotics (including multidrug, aminoglycoside, macrolide-lincosamide-streptogramin B (MLSB), and β-Lactamase) in water and soil in different agricultural types, as well as within water-soil interfaces in small rural watersheds in Southwest China. The results revealed that the most abundant ARGs in water and soil were consistent, but different in subtypes, and anthropogenic activities affect the transport of ARGs between water and soils. Livestock wastewater discharges influenced the diversity and abundance of ARGs in water, while in soil it is planting type and fertilizer management, and thus interfered with the co-occurrence patterns between bacteria and ARGs. Co-occurrence analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant ARG hosts in water and soil, but soil exhibited a more intricate ARG-bacterial association. Overall, this study provides integrated profiles of ARGs in water and soil influenced by anthropogenic activities at the small watershed scale in a typical rural area and provides a baseline for comparisons of ARGs.

Promotion of antibiotic-resistant genes dissemination by the micro/nanoplastics in the gut of snail Achatina fulica

Terrestrial animal intestines are hotspots for the enrichment of micro/nano plastics (M/NPs) and antibiotic-resistant genes (ARGs). However, little is known about the further impact of M/NPs on the spread of ARGs in animal guts. This study investigates the role of M/NPs (polystyrene) with varying particle sizes (0.082, 42, and 182 μm), concentrations (10 and 100 mg/L), and exposure durations (4 and 16 days) in the ARGs dissemination via conjugation in the edible snail (Achatina fulica) gut. Combination of qPCR with 16S rRNA-based sequencing, we found that PS exposure caused intestinal cell impairment and shifts in the gut microbial community of snails. Conjugation rate increased with PS particle sizes in the snail gut. After 4 days of exposure, significantly higher conjugation rates were observed in the gut exposed to 100 mg/L PS compared to 10 mg/L, however, this trend reversed after 16 days. Consistently, the abundances of conjugation relevant genes trfA and trbB shared similar trends to the conjugation ratios in the snail gut after PS exposure. Transconjugant diversity was much lower in 10 mg/L PS groups than in 100 mg/L PS treatments. Therefore, this study suggests that the presence of M/NPs would complicate management of ARG spread. The selection pressure exerted by M/NPs may sustain or even amplify the spread of ARGs in the gut of terrestrial animals even in the absence of antibiotics. It highlights the necessity of avoiding M/NPs intake as a part of comprehensive strategy for cubing ARG dissemination in the gut of animals.

Co-selective effect of dissolved organic matter and chlorine on the bacterial community and their antibiotic resistance in biofilm of drinking water distribution pipes

The proliferation of pathogenic bacteria and antibiotic resistance genes (ARGs) in the biofilm of drinking water distribution pipes poses a serious threat to human health. This work adopted 15 polyethylene (PE) pipes to study the co-selective effect of dissolved organic matter (DOM) and chlorine on the bacterial community and their antibiotic resistance in biofilm. The results indicated that ozone and granular activated carbon (O3-GAC) filtration effectively removed lignins and proteins from DOM, and chlorine disinfection eliminated carbohydrate and unsaturated hydrocarbons, which both contributed to the inhibition of bacterial growth and biofilm formation. After O3-GAC and disinfection treatment, Porphyrobacter, unclassified_d_bacteria, and Sphingopyxis dominated in the biofilm bacterial community. Correspondingly, the bacterial metabolism pathways, including the phosphotransferase system, phenylalanine, tyrosine and tryptophan biosynthesis, ABC transporters, and starch and sucrose metabolism, were downregulated significantly (p < 0.05), compared to the sand filtration treatment. Under such a situation, extracellular polymeric substances (EPS) secretion was inhibited in biofilm after O3-GAC and disinfection treatment, postponing the interaction between EPS protein and pipe surface, preventing bacteria, especially pathogens, from adhering to the pipe surface to form biofilm, and restraining the spread of ARGs. This study revealed the effects of various water filtration and disinfection processes on bacterial growth, metabolism, and biofilm formation on a molecular level, and validated that the O3-GAC filtration followed by chlorine disinfection is an effective and promising pathway to control the microbial risk of drinking water.

Prevalence and antimicrobial resistance of Pseudomonas aeruginosa in food in Ho Chi Minh City

Pseudomonas aeruginosa is a bacterium that commonly found in various environments, including food, soil, and water. The significant concern is it&amp;rsquo;s resistance to many antimicrobial agents and it&amp;rsquo;s role in the spread of antibiotic resistance genes. This study investigated P. aeruginosa contamination in food products in Ho Chi Minh City and found the following contamination rates: pork (44.8%; 13/29), beef (38.5%; 10/26), fish (30.0%; 9/30), chicken (25.9%; 7/27), street drinks (25.9%; 7/27), shrimp (17.9%; 5/28), raw milk (10.7%; 3/28). The highest average quantity of P. aeruginosa contamination was observed in beef samples, with over 104 CFU/g, while shrimp samples had the lowest, nearly 103 CFU/g. Among the 94 isolates examined, 63 were sensitive or showed intermediate resistance to ten antimicrobial agents. Resistance was observed in 32 isolates, with the hightest resistance rates to aztreonam (28.9%), followed by ciprofloxacin (11.7%), and gentamicin (2.1%). The antimicrobial resistance rates of P. aeruginosa isolates varied by food type: pork (27.6%), fish (16.7%), shrimp (10.7%), chicken (7.4%), street drinks (7.4%), and beef (3.9%). All P. aeruginosa isolates from raw milk were sensitive to the tested antimicrobials. The findings suggest a need for stricter regulations to control P. aeruginosa contamination in food products. Further research is also recommended to explore the potential for transmission of drug resistance genes from P. aeruginosa in contaminated food.

Distribution of tetracyclines and sulfonamides resistance genes around a smallholder pig farm: Modeling and attribution

Livestock farm is a major source of antibiotics and antibiotic resistance genes (ARGs) pollution. ARGs can directly enter the environment through runoff and air deposition. The impact extent and the driving factors require further investigation to inform effective policies and actions to mitigate their spread. This study investigated a smallholder pig farm and its surrounding areas to understand the spread of ARGs. Topsoil samples were collected from 56 different sites within one kilometer of the farm, and a comprehensive analysis was conducted to reveal effects of soil properties, antibiotic residues, microbiome, mobilome on the variation of typical ARGs. The results confirmed that the ARGs reduced exponentially with increasing distance from the farm, with a goodness of fit (R2) of 0.7 for total ARGs. For tetracyclines (TC) and sulfonamides (SA) resistance genes, the fitting R2 exceeded 0.9. Model estimates allowed for quantitative comparisons of in-farm increments, out-farm background levels, and spread abilities of ARGs with distinct resistance mechanisms. SA-specific resistance genes (SRGs, 0.097 copies/16S rRNA gene) and TC-specific resistance genes (TRGs, 0.036 copies/16S rRNA gene) showed higher within-farm increases compared to multidrug resistance genes (MDRGs, 0.020 copies/16S rRNA gene). MDRGs, however, had a higher background level and a greater impact distance (0.18 km, 4.4 times the farm radius). Additionally spread abilities of TRGs varied by resistance mechanism, with ribosome protection proteins showing greater spread than TC inactivating enzymes and TC efflux pumps, likely due to different fitness costs. Correlation analysis and structural equation modeling indicated that changes in bacterial community composition and mobilome are primary factors influencing ARGs variation during their spread. Abiotic factors like soil nutrients and antibiotics also selectively enriched ARGs within the farm. These findings provide insights into the ARGs dissemination and could inform strategies to prevent their spread from smallholder livestock farms.

Mechanisms of horizontal gene transfer and viral contribution to the fate of intracellular and extracellular antibiotic resistance genes in anaerobic digestion supplemented with conductive materials under ammonia stress

The addition of conductive materials (CMs) is an effective strategy for mitigating ammonia inhibition during anaerobic digestion (AD). However, the introduction of CMs can result in increased antibiotic resistance genes (ARGs) pollution, potentially facilitated by enhanced horizontal gene transfer (HGT). The complex dynamics of intracellular and extracellular ARGs (iARGs/eARGs) and the mechanisms underlying their transfer, mediated by CMs, in ammonia-stressed AD systems remain unclear. In this study, we investigated the effects of three commonly used CMs—nano magnetite (Mag), nano zero-valent iron (nZVI), and granular activated carbon (GAC)—on the fate of iARGs and eARGs during the AD of waste activated sludge under ammonia stress. The results revealed an unexpected enrichment of iARGs by 1.5 %–10.9 % and a reduction of eARGs by 14.1 %–25.2 % in CM-supplemented AD. This discrepancy in the dynamics of iARGs and eARGs may be attributed to changes in microbial hosts and the horizontal transfer of ARGs. Notably, CMs activated prophages within antibiotic-resistant bacteria (ARB) and their symbiotic partners involved in vitamin B12 provision, leading to the lysis of ARB and the subsequent release of eARGs for transformation. Additionally, the abundance of potentially mobile ARGs, which co-occurred with mobile genetic elements, increased by 56.6 %–134.5 % with CM addition, highlighting an enhanced potential for the HGT of ARGs. Specifically, Mag appeared to promote both transformation and conjugation processes, while nZVI only promoted conjugation. Moreover, none of the three CMs had any discernible impact on transduction. GAC proved superior to both nano Mag and nZVI in controlling the enrichment of iARGs, reducing eARGs, and limiting HGTs simultaneously. Overall, these findings provide novel insights into the role of viruses and the mechanisms of ARG spread in CM-assisted AD, offering valuable information for developing strategies to mitigate ARG pollution in practical applications.

Absence of synergistic effects between microplastics and copper ions on the spread of antibiotic resistance genes within aquatic bacteria at the community level

Microplastics and copper ions (Cu2+) are favorable in accelerating the propagation of antibiotic resistance genes (ARGs) in the plastisphere, however, their combined effects on the ARG spread within the bacterial community of the natural environment were less understood. The influence of microplastic types and Cu2+ concentrations on the horizontal gene transfer (HGT) of ARGs mediated by RP4 plasmid within natural bacterial communities in aquatic environments was investigated. Both biodegradable polybutylene succinate (PBS) and non-biodegradable polyvinyl chloride (PVC) microplastics significantly enhanced the transfer of ARGs, with PBS showing a significant higher effect compared to PVC. Cu2+ also increased transconjugation rates at environmentally relevant concentrations (5 μg L−1), but higher levels (50 μg L−1) lead to decreased rates due to severe bacterial cell membrane damage. The transconjugation rates in the presence of both microplastics and Cu2+ were lower than the sum of their individual effects, indicating no synergistic effects between them on transconjugation. Proteobacteria dominated the composition of transconjugates for all the treatment. Transmission electron microscope images and reactive oxygen species production in bacterial cells indicated that the increased contact frequency due to extracellular polymeric substances, combined with enhanced membrane permeability induced by microplastics and Cu2+, accounted for the increasing transconjugation rates. The study provides valuable insight into the potential effects of microplastics and heavy metals on the spread of ARGs from donors to bacterial communities in natural environments.

Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments

The spread of antibiotic resistance genes (ARGs) poses a substantial threat to human health. Phage-mediated transduction could exacerbate ARG transmission. While several case studies exist, it is yet unclear to what extent phages encode and mobilize ARGs at the global scale and whether human impacts play a role in this across different habitats. Here, we combine 38,605 bacterial genomes, 1432 metagenomes, and 1186 metatranscriptomes across 12 contrasting habitats to explore the distribution of prophages and their cargo ARGs in natural and human-impacted environments. Worldwide, we observe a significant increase in the abundance, diversity, and activity of prophage-encoded ARGs in human-impacted habitats linked with relatively higher risk of past antibiotic exposure. This effect was driven by phage-encoded cargo ARGs that could be mobilized to provide increased resistance in heterologous E. coli host for a subset of analyzed strains. Our findings suggest that human activities have altered bacteria-phage interactions, enriching ARGs in prophages and making ARGs more mobile across habitats globally.

Vertical variation of antibiotic resistance genes and their interaction with environmental nutrients in sediments of Taihu lake

Antibiotic resistance is a growing environmental issue. As a sink for antibiotic resistance genes (ARGs), lake surface sediments are well known for the spread of ARGs. However, the distribution pattern of ARGs and their relationship with environmental factors in vertical sediment layers are unclear. In this study, we investigated the resistome distribution in sediment cores from Taihu Lake using metagenomic analysis. The results showed that the abundance of total ARGs increased by 153% as the sediment depth rose from 0 to 50 cm, and the ARG Shannon index significantly increased. Among all the ARG types, efflux pump genes (e.g., mexT and mexW) were dominant, especially in 40–50 cm sediment. The variation in ARG with depth described above was related to the changes in bacterial adaptation to environmental gradients. Specifically, sulfate and nitrate concentrations decreased with depth, and random forest analysis showed that they were the main factors affecting the changes in ARG abundance. Environmental factors were also found to indirectly impact the distribution of ARGs by affecting the bacterial community. Potential sulfate-reducing gene/nitrate-reducing gene-ARG co-hosts were annotated through metagenomic assembly. The dominant co-hosts, Curvibacter, and Comamonas, which were enriched in deeper sediments, may have contributed to the enrichment of ARGs in deep sediments. Overall, our findings demonstrated that bacterial-mediated sulfate and nitrate reduction was closely related to sediment resistance, which provided new insights into the control of antibiotic resistance.

Distribution and driving mechanisms of antibiotic resistance genes in urbanized watersheds

Antibiotic resistance genes (ARGs) have emerged as a global concern, posing significant threats to human health and safety. Understanding the contamination levels and driving mechanisms behind ARG proliferation is urgently needed. Urban watersheds, influenced by human activities, serve as critical reservoirs for ARGs; however, the impact of urbanization on ARG spread of and the underlying driving mechanisms remain unclear. This study evaluates the diversity and abundance of ARGs in water and sediment samples from the Jialing River watershed in Chongqing City, China. The obtained results indicate that aminoglycoside and multidrug ARGs are the primary contributors to ARG presence in both sediments and water. Additionally, the diversity and abundance of ARGs are higher in water than in sediments. ARGs in watershed show a significant positive correlation with mobile genetic elements (MGEs). While environmental factors in urbanized watersheds affect ARG abundance and distribution to some extent, they are not the primary drivers. Urbanization itself emerges as a prominent factor influencing ARG diversity and abundance in river basins. Specifically, livestock, healthcare, and agriculture are identified as the main social factors influencing ARG proliferation in the highly urbanized areas of the Jialing River watershed. Further investigation into other contributing social factors, such as industrial development, is warranted. This study reveals the factors driving ARG distribution in urbanized watersheds, providing a foundation for future efforts to maintain ecological health in these environments.

The interplay between mobilome and resistome in Staphylococcus aureus.

Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.