Abundance Of Antibiotic Resistance Genes Research Articles

Increased Transmission of Antibiotic Resistance Occurs in a Soil Food Chain under Pesticide Stress.

The rising spread of antibiotic resistance is a global concern, but the pathways of dissemination within soil ecosystems remain poorly understood. Here, we quantified the occurrence of antibiotic resistance genes (ARGs) in gut microbiomes of soil collembolans (Folsomia candida) under pesticide stress (zinc thiazole, ZT) and analyzed the trophic transfer of ARGs to the microbiomes of predatory mites (Hypoaspis aculeifer), natural predators of collembolans. High throughput quantitative PCR was used to quantify ARGs, whereas gut microbiomes of collembolans and mites were characterized using 16S rRNA gene amplicon sequencing, and potential pathogens were identified. Our results revealed that ZT exposure significantly elevated the abundance of ARGs (e.g., AAC(6')-Ir) in soil collembolan microbiomes. With the increase of ARGs in prey collembolan microbiomes, an increase of ARGs in predatory mite microbiomes was observed through trophic transfer. Mobile genetic elements (MGEs) significantly contribute to the transmission of ARGs within this food chain. Additionally, co-occurrence analysis indicated a strong association between gut resistomes and pathogens, such as Brevundimonas diminuta, in the collembolans and predatory mites. Overall, our study provides evidence for the dissemination of ARGs through the collembolan-predatory mite food chain following pesticide exposure, which is important for understanding the broader dynamics of antibiotic resistance spreading in soil ecosystems.

Biochar Reduced the Risks of Human Bacterial Pathogens in Soil via Disturbing Quorum Sensing Mediated by Persistent Free Radicals.

Biochar has great potential in reducing the abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from soil. However, its efficiency in removing other biological pollutants, such as human bacterial pathogens (HBPs) and virulence factor genes (VFGs), is rarely studied. Herein, by pyrolyzing rice straw (RS) and pine wood (PW) at 350 and 700 °C, we prepared a series of biochar (RS350, RS700, PW350, and PW700) and investigated their impacts on the abundance and pathogenicity of HBPs. Compared with PW biochar, RS biochar effectively reduced the abundance of HBPs by 6.3-40.1%, as well as their pathogenicity, evidenced by an 8.2-10.1% reduction in the abundance of VFGs. Mechanistically, more persistent free radicals (PFRs) were formed in RS biochar than that of PW biochar during pyrolysis, and PFRs triggered the degradation of N-butyryl-l-homoserine lactone (C4-HSL) from 1.05 to 0.68 ng/kg, thereby disturbing the quorum sensing (QS) of HBPs. Once the QS was disturbed, the communications among HBPs were hindered, and their virulence factors were reduced, which ultimately lowered the abundance and pathogenicity of HBPs. Collectively, our study provides insights into the role of biochar in decreasing the risks of HBPs, which is significant in the development of biochar-based technologies for soil remediation.

Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient.

Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.

Hot spots of resistance: Transit centers as breeding grounds for airborne ARG-carrying bacteriophages

The presence of pathogenic bacteria and antibiotic resistance genes (ARGs) in urban air poses a significant threat to public health. While prevailing research predominantly focuses on the airborne transmission of ARGs by bacteria, the potential influence of other vectors, such as bacteriophages, is often overlooked. This study aims to investigate the characteristics of phages and ARGs in aerosols originating from hospitals, public transit centers, wastewater treatment plants, and landfill sites. The average abundance of ARGs carried by phages in the public transit centers was 8.81 ppm, which was 2 to 3 times higher than that at the other three sites. Additionally, the abundance of ARGs across different risk levels at this site was also significantly higher than at the other three sites. The assembled phage communities bearing ARGs in public transit centers are chiefly governed by homogeneous selection processes, likely influenced by human movement. Furthermore, observations at public transit sites revealed that the average abundance ratio of virulent phages to their hosts was 1.01, and the correlation coefficient between their auxiliary metabolic genes and hosts' metabolic genes was 0.59, which were 20 times and 3 times higher, respectively, than those of temperate phages. This suggests that virulent phages may enhance their survival by altering host metabolism, thereby aiding the dispersion of ARGs and bacterial resistance. These revelations furnish fresh insights into phage-mediated ARG transmission, offering scientific substantiation for strategies aimed at preventing and controlling resistance within aerosols.

Metagenomic analysis reveals houseflies as indicators for monitoring environmental antibiotic resistance genes.

Given the threat to public health posed by antibiotic resistance transmission, environmental monitoring is essential for tracking antibiotic resistance genes (ARGs). Houseflies, being ubiquitous organisms capable of carrying and disseminating ARGs, serve as suitable indicators for environmental monitoring. In this study, we employ metagenomic approaches to investigate housefly body surface samples from five typical sites associated with human activities. The investigation reveals microbiome diversity among the samples, along with variations in the occurrence and mobility potential of ARGs. Metagenomic analysis indicates that the composition of ARGs on housefly body surfaces is influenced by environmental ARGs, which may be enriched on the housefly body surface. The resistance genes related to multidrug, β-lactam, bacitracin, and tetracycline were the predominant ARGs detected, with multidrug-related ARGs consistently exhibiting dominance. Furthermore, the abundance of ARGs in the different housefly body surface samples was found to correlate with the population density and mobility of the sampling site. Natural environments exhibited the lowest ARG abundance, while areas with higher population density and limited population mobility displayed higher ARG abundance. This study emphasizes the effectiveness of houseflies as monitors for environmental ARGs and underscores their potential for assessing and controlling antibiotic resistance risks in urban environments.

Unveiling the critical role of overlooked consumer protist-bacteria interactions in antibiotic resistance gene dissemination in urban sewage systems

Antibiotic resistance genes (ARGs) are emerging contaminants of significant concern due to their role in facilitating the spread of antibiotic resistance, especially high-risk ARGs, which are characterized by high human accessibility, gene mobility, pathogenicity, and clinical availability. Studies have shown that cross-domain interactions, such as those between consumer protists (consumers) and bacteria, can influence bacterial diversity, distribution, and function through top-down power. The consumers-bacteria interactions may also affect the occurrence and distribution of ARGs, yet this has been scarcely explored in field investigations. We conducted a city-scale investigation of ARGs, protists, and bacterial communities across each unit of the urban sewage system (USS), including 49 sewage pumping stations (SW), as well as influent (IF), activated sludge (AS), and effluent (EF) from seven wastewater treatment plants. Interestingly, consumers-bacteria interactions, as indicated by indices of bipartite relevance networks (i.e., connectedness and cohesion), increased from SW and IF to AS and EF. Structural equation modelling (SEM) revealed that consumers-bacteria interactions had a greater influence on the abundance of total ARGs and high-risk ARGs than seasonal or environmental factors. Notably, the total effects of consumers-bacteria interactions in SEM were significant (P < 0.05) and comparable in both IF and EF, even with the decrease in ARG abundance from IF to EF. This suggests a potential risk of ARG spread to the environment, facilitated by consumer protists in the EF. Additionally, the relevance network also demonstrated an increasing trend in the relationships between consumer protists and potential hosts of high-risk ARGs from raw sewage (SW and IF) to AS and EF. Overall, this study emphasizes the importance of integrating multitrophic microbial interactions to better understand and mitigate the dissemination of ARGs in sewage systems.

Antibiotic resistance genes and virulence factors in the plastisphere in wastewater treatment plant effluent: Health risk quantification and driving mechanism interpretation

Microplastics (MPs) are ubiquitous in wastewater treatment plants (WWTPs) and provide a unique niche for the spread of pollutants. To date, risk assessments and driving mechanisms of pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in the plastisphere are still lacking. Here, the microbiota, ARGs, VFs, their potential health risks, and biologically driving mechanisms on polythene (PE), polyethylene terephthalate (PET), poly (butyleneadipate-co-terephthalate) and polylactic acid blends (PBAT/PLA), PLA MPs, and gravel in WWTP effluent were investigated. The results showed that plastisphere and gravel biofilm harbored more distinctive microorganisms, promoting the uniqueness of pathogens, ARGs, and VFs compared to WWTP effluent. The abundance of major pathogens, ARGs, and VFs in the plastisphere was 1.01–1.35 times higher than that in the effluent. The high health risk of ARGs (HRA) calculated by fully considering the abundance, clinical relevance, pathogenicity, accessibility and mobility, and the high proportion of resistance contigs with mobile genetic elements confirmed that the plastisphere posed the highest potential health risk. Candidatus Microthrix and Candidatus Promineifilum were the essential hosts of ARGs and VFs in the plastisphere and gravel biofilm, respectively. High metabolic activity such as amino acid metabolism and biosynthesis of secondary metabolites, and highly expressed key genes increased the synthesis of ARGs and VFs. The primary mechanisms driving ARG enrichment in the plastisphere were enhanced microbial metabolic activity, increased frequency of horizontal gene transfer, heightened antibiotic inactivation and efflux, and reduced cell permeability. This study provided new insights into the ARGs, VFs, and health risks of the plastisphere and emphasized the importance of strict control of wastewater discharge.

Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing

Night-time outdoor illumination in combination with natural sunlight can influence the visible phototrophic colonizers (mainly algae) growing on stone facades; however, the effects on the microbiome (invisible to the naked eye) are not clear. The presence of stone-dwelling microbes, such as bacteria, diatoms, fungi, viruses and archaea, drives further biological colonization, which may exacerbate the biodeterioration of substrates. Considering the microbiome is therefore important for conservation of the built heritage. The impact of the following types of lighting on the relative abundance and diversity of the microbiome on granite ashlars was evaluated in a year-long outdoor pilot study: no lighting; lighting with a metal halide lamp (a traditional lighting system currently used to illuminate monuments); and lighting with a novel LED lamp (an environmentally sound prototype lamp with a biostatic effect, halting biological colonization by phototrophs, currently under trial). Culturable fractions of microbiome and whole-genome sequencing by metabarcoding with Oxford Nanopore Sequencing (MinION) was conducted for bacteria and fungi in order to complement both community characterization strategies. In addition, the possible biodeteriorative profiles of the isolated strains, relative to calcium carbonate precipitation/solubilisation and iron oxidation/reduction, were investigated by plate assays. Alpha and beta diversity indexes were also determined, along with the abundance of biocide and antibiotic resistance genes. Culture-dependent microbiological analysis failed to properly show changes in community composition, for which metagenomic approaches like MinION are better suited. Thus, MinION analysis identified shifts in the granite microbiome elicited by ornamental lighting. The novel LED lamp with the biostatic effect on phototrophs caused an increase in the diversity of bacteria and fungi. In this case, the microbiome was more similar to that in the unlit samples. In the samples illuminated by the metal halide lamp, dominance of bacteria was favoured and the presence of fungi was negligible.

Effects of aging of polyethylene microplastics and polystyrene nanoplastics on antibiotic resistance gene transfer during primary sludge fermentation

The increasing presence of nano and microplastics (NPs/MPs) in wastewater treatment plants and their inevitable accumulation in the sludge has raised serious concerns in recent years. This study investigated the effects of pristine and aged polyethylene microplastics (PEMPs), polystyrene nanoplastics (PsNPs), and their mixtures on the primary sludge fermentation process. Pristine MPs/NPs (150 μg/L and 2 g/L for PsNPs and PEMPs, respectively) underwent two weeks of weathering in the presence of humic and alginic acids. The results from a batch fermentation experiment (15 days, pH 10) revealed that the exposure to aged PEMPs/PsNPs experienced greater VFA production than pristine samples. Notably, the aged PEMPs/PsNPs mixture showed a 23.12% increase in VFA production over the pristine mixture. The relative abundance and total concentration of antibiotic resistance genes (ARGs) increased in all PEMPs/PsNPs batches compared to the control, with the most significant rise in total ARGs observed in the aged PEMPs sample. Aged PEMPs exhibited a 26.22-fold increase in tetA genes, while aged mix samples showed a 19.68-fold increase in tetM genes compared to their pristine counterparts. Both pristine and aged PEMPs/PsNPs, particularly the aged PEMPs adversely affected the microbial communities at the genus level and altered the microbial structure. Microbial richness and diversity were enhanced in samples exposed to pristine PEMPs/PsNPs and aged PsNPs but decreased in aged PEMPs and in the aged mixture group, suggesting a negative impact of aged polyethylene microplastics on microbial communities. Correlation analysis suggested that phyla Planctomycetes, Proteobacteria, and TM7 are potential hosts of ARGs. These findings manifest the substantial effects of aged nano/microplastics compared to their pristine forms, emphasizing the complex interplay between various forms of PEMPs/PsNPs and microbial dynamics in sludge fermentation processes.

Effect of Cow Bone Addition on the Humification, Heavy Metals Passivation and Fate of Resistance Genes During Swine Manure Composting

Bone meal has been used as economic and effective additive for heavy metals (HMs) pollution remediation due to the distinct components and structures that enable their favorable properties, such as its low cost, high adsorption capacity, acid-base adjustability, and ion-exchange capability. However, no attempt has been made to establish whether cow bone could promote the passivation of HMs and the removal of metal resistance genes (MRGs) and antibiotics resistance genes (ARGs) during the composting process. Two sizes of cow bone (meal (T2) and granule (T3)) were added to investigate their effects on humification, HMs passivation and the abundance of ARGs and MRGs during swine manure composting. Excitation-emission matrix (EEM)-parallel factor analysis showed that the percentage of maximum fluorescence intensity of humic-like substances were higher in T2 (91.82%) than in T3 (88.46%), implying that T2 could promote the humification process compared to T3. In comparison with control (T1), the addition of T2 and T3 could promote the change of exchangeable Cu and reducible Cu into oxidizable Cu, thus reducing the mobility factors (MF) of Cu in T2 and T3 treatments by 10.48% and 6.98%, respectively. In addition, T2 and T3 could increase exchangeable Zn into reducible Zn and oxidizable Zn, thereby reducing the MF of Zn in T2 and T3 treatments by 18.80% and 2.0%, respectively. Quantitative Real-time PCR (qPCR) analysis revealed that the total abundances of MRGs were decreased by 100% in T2 and T3 treatments, and T2 decreased the total relative abundance of ARGs. Furthermore, the relative abundance of ARGs and MRGs had significantly correlated with intI1 and bio-available of Cu and Zn, which was triggered by selective pressure of HMs and horizontal gene transfer. The present study suggested that cow bone meal as additives can be a feasible approach to promote the passivation of HMs and enhance the removal of MGRs and ARGs by decreasing horizontal gene transfer and selective pressure by bioavailable HMs.

Metagenomics reveals the profiles and drivers of antibiotic resistance genes and virulence factors in Glebionis coronaria L. planting soil

Due to the application of contaminated water irrigation and bio-amendments, the emergence and spread of antibiotic resistance genes (ARGs) and virulence factors (VFs) in soil have become a global problem, thus having potential threats to human health and ecology. However, limited knowledge exists regarding how variations in the soils of Glebionis coronaria L. (previously called Chrysanthemum coronarium L., or the crown daisy) planting sites influence the profiles of ARGs and VFs. In this study, ARGs, VFs, mobile genetic elements (MGEs), and microbial communities were comprehensively characterized using metagenomic methods in the soils from five different Glebionis coronaria L. planting sites in Shanghai. The dominant microbial populations in Glebionis coronaria L. planting soil were not affected by different planting sites, but there were changes in their relative abundance. The abundance and diversity of ARGs, VFs, and MGEs were different among the soils of five planting sites. The overall distribution characteristics of ARGs and VFs in the soils of each planting site remained consistent. Potential hosts shared by ARGs and VFs were present at each site, raising the risk of soil antibiotic resistance. Fe and T were the primary driving factors for the changes in ARGs and VFs, contributing to 11.32 % and 10.74 % of the overall variation in ARGs and VFs, respectively. Taken together, the identification of biological and non-biological factors that affect ARGs and VFs in the soils from different planting sites could provide valuable perspectives for controlling the dissemination of these genes. This study underscored the necessity for accurate and coordinated strategies to tackle the worldwide antibiotic resistance challenge.

Effects of glyphosate on antibiotic resistance in soil bacteria and its potential significance: A review.

The evolution and spread of antibiotic resistance are problems with important consequences for bacterial disease treatment. Antibiotic use in animal production and the subsequent export of antibiotic resistance elements in animal manure to soil is a concern. Recent reports suggest that exposure of pathogenic bacteria to glyphosate increases antibiotic resistance. We review these reports and identify soil processes likely to affect the persistence of glyphosate, antibiotic resistance elements, and their interactions. The herbicide molecular target of glyphosate is not shared by antibiotics, indicating that target-site cross-resistance cannot account for increased antibiotic resistance. The mechanisms of bacterial resistance to glyphosate and antibiotics differ, and bacterial tolerance or resistance to glyphosate does not coincide with increased resistance to antibiotics. Glyphosate in the presence of antibiotics can increase the activity of efflux pumps, which confer tolerance to glyphosate, allowing for an increased frequency of mutation for antibiotic resistance. Such effects are not unique to glyphosate, as other herbicides and chemical pollutants can have the same effect, although glyphosate is used in much larger quantities on agricultural soils than most other chemicals. Most evidence indicates that glyphosate is not mutagenic in bacteria. Some studies suggest that glyphosate enhances genetic exchange of antibiotic-resistance elements through effects on membrane permeability. Glyphosate and antibiotics are often present together in manure-treated soil for at least part of the crop-growing season, and initial studies indicate that glyphosate may increase abundance of antibiotic resistance genes in soil, but longer term investigations under realistic field conditions are needed. Although there are demonstratable interactions among glyphosate, bacteria, and antibiotic resistance, there is limited evidence that normal use of glyphosate poses a substantial risk for increased occurrence of antibiotic-resistant, bacterial pathogens. Longer term field studies using environmentally relevant concentrations of glyphosate and antibiotics are needed.

Antibiotic resistance in the Ganga River: Investigation of antibiotic resistant bacteria and antibiotic resistance genes, and public health risk assessment

The Ganga River, sacred to India and supporting 440 million people, faces a severe threat from antibiotic resistance. Here, we have investigated the abundance of antibiotic resistant bacteria (ARB), antibiotic resistant genes (ARGs), and mobile genetic elements (MGEs) in water and sediment samples at 16 different sites across the Ganga River biannually. Furthermore, we investigated the presence of potentially pathogenic ARB at genus level in the Ganga River and conducted a risk assessment for human exposure to ESKAPE pathogens during swimming activities. Among the sites studied, a notably higher abundance of ARB, ARGs, and MGEs was observed downstream of the pristine sites (G1 and G2) due to anthropogenic inputs. A significant positive correlation (p < 0.05) was observed between ARB, ARGs, MGEs, and coliforms, suggesting a close association between faecal contamination and MGEs in the spread of antibiotic resistance in the river. Of the identified, 10,340 isolates, Pseudomonas, Bacillus, Acinetobacter, Pseudoxanthomonas, and Aeromonas were the top five most abundant genera. The dominant potentially pathogenic ARB were Pseudomonas, Acinetobacter, Aeromonas, Stenotrophomonas, and Brevundimonas. The results of the Quantitative Microbial Risk Assessment (QMRA) and the analysis of disability-adjusted life years (DALYs) indicated that Enterobacter cloacae posed the highest risk, followed by Acinetobacter baumannii and Klebsiella pneumoniae. Overall, this study provides quantitative data on antibiotic resistance and human health risks in the Ganga River. The data from this study can serve as a foundational basis for guiding crucial actions and policy recommendations for safeguarding the Ganga River and the well-being of its users.

Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses

Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from nine European countries and employed metagenomic assembly methods to investigate the dynamics and distribution of ARGs and viruses within the pig intestinal microbiota, aiming to observing their associations with potential bacterial hosts. We identified 4605 metagenome-assembled genomes (MAGs), corresponding to 19 bacterial phyla, 97 families, 309 genera, and a total of 449 species. Additionally, 44 MAGs were classified as archaea. Analysis of ARGs revealed 276 ARG types across 21 ARG classes, with Glycopeptide being the most abundant ARG class, followed by the class of Multidrug. Treponema D sp016293915 was identified as a primary potential bacterial host for Glycopeptide. Aligning nucleotide sequences with a viral database, we identified 1044 viruses. Among the viral genome families, Peduoviridae and Intestiviridae were the most prevalent, with CAG-914 sp000437895 being the most common potential host species for both. These findings highlight the importance of MAGs in enhancing our understanding of the gut microbiome, revealing microbial diversity, antibiotic resistance, and virus–bacteria interactions. The data analysis for the article was based on the public dataset PRJEB22062 in the European Nucleotide Archive.

Elevated CO2 alters antibiotic resistome in soil amended with sulfamethazine via chemical-organic fertilization

Rising antimicrobial resistance (AMR) is an enormous challenge for global healthcare systems. The effects of elevated CO2 (eCO2) on AMR are poorly characterized. Using a free-air CO2 enrichment system and high-throughput qPCR arrays, we investigated the response of soil antibiotic resistome and bacterial communities to eCO2 (ambient+200ppm) in soils amended with sulfamethazine (SMZ) at 0.1 and 1mgkg-1 via chemical-organic fertilizer (COL, COH). Results showed that under ambient condition, COH significantly enhanced the diversity of high-risk antibiotic resistance genes (ARGs), relative abundance of low risk ARGs, unassessed ARGs and total ARGs compared to COL. Nevertheless, eCO2 mitigated the effects of COH, with no significant difference found between COL and COH on the above high risk, low risk, unassessed and total ARGs. Meanwhile, eCO2 decreased the relative abundance of spcN, ermA, olec, oprD, sulA-olP, tetB, tetT and vanXD in COL, and alleviated the enrichment of pikR2, ampC, lunC, oprD and pncA caused by the application of SMZ at 1mgkg-1. Correlation and network analysis illustrated that changes of certain bacteria biomarkers and horizontal gene transfer of integrase gene were associated with the altered response of ARGs abundance to eCO2. This study adds knowledge of the potential risk of antibiotic resistance in agricultural exposure scenarios under increasing CO2 concentration.

Bacterial communities and tetracycline resistance genes in the soil-rice continuum upon tetracycline exposure

Edible plants are known as key vectors for transmission of antibiotic resistance genes (ARGs) to humans. However, little is known about how antibiotic exposure affects the abundance of ARGs in the soil-rice continuum. This study assessed tetracycline (TC) content, tetracycline resistance genes (TRGs), class 1 integron-integrase gene (intI1), and bacterial communities in the mature soil-rice continuum exposed to varying concentrations of TC (0, 50, 100, and 300 ppm). As TC exposure levels increased, the TC content in rhizosphere soils and roots increased accordingly. However, TC residue was not detected in the grains. Additionally, sample type (rhizosphere soils, roots, and grains) was the key determinant of bacterial communities and TRGs profiles in the soil-rice continuum. The bacterial communities and TRGs profiles in the rhizosphere soils and roots exposed to TC >50 ppm were more dissimilar to those without TC than to those exposed to TC <50 ppm. The abundance of TRGs in the soil-rice continuum increased with the TC concentrations but declined when TC > 50 ppm. This decline was primarily due to changes in the abundance of tetX and tetZ. Variation partitioning analysis revealed that the TRGs profiles in rhizosphere soils is strongly affected by bacterial communities. In contrast, the variation in TRGs profiles in roots was predominantly explained by bacterial communities-TC interactions. However, the changes in TRGs profiles of grains could not be attributed to the bacterial communities, TC, or intI1. This study provides valuable insights into the response of TRGs profiles in the soil-rice continuum to TC exposure.

A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli.

Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance. In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity. Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread. This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.

Microplastic diversity increases the abundance of antibiotic resistance genes in soil

The impact of microplastics on antibiotic resistance has attracted widespread attention. However, previous studies primarily focused on the effects of individual microplastics. In reality, diverse microplastic types accumulate in soil, and it remains less well studied whether microplastic diversity (i.e., variations in color, shape or polymer type) can be an important driver of increased antibiotic resistance gene (ARG) abundance. Here, we employed microcosm studies to investigate the effects of microplastic diversity on soil ARG dynamics through metagenomic analysis. Additionally, we evaluated the associated potential health risks by profiling virulence factor genes (VFGs) and mobile genetic elements (MGEs). Our findings reveal that as microplastic diversity increases, there is a corresponding rise in the abundance of soil ARGs, VFGs and MGEs. We further identified microbial adaptive strategies involving genes (changed genetic diversity), community (increased specific microbes), and functions (enriched metabolic pathways) that correlate with increased ARG abundance and may thus contribute to ARG dissemination. Additional global change factors, including fungicide application and plant diversity reduction, also contributed to elevated ARG abundance. Our findings suggest that, in addition to considering contamination levels, it is crucial to monitor microplastic diversity in ecosystems due to their potential role in driving the dissemination of antibiotic resistance through multiple pathways.

Impact of salmon farming in the antibiotic resistance and structure of marine bacterial communities from surface seawater of a northern Patagonian area of Chile

BackgroundAquaculture and salmon farming can cause environmental problems due to the pollution of the surrounding waters with nutrients, solid wastes and chemicals, such as antibiotics, which are used for disease control in the aquaculture facilities. Increasing antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is linked to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the primary source of antibiotics residues in the coastal waters of northern Patagonia. Here, we evaluated whether the structure and diversity of marine bacterial community, the richness of antibiotic resistance bacteria and the frequency of antibiotic resistance genes increase in communities from the surface seawater of an area with salmon farming activities, in comparison with communities from an area without major anthropogenic disturbance.ResultsThe taxonomic structure of bacterial community was significantly different between areas with and without aquaculture production. Growth of the culturable fraction under controlled laboratory conditions showed that, in comparison with the undisturbed area, the bacterial community from salmon farms displayed a higher frequency of colonies resistant to the antibiotics used by the salmon industry. A higher adaptation to antibiotics was revealed by a greater proportion of multi-resistant bacteria isolated from the surface seawater of the salmon farming area. Furthermore, metagenomics data revealed a significant higher abundance of antibiotic resistant genes conferring resistance to 11 antibiotic families in the community from salmon farms, indicating that the proportion of bacteria carrying the resistance determinants was overall higher in salmon farms than in the undisturbed site.ConclusionsOur results revealed an association between bacterial communities and antibiotic resistance from surface seawater of a coastal area of Chile. Although the total bacterial community may appear comparable between sites, the cultivation technique allowed to expose a higher prevalence of antibiotic resistant bacteria in the salmon farming area. Moreover, we demonstrated that metagenomics (culture-independent) and phenotypic (culture-dependent) methods are complementary to evaluate the bacterial communities’ risk for antibiotic resistance, and that a human—influenced environment (such as salmon farms) can potentiate bacteria to adapt to environmental stresses, such as antibiotics.

The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants

Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.