Abundance Of Antibiotic Resistance Genes Research Articles

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

IntroductionEscherichia 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.MethodsIn 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.ResultsOur 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.DiscussionThis 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.

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.

Viral community and antibiotic resistance genes carried by virus in soil microbial fuel cells

Soil microbial fuel cells (MFCs) can control the horizontal transfer of antibiotic resistance genes (ARGs) by reducing the abundance of mobile genetic elements. However, little is known about the effect of soil MFCs on the horizontal transfer pathway of ARGs transduced by viruses. In this study, the average abundance of ARGs in soil MFCs was 11 % lower than that in the open-circuit control. Lower virus abundance in soil MFCs suggested less detriment of microbial communities. The structure of the viral community was respectively shifted by the introduction of electrodes and the stimulation of biocurrent, especially for the top three viral genera Oslovirus, Tequatrovirus and Incheonvrus in soil. The ARGs aac(6)-I, cat chloramphenicol acetyltransferase, qnrA and vanY were found as the highest health risk (Rank I), and their total abundance showed the lowest in MFCs, with a decrease of 91–99 % compared to the controls. As the main carrier of ARGs, the abundance of Caudoviricetes showed a significant positive correlation with ARGs. Viral integrase was identified respectively coexisting with arnA and vanR (Rank III) in the same contig, which might aggravate their horizontal transfer. Proteobacteria was the main host of viruses carrying ARGs, which exhibited the lowest abundance in the soil MFC. The genus Pseudomonas was the host of viruses carrying ARGs, whose amount reduced by soil MFCs. This study provides an insight into the bioelectrochemical control of ARGs horizontal transfer.

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.

Normal levels of Cu and Zn contamination present in swine manure increase the antibiotic resistance gene abundances in composting products

Normal levels of Cu and Zn contamination present in swine manure increase the antibiotic resistance gene abundances in composting products

Assessing the pig microbial health impacts of smallholder farming

The livestock industry has long been a hotspot environment for antibiotic resistance genes, with smallholder farming still holding a significant position in pig farming. However, the microbial antibiotic resistance and pathogen risks in pigs under the smallholder farming model remain unclear. We systematically analyzed the antibiotic resistance and microbial composition of pig feces from smallholder and large-scale farming models in Sichuan. The results indicated a lower abundance of antibiotic resistance genes (ARGs) and similar microbial composition in smallholder farming compared to large-scale farming. Beneficial bacteria were more abundant in small-scale farming, whereas large-scale farming exhibited more ARGs, virulence genes, and human pathogenic bacteria (HPBs), including ESBL Escherichia coli strains closely related to human strains, indicating higher zoonotic risk. The findings suggest that smallholder farming presents a relatively better microbial composition and resistance profile, highlighting its advantages over large-scale farming in terms of pig and human health. It is noteworthy that a considerable proportion of HPBs carrying ARGs still exist in the feces from smallholder farming, and given the openness of fecal handling, there remains a high risk of transmitting ARGs and pathogens to humans.

Silver nanoparticles regulate antibiotic resistance genes by shifting bacterial community and generating anti-silver genes in estuarine biofilms

Biofilms are thought to be sinks for antibiotic resistance genes (ARGs) and nanoparticles (NPs), however, studies on the interactions between NPs and ARGs in biofilms are limited. This study focused on the occurrence and regulatory mechanisms of ARGs during the formation of biofilms with continuous treatment of zero-valent silver nanoparticles (Ag0-NPs) and Ag ions at an environmental concentration of 10 µg/L in the Yangtze Estuary. The biofilms could enrich large amounts of Ag, with the highest concentration of 97.60 mg/kg and 111.08 mg/kg in the Ag0-NPs and Ag ions group at 28 days. Compared to the blank at 28 days, the abundance of ARGs was reduced 2.2 times in the Ag0-NPs group, whereas it increased 1.3 times in the Ag ion group. Ag0-NPs and Ag ions induced the production of silver resistance genes (SRGs) or selected bacteria with SRGs in biofilms. Based on machine learning, the bacterial community, SRGs, and Ag concentration were the top three dominant regulators of ARGs, with 27.74 %, 25.57 %, and 17.93 % contributions, respectively. Structural equation modeling revealed that Ag could indirectly regulate ARGs by regulating the bacterial community in the Ag0-NPs group. Metagenomic sequencing further showed that most of the decreased ARGs were hosted by Betaproteobacteria in the Ag0-NPs groups. According to the KEGG pathway database, the possible molecular mechanism of Ag0-NPs/Ag ions regulating ARGs may be through the two-component system (arlS/silS-arlR) and beta-lactam resistance system (mexI-mexV-oprM/oprZ/smeF). Overall, this study provides new insights into the effects of Ag0-NPs at environmental concentrations on the ecological environment, especially regarding the mechanism of regulating ARGs in estuarine biofilms.

Metagenomic analysis of sedimentary archives reveals ‘historical’ antibiotic resistance genes diversity increased over recent decades in the environment

Abstract Antibiotic Resistance Genes (ARGs) are widespread in freshwater environments and represent a concealed threat to public health and aquatic eco-system safety. To date, only a limited number of studies have investigated the historical distribution of ARGs and their hosts through the analysis of freshwater sedimentary archives. This research gap constrains our comprehensive of the mechanisms underlying natural bacterial resistance formation during pre-antibiotic era (prior to the 1940s) and the development of human-induced bacterial resistance in post-antibiotic era (since the 1940s). In this study, we examined the vertical distribution patterns of ARGs and their associated hosts within a sedimentary core from a eutrophic lake, employing shotgun sequencing methodology. The findings revealed a marked increase in ARG diversity during post-antibiotic era, and the predominant ARG types identified included those conferring resistance to multidrug, bacitracin, macrolide–lincosamide–streptogramin, beta-lactam, tetracycline, fluoroquinolone, glycopeptide and aminoglycoside, collectively accounting for 78.3%–85.6% of total ARG abundance. A total of 127 ARG subtypes were identified in samples, and 48 ARG subtypes shared across vertical sediment resistome profile with two of them, bacA and bcrA, occurring only in post-antibiotic era. Further, 137 metagenome-assembled genomes (83 species belonging to 12 phyla) were identified as ARG hosts, mainly belonging to the phyla Proteobacteria, Nitrospirota, Chloroflexota, Bacteroidota, Actinobacteriota, Cyanobacteria, and Firmicutes. Significant correlation was found between the diversity of ARG and the concentrations of organic matter and heavy metals, suggesting a common source of contamination. Aside the fact that human-induced eutrophication is a forcing factor acting in parallel to increase ARGs releases in water systems, both being indicators of increased urbanization in the catchment, eutrophication may significantly increase bacterial activity, thereby facilitating the spread of antibiotic-resistant bacteria in environment. This study reveals the marked increased in ARG diversity with the onset of antibiotic use by human societies with potential impact of aquatic ecosystem.

Antibiotics and Pesticides Enhancing the Transfer of Resistomes among Soil-Bayberry-Fruit Fly Food Chain in the Orchard Ecosystem.

While substantial amounts of antibiotics and pesticides are applied to maintain orchard yields, their influence on the dissemination and risk of antibiotic resisitome in the orchard food chain remains poorly understood. In this study, we characterized the bacterial and fungal communities and differentiated both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the soil, Chinese bayberry (matured and fallen), and fruit fly gut, collected from five geographic locations. Our results showed that fruit fly guts and soils exhibit a higher abundance of ARGs and VFGs compared with bayberry fruits. We identified 112 shared ARGs and 75 shared VFGs, with aminoglycoside and adherence factor genes being among the most abundant. The co-occurrence network revealed some shared microbes, such as Bacillus and Candida, as potential hosts of ARGs, highlighting the vector risks for both above- and below-ground parts of the orchard food chain. Notably, the elevated levels of antibiotics and pesticide residues in orchard soils increase ARGs, mobile genetic elements (MGEs), and VFGs in the soil-bayberry-fruit fly food chain. Our study highlighted that agricultural management, including the overuse of antibiotics and pesticides, could be the key factor in accumulating resistomes in the orchard food chain.

Metagenomic assemblies tend to break around antibiotic resistance genes

BackgroundAssembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs) and inform interventions to prevent further spread of resistant bacteria. However, similar to other conserved regions, such as ribosomal RNA genes and mobile genetic elements, almost identical ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.ResultsThe results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.ConclusionsOur study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.

Antibiotic Resistance Genes in Global Food Transformation System: Edible Insects vs. Livestock.

Antibiotic-resistant genes (ARGs) pose a significant threat to the global food transformation system. The increasing prevalence of ARGs in food has elicited apprehension about public health safety. The widespread dissemination of ARGs in food products, driven by the inappropriate use of antibiotics, presents significant adversity for the safety of emerging future food sources such as edible insects. As the world faces increasing challenges related to food security, climate change, and antibiotic resistance, edible insects offer a sustainable and resilient food source. The intriguing possibility of edible insects serving as a less conducive environment for ARGs compared to livestock warrants further exploration and investigation. In this recent work, we listed ARGs from edible insects detected so far by in vitro approaches and aimed to construct a fair comparison with ARGs from livestock based on relevant genes. We also presented our argument by analyzing the factors that might be responsible for ARG abundance in livestock vs. edible insects. Livestock and edible insects have diverse gut microbiota, and their diets differ with antibiotics. Consequently, their ARG abundance may vary as well. In addition, processed edible insects have lower levels of ARGs than raw ones. We hypothesize that edible insects could potentially contain a lower abundance of ARGs and exhibit a diminished ability to disseminate ARGs relative to livestock. A regulatory framework could help intercept the increasing prevalence of ARGs. Due diligence should also be taken when marketing edible insects for consumption.

How nanoscale plastics facilitate the evolution of antibiotic resistance?

The plastic can enhance the proliferation of antibiotic resistance genes (ARGs), however, the effect of nanoplastics (NPLs) on bacterial antibiotic resistance has not been clearly explained. Herein, we explored the effects and mechanisms of NPLs of different sizes (200 and 600 nm) on the evolution of antibiotic resistance in Serratia marcescens. The results indicated that the evolution of bacterial antibiotic resistance could be promoted under NPLs exposure, which the median of relative abundance of ARGs was 1.11–1.46 times compared to the treatment without NPLs. Transcriptomic analysis showed that the larger size of NPLs mainly increased the permeability of bacterial cell membranes to efflux antibiotics, thus potentiating antibiotic resistance. While, the smaller NPLs is more than that, its enhanced the expression of antibiotic resistance by modulating bacterial metabolic processes. The genome SNP analysis found that the NPLs could cause the genetic mutation occurrence to alter the membrane transport and metabolism processes, and it increased at a size of 200 nm more than at 600 nm NPLs. Importantly, we demonstrated that the horizontal transfer of ARGs was augmented due to the NPLs could dock to bacterial surface proteins and pull their movement to contact with other bacteria (binding energy of membrane proteins: −8.54 kcal/mol), especially the smaller size. It suggests that NPLs will also contribute to the proliferation of ARGs in the environment. This study provides data for understanding the risk of bacterial resistance.

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.

Effects of exogenous signaling molecules on anaerobic sludge digestion: Quorum sensing and antibiotic resistance genes

Regulating quorum sensing (QS) signaling molecules could improve wastewater treatment but might increase antibiotic resistance. This study investigated the effects of exogenous C6-HSL on anaerobic sludge under oxytetracycline stress, with a focus on antibiotic resistance genes (ARGs) and the QS response. The results revealed that exogenous oxytetracycline increased the copy number of ARGs by more than 68.8 %. It also facilitated a 3.04-fold increase in the concentration of signaling molecules and increased the abundance of QS genes. Further addition of the C6-HSL accelerated oxytetracycline degradation, and reduced its residual concentration by 70.9 %, alleviating oxytetracycline stress on microbial communities, and correspondingly reducing stress release from AHL by 75.4 %. Importantly, this did not exacerbate antibiotic resistance, with no significant difference (p > 0.05) in the ARG abundance. These findings may provide valuable insights into the relationship between QS process and antibiotic resistance.

Seasonal variation of antibiotic resistance genes in activated sludge of a full-scale municipal wastewater treatment plant: Contribution of activated sludge functional taxa and clinically relevant taxa

It has been demonstrated that antibiotic resistance genes (ARGs) exhibit seasonal variations in municipal wastewater treatment plants (MWTPs), but their relationship to bacterial phylogeny structure remains unclear. Using advanced metagenomic techniques and machine learning approach, the current study conducted a year-long investigation to explore the relationship between ARGs and the bacterial community of activated sludge in a full-scale MWTP in Beijing, where seasonal dynamics are remarkable. High abundance of ARGs, notably the clinically relevant high-risk ARGs, was observed in winter and spring, the cold season in Beijing. Seasonal patterns were also observed in the diversity of ARGs and the overall bacterial community. Machine learning-based random forest classification models were utilized to identify biomarkers for ARGs and bacterial genera as indicators of seasonal differences. Subsequent analysis of the relationship between ARGs and bacterial biomarkers was examined using random forest regression models. Results showed that the enrichment of potential pathogens such as Mycobacterium, Clostridium and Pseudomonas was high in winter and spring, strongly contributing to the abundance of high-risk ARGs (ermB, aac(6′)-I, tetM, blaTEM, and mefA) during cold season. Conversely, functional taxa associated with activated sludge, such as Thauera, displayed seasonal fluctuations and a preference for ARGs with minor clinical implications. Metagenomic binning further illustrated the contribution of Mycobacterium to ARG enrichment in cold season. Our findings highlight the collective impact of human-derived clinically relevant taxa and functional bacterial taxa in activated sludge on the seasonal dynamics of ARGs in MWTPs. Additionally, this study offers valuable insights into the safe disposal of the excess sludge from MWTPs.

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.

Antibiotic resistomes and ecological risk elimination in field-scale constructed wetland revealed by integrated metagenomics and metatranscriptomics

Constructed wetlands (CWs) are identified as significant ecological systems for the potential control of antibiotic resistance genes (ARGs) in the environment. However, the precise mechanisms governing removal, persistence, expression, and associated risks of ARGs during wetland treatment remain poorly understood. In this study, the distribution, mobility, expression, and hosts of ARGs in water, sediments, and plants of a field-scale CW and its parallel natural river were systematically investigated through metagenomic and metatranscriptomic approaches. Results showed that both the abundance and diversity of ARGs in water gradually decreased along the way of CW, reaching a final abundance removal rate of 72.28 % in the effluent. Source tracking analysis indicted that the reduction of ARGs in water was mainly achieved by the dynamic accumulation of ARGs in sediments and plants of the CW. Proteobacteria were identified as primary hosts for ARGs, particularly in sediments and plants during CW treatment. Moreover, although ESKAPE pathogens carrying multiple ARGs persisted in all media throughout the CW treatment, ARG expression levels and risk of water were also significantly decreased after CW treatment. Collectively, our comprehensive multi-omics study would enhance the understanding of ARG removal by CWs, offering insights for controlling antimicrobial resistance in wastewater treatment system.