Copies Of Antibiotic Resistance Genes Research Articles

Global Trends of Antibiotic Resistance Genes in Staphylococcus aureus: A Comprehensive Genomic Analysis.

Staphylococcus aureus (S. aureus) is a pathogen capable of causing severe diseases and exhibiting resistance to multiple antibiotics. However, there is a significant lack of comprehensive research on the global prevalence of its antibiotic resistance genes (ARGs). This study provided a comprehensive analysis of ARGs in S. aureus, using 113,842 S. aureus genome sequences from the National Center for Biotechnology Information database. The results revealed that a significant majority (84%) of these genomes harbored at least one ARG, with a total of 389,464 ARG sequences identified across 19 major types and 103 subtypes. These ARGs exhibited varied abundances and diversities, linked primarily to clinical cases worldwide. ARGs for fluoroquinolones, multidrug resistance, bacitracin, tetracyclines, beta-lactams, and aminoglycosides were notably abundant, ranging from 3.16 × 10-5 to 1.49 copies of ARG per million bp. Variations in the abundance and diversity of ARGs were observed between countries, with middle- and low-income countries showing higher gene abundance but lower diversity compared with high-income countries. Temporal analysis over 30 years showed a fluctuating decline in ARG abundance alongside an increase in diversity, suggesting evolving resistance mechanisms. The study also explored the role of mobile genetic elements in ARG dissemination, finding a substantial proportion of ARG subtypes associated with plasmids and insertion sequence elements, indicating their potential for spread across borders. The global distribution of mobile ARGs was further analyzed, revealing the extensive reach of certain ARGs across countries. This research provides valuable insights into the prevalence and dissemination of antibiotic resistance in S. aureus on a global scale, aiding in the development of effective monitoring and control strategies to combat ARGs in S. aureus and other pathogens.

Transmission of antibiotic resistance through organic amendments in arable land: A 3-year field study with pigeonpea–wheat cropping system

The worldwide emergence of antimicrobial resistance (AMR) poses a substantial risk to human health and environmental stability. In agriculture, organic amendments (derived from organic sources such as manure, and plant residues) are beneficial in restoring soil properties and providing essential nutrients to crops but raise concerns about harboring antibiotic resistance, which emphasizes the need for vigilant monitoring and strategic interventions in their application. The current study assessed the impact of farming practices (organic and conventional) in a three-year field experiment with pigeonpea-wheat cropping system, focusing on the transmission of AMR using culture-dependent and -independent approaches, and soil nutrient content. Markers for antibiotic resistance genes (ARGs) (aminoglycoside-aacA, β-lactam-blaTEM, chloramphenicol-cmlA1, macrolide-ermB, sulfonamides-sul1, sul2, and tetracycline-tetO) and integrons (intl1 and intl2) were targeted using qPCR. Manure amendments, particularly FYM1, exhibited a higher abundance of copies of ARGs compared to the rhizospheric soil. Organic farming was associated with higher copies of intl2, sul1, blaTEM, and tetO genes, while conventional farming showed increased copies of sul2 and ermB genes in the rhizosphere. Significant positive correlations were observed among soil nutrient contents, ARGs, and MGEs. The notable prevalence of ARGs linked to manure amendments serves as a cautionary note, demanding responsible management practices.

Exploring the dynamics of antibiotic resistome on plastic debris traveling from the river to the sea along a representative estuary based on field sequential transfer incubations

The environmental risks arising from ubiquitous microplastics or plastic debris (PD) acting as carriers of antibiotic resistance genes (ARGs) have attracted widespread attention. Enormous amounts of plastic waste are transported by rivers and traverse estuaries into the sea every year. However, changes in the antibiotic resistome within the plastisphere (the biofilms formed on PD) as PD travels through estuaries are largely unknown. In this study, we performed sequential migration incubations for PD along Haihe Estuary to simulate the natural process of PD floating from rivers to the ocean. Metagenomic sequencing and analysis techniques were used to track microbial communities and antibiotic resistome on migrating PD and in seawater representing the marine environment. The total relative gene copies of ARGs on traveling PD remained stable. As migration between greatly varied waters, additional ARG subtypes were recruited to the plastisphere. Above 80 % ARG subtypes identified in the plastisphere were persistent throughout the migration, and over 30 % of these persistent ARGs were undetected in seawater. The bacterial hosts composition of ARGs on PD progressively altered as transported downstream. Human pathogenic bacteria carrying ARGs (HPBs-ARG) exhibited decreasing trends in abundance and species number during transfer. Individual HPBs-ARG persisted on transferred PD and were absent in seawater samples, comprising Enterobacter cloacae, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Vibrio parahaemolyticus. Based on all detected ARGs and HPBs-ARG, the Projection Pursuit model was applied to synthetically evaluate the potential risks of antibiotic resistance on migrating PD. Diminished risks on PD were observed upon the river-to-sea journey but consistently remained significantly higher than in seawater. The potential risks posed to marine environments by drifting PD as dispersal vectors for antibiotic resistance deserve greater attention. Our results provide initial insights into the dynamics or stability of antibiotic resistome on PD crossing distinct aquatic systems in field estuaries.

Potential of novel zinc-based nanomaterials on the microbial community, antibiotic resistance genes, and DNA replication in animal manure

The existence of Antibiotic Resistance Genes (ARGs) in diverse everyday environments, such as animal agriculture, natural surroundings, and waste products, presents potential threats to both human health and food safety. Herein, metagenomic sequencing technique was employed to investigate the impact of two zinc-based nanoparticles, Graphene Oxide-modified Zinc Oxide (GOnZnO) and Microorganism-mediated Zinc Oxide (Micro-ZnO), on the microbial community, ARGs, and DNA replication. The results showed that both GOnZnO and Micro-ZnO significantly reduced zinc levels in animal manure when compared to the control group of nano zinc oxide (nZnO). The order of ARGs copy numbers was nZnO > GOnZnO > Micro-ZnO, with a significant difference between the GOnZnO and Micro-ZnO groups. Additionally, the expression levels of various DNA replication genes, including DNA polymerase III holoenzyme, dnaB, dnaG, RNeseH, polA, and Lig, were significantly lower in the GOnZnO group compared to the nZnO group. The Micro-ZnO group exhibited even lower expression levels of these genes compared to the GOnZnO group. In contrast, GOnZnO and Micro-ZnO had no significant impact on archaeal DNA replication pathway-related genes. Specifically, the expression of RNASEH1 was significantly higher in the Micro-ZnO group compared to the GOnZnO and nZnO groups. Co-occurrence network analysis revealed changes in ARGs driven by bacterial and eukaryotic DNA replication and microbial community dynamics. However, there was no correlation observed between ARGs and archaeal DNA replication genes. Overall, these findings add to the existing literature regarding the application of GOnZnO and Micro-ZnO as potential agents for reducing ARGs pollution.

The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang.

Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 108 total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.

Biofilm electrode reactor coupled manganese ore substrate up-flow microbial fuel cell-constructed wetland system: High removal efficiencies of antibiotic, zinc (II), and the corresponding antibiotic resistance genes

A coupled system comprised of a biofilm electrode reactor (BER) and a manganese ore substrate microbial fuel cell-constructed wetland (MFC-CW) system was used to remove co-exposed antibiotic and Zn (II), as well as simultaneously reduce copies of antibiotic resistance genes (ARGs) in the current study. In this system, BER primarily reduced the concentrations of antibiotics and Zn (II), and the effluent was used as the input to the MFC-CW, thereby providing electricity to BER. Co-exposure to a high concentration of Zn (II) decreased the relative abundances (RAs) of ARGs in the BER effluent, whereas the remaining sub-lethal concentration of Zn (II) increased the RAs of ARGs in the MFC-CW effluent. Even though the absolute copies of ARGs in the effluents increased during co-exposure, the total number of target ARG copies in the effluent of MFC-CW was significantly lower than that of BER. Moreover, BER pre-treatment eliminated most of Zn (II), which improved the electrical power generation characteristic of the MFC-CW unit. Correspondingly, the bacterial community and the ARGs hosts were analyzed to demonstrate the mechanism. In conclusion, the coupled system demonstrates significant potential to reduce antibiotics, Zn (II) and environmental risks posed by ARGs.

Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.

Metagenomic insights into the potential risks of representative bio/non-degradable plastic and non-plastic debris in the upper and lower reaches of Haihe Estuary, China

As vectors for microorganisms and genetic elements, vast amounts of solid wastes, including plastics and non-plastics, enter oceans through estuaries globally. The heterogeneity of microbiomes developed on different types of plastic and non-plastic matrices and their potential environmental risks in field estuarine regions have not been fully explored. Here, microbial communities, antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) on substrate debris (SD) covering non-biodegradable plastics, biodegradable plastics, and non-plastics were first comprehensively characterized based on metagenomic analyzes (substrate identity). These selected substrates were field-exposed at both ends of the Haihe Estuary, China (geographic location). For substrate identity: conspicuously diverse functional gene profiles on different substrates were obtained; the relative gene copies of ARGs, VFs, and MGEs on non-biodegradable plastics were highest at both locations; non-biodegradable plastic matrices recruited the most abundant unique ARGs from ambient waters; the relative abundance of potential bacterial hosts carrying multiple ARGs and VFs (BH-AV) was much higher on non-biodegradable plastic surfaces than on the other two substrates, especially in the coastal water environment. For geographic locations: more abundant specific ARGs, VFs, and MGEs were significantly enriched on SD from the upper estuary; the average relative abundance of identified BH-AV on SD from the upper estuary was 1.99–7.14 folds from the lower estuary. Finally, the results of the Projection Pursuit Regression model verified the higher comprehensive potential risks arising from non-biodegradable plastics (substrate identity) and SD from the upstream of the estuary (geographic location). Based on comparative analysis, our results alert us to pay particular attention to ecological risks triggered by conventional non-biodegradable plastics in rivers and coastal environments and highlight the microbiological risk from terrestrial solid waste to the downstream marine environment.

Characteristics of antibiotic resistance gene distribution in rainfall runoff and combined sewer overflow.

Rainfall runoff and combined sewer overflow (CSO) converge with organic waste, nutrients, and microbes from the ground and wastewater. These pollutants promote the spread and transformation of antibiotic resistance genes (ARGs). In this study, four rainfall runoff and one CSO outfall were chosen, and samples were collected to explore the occurrence and distribution of ARGs. The ARGs were extracted from suspended solids and analyzed using metagenomic sequencing. A total of 888 ARG subtypes, belonging to 17 ARG types, were detected in all samples. Eleven ARG types were shared by all the samples. Multidrug resistance genes had the highest relative abundance. Their total relative abundance reached 1.07 ratio (ARG copy number/16S rRNA gene copy number) and comprised 46.6% of all the ARGs. In all samples, the CSO outfall had the highest total relative abundance (8.25 × 10-1 ratio) of ARGs, with a ratio ranging ND (not detected)-3.78 × 10-1 ratio. Furthermore, the relationship between ARG types and environmental factors was determined using redundancy analysis. The results showed that chemical organic demand (COD) and bacterial abundance were positively correlated with most ARG types, including multidrug, bacitracin, aminoglycoside, β-lactam, tetracycline, and sulfonamide. NH3-N, TN, and TP were positively correlated with rifamycin, fosmidomycin, and vancomycin resistance genes. The relationship among the ARG subtypes was investigated using network analyses. The multidrug resistance gene subtypes had the highest frequency of co-occurrence. This study provides insights into the occurrence and distribution of ARGs under non-point source pollution and may contribute to the control of ARGs.

Seasonal variation in antibiotic resistance genes and bacterial phenotypes in swine wastewater during three-chamber anaerobic pond treatment

Antibiotic resistance is a global public health concern. Antibiotic usage in pigs makes swine wastewater (SW) a reservoir for antibiotic resistance genes (ARGs). SW is usually stored and treated in a three-chamber anaerobic pond (3-CAP) in medium and small pig farms in northern China. However, the yet unexplored presence of ARGs in SW during 3-CAP treatment may result in ARGs spreading into the environment if farmers apply SW to farmland as a liquid organic fertilizer. This study investigated the profiles of and changes in ARGs in SW during its treatment in 3-CAP over four seasons and analyzed the correlation between ARGs and bacterial phenotypes, along with the physicochemical parameters of the water. The results revealed that ARG abundance decreased considerably after 3-CAP treatment in April (47%), October (47%), and December (62%) but increased in May (43%) and August (73%). The ARG copies in the influent and other SW samples increased significantly from 107 copies/mL in April to 109 copies/mL in October and were maintained in December. The increase in ARG abundance was not as rapid as the growth of the bacterial population, resulting in lower relative abundance in October and December. Bacterial communities possessed more sul1 and tetM genes, which were also positively correlated with mobile genetic elements. After the 3-CAP treatment, 16% of antibiotics and 60% of heavy metals were removed, and both had a weak correlation with ARGs. Predicted phenotypes showed that gram-positive (G+) and gram-negative (G−) bacteria have different capacities for carrying ARGs. G+ bacteria carry more ARGs than G− bacteria. This study revealed the persistence of ARGs in SW after 3-CAP treatment over different seasons. Applying SW in the proper month will mitigate ARG dissemination to the environment.

Uncover landfilled antimicrobial resistance: a critical review of antibiotics flux, resistome dynamics and risk assessment

Municipal solid waste (MSW) landfill is one of the most important reservoirs of antimicrobial resistance (AMR) in urban environments. By reviewing ~120 published cases worldwide, we found that leachate-borne antibiotics were at the μg/L level, and meanwhile, around 8 tons of antibiotics (including the clinically relevant ones) annually leached from the MSW landfills in China. During a decade-long landfilling process, the leachate-borne bacteria mainly originating from human-associated waste (&gt;40%) formed a community network being versatile to the drastic environmental changes. Among them, the keystone species (<italic>Proteobacteria</italic> subtaxa) functioned for metabolizing the most available substrate in leachates and were also the hosts of mobile antibiotic resistance genes (ARGs), which suggested the enduring and close associations between bacterial community and resistome. These leachate-borne ARGs were highly mobile via plasmid-mediated horizontal gene transfer, especially in less aged leachates (&lt;10 yr). MetaCompare showed that the AMR-hazard index of landfill-specific airborne particles (index=20.5) was significantly higher than that of drinking water (index=17.81, <italic>P</italic>&lt;0.01). Human daily exposure of ARGs amounted to an inhalation of (5.83±0.16)×10⁵ copies of ARGs, being tenfold higher than that ingestion of drinking water, which implies landfills as a non-ignorable AMR source.

Wastewater Treatment Works: A Last Line of Defense for Preventing Antibiotic Resistance Entry Into the Environment

With their large, diverse microbial communities chronically exposed to sub-inhibitory antibiotic concentrations, wastewater treatment works (WWTW) have been deemed hotspots for the emergence and dissemination of antimicrobial resistance, with growing concern about the transmission of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) into receiving surface waters. This study explored (1) the prevalence of ARG and ARB in local WWTW, (2) the effect of sub-inhibitory antimicrobial exposure on ARG copy numbers in pure cultures from WWTW, and (3) two WWTW with different treatment configurations. For each WWTW, qPCR determined the prevalence ofmcr3, sul1, sul2, andblaKPCduring the treatment process, and culture methods were used to enumerate and identify ARB. Bacterial colonies isolated from effluent samples were identified by 16S rDNA sequencing and their respective minimum inhibitory concentrations (MIC) were determined. These were compared to the MICs of whole community samples from the influent, return activated sludge, and effluent of each WWTW. Resistance genes were quantified in 11 isolated cultures before and after exposure to sub-MIC concentrations of target antibiotics. The numbers of ARG and ARB in both WWTW effluents were notably reduced compared to the influent.Sul1andsul2gene copies increased in cultures enriched in sub-MIC concentrations of sulfamethoxazole, whileblaKPCdecreased after exposure to amoxicillin. It was concluded, within the parameters of this study, that WWTW assist in reducing ARG and ARB, but that sub-inhibitory exposure to antimicrobials has a varied effect on ARG copy number in pure cultures.

Nitrogen Regulates the Distribution of Antibiotic Resistance Genes in the Soil-Vegetable System.

The increasing antibiotic resistance genes (ARGs) in fertilizer-amended soils can potentially enter food chains through their transfer in a soil–vegetable system, thus, posing threats to human health. As nitrogen is an essential nutrient in agricultural production, the effect of nitrogen (in the forms NH4+-N and NO3−-N) on the distribution of ARGs (blaTEM-1, sul1, cmlA, str, and tetO) and a mobile genetic element (MGE; tnpA-4) in a soil–Chinese cabbage system was investigated. Not all the tested genes could transfer from soil to vegetable. For transferable ones (blaTEM-1, sul1, and tnpA-4), nitrogen application influenced their abundances in soil and vegetable but did not impact their distribution patterns (i.e., preference to either leaf or root tissues). For ARGs in soil, effects of nitrogen on their abundances varied over time, and the positive effect of NH4+-N was more significant than that of NO3−-N. The ARG accumulation to vegetables was affected by nitrogen application, and the nitrogen form was no longer a key influencing factor. In most cases, ARGs were found to prefer being enriched in roots, and nitrogen application may slightly affect their migration from root to leaf. The calculated estimated human intake values indicated that both children and adults could intake 106–107 copies of ARGs per day from Chinese cabbage consumption, and nitrogen application affected ARG intake to varying degrees. These results provided a new understanding of ARG distribution in vegetables under the agronomic measures such as nitrogen application, which may offer knowledge for healthy vegetable cultivation in future.

Antibiotic Resistance in Black Sea Microbial Communities

Background: Antibiotic resistance genes (ARGs) are considered as pollutants and are found in natural and anthropogenically impacted environments. Distribution of ARGs in marine environment poses a threat to human health turning the water body into a pool for the ARGs’ transmission.Objectives: A large-scale study of antibiotic resistance in microbial communities has been performed in the Black Sea, both in the coastal and offshore regions.Methods: The quantitative distribution of the genes responsible for the inactivation of the beta-lactam (blaCMY, blaSHV), vancomycin (vanA, vanB), macrolides (ermB) and colistin (mcr-1) was assessed with real-time quantitative PCR. Concentrations of the antibiotics belonging to the classes of beta-lactam/cephalosporin/carbapenem, macrolides and glycopeptides were determined by LC-ESI-QTOF-MS.Results: The present study revealed the distribution of antibiotic resistance genes targeting the response to all antibiotics included in our analysis at various locations across the Black Sea. According to the ARGs copy number normalized to the 16S rRNA, vanB (2 × 10−1 ± 1 × 10−1) and blaSHV (4 × 10−2 ± 1 × 10−2) were the most numerous genes, followed by blaCMY (1 × 10−2 ± 3 × 10−3) and mcr-1 (3 × 10−2 ± 2 × 10−2). The less abundant gene was ermB (1 × 10−3 ± 5 × 10−4) and vanA (1 × 10−5 ± 5 × 10−4). The mcr-1, blaCMY and blaSHV had moderate positive correlation with markers of ruminant faecal pollution. The concentration of antibiotics in seawater was below the detection limit. The abundance of all ARGs included in the study was significantly higher (p-value&amp;lt;0.05) within the northwest coastal area when compared to the offshore stations. The results clearly indicate an alarming antibiotic resistance problem in the region and call for a regular monitoring of ARGs abundance in the Black Sea and its major freshwater tributaries.

Estuarine salinity gradient governs sedimentary bacterial community but not antibiotic resistance gene profile

Antibiotic resistance gene (ARG) pollution in estuarine environment has drawn great attention, and it is not clear if the physical and chemical parameters such as salinity, total organic carbon, total nitrogen, total phosphorus and antibiotics affects the distribution of ARGs. Herein, we deciphered the ARG profiles and microbial community compositions in sediments from Jiulong River Estuary (JRE) and Min River Estuary (MRE) of China using high-throughput sequencing-based metagenomics analysis. Furthermore, we explored the influence of salinity on bacterial community and ARG profiles. The results showed that Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these two estuaries. The abundance of ARGs ranged from 1.05 × 10−1 to 2.93 × 10−1 copy of ARG per copy of 16S rRNA gene in all the sediment samples and the profiles of ARGs presented similar patterns in two estuaries. Multidrug resistance genes were the dominant ARG types in both estuaries, with an overall abundance of 2.39 × 10−2–1.07 × 10−1 copy of ARG per copy of 16S rRNA gene, followed by genes conferring resistance to bacitracin and macrolide-lincosamide-streptogramin. Salinity was an important influencing factor on the bacterial community but not on the ARG profiles. Instead, stochastic processes exerted the main influence on the distribution of ARGs. The comparison of ARG profiles among estuary sediments, marine sediments, and samples from anthropogenic pollution environments revealed remarkable similarity of ARG profiles between samples from estuary sediments and those from municipal wastewater treatment plants. These results suggested that the complex emission of anthropogenic pollution could cause the stochastic ecological pattern of ARGs.

Safety of composts consisting of hydrothermally treated penicillin fermentation residue: Degradation products, antibiotic resistance genes and bacterial diversity

Combining hydrothermal treatment and composting is an effective method to dispose of penicillin fermentation residue (PFR), but the safety and related mechanism are still unclear. In this study, penicillin solution was hydrothermally treated to decipher its degradation mechanism, and then hydrothermally treated PFR (HT-PFR) was mixed with bulking agents at ratios of 2:0 (CK), 2:1.5 (T1), and 2:5 (T2) to determine the absolute abundance of antibiotic resistance genes (ARGs) and the succession of bacterial community. Results showed that penicillin was degraded to several new compounds without the initial lactam structure after hydrothermal treatment. During composting, temperature and pH of the composts increased with the raising of HT-PFR proportion, except the pH at days 2. After 52 days of composting, the absolute copies of ARGs (blaTEM, blaCMY2, and blaSFO) and the relative abundance of bacteria related to pathogens were reduced significantly (P < 0.05). Especially, the total amount of ARGs in the samples of CK and T1 were decreased to equal level (around 5 log10 copies/g), which indicated that more ARGs were degraded in the latter by the composting process. In the CK samples, Bacteroidetes and Proteobacteria accounted for ~69.8% of the total bacteria, but they were gradually replaced by Firmicutes with increasing proportions of HT-PFR, which can be caused by the high protein content in PFR. Consisting with bacterial community, more gram-positive bacteria were observed in T1 and T2, and most of them are related to manganese oxidation and chitinolysis. As composting proceeded, bacteria having symbiotic or pathogenic relationships with animals and plants were reduced, but those related to ureolysis and cellulolysis were enriched. Above all, hydrothermal treatment is effective in destroying the lactam structure of penicillin, which makes that most ARGs and pathogenic bacteria are eliminated in the subsequent composting.

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems

BackgroundSoil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively.ResultsHigh diversity (242 ARG subtypes) and abundance (0.184–0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13–35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition.ConclusionsOur results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future.Aify4ac4FW_3-HKjdJXvGWVideo abstract

In-situ remediation of oxytetracycline and Cr(VI) co-contaminated soil and groundwater by using blast furnace slag-supported nanosized Fe0/FeSx

The combined pollution of heavy metals and antibiotics in soil and groundwater has caused widespread concern. In this study, a blast furnace slag-supported nanosized Fe0/FeSx composite (Fe0/FeSx@BFS) was synthesized and used for the in-situ remediation of Cr(VI) and oxytetracycline (OTC) co-contaminated soil and groundwater. The effects of pH and initial concentration of contaminants on Cr(VI) and OTC co-adsorption in simulated contaminated groundwater were investigated. Consequently, the adsorption of both Cr(VI) and OTC was highly pH-dependent, while the lower pH value favored the adsorption. Meanwhile, 0.5 g/L of Fe0/FeSx@BFS could efficiently remove approximately 38 mg/g Cr(VI) and 95 mg/g OTC in simulated groundwater at an initial pH of 3.5, initial Cr(VI) concentration of 20 mg/L, and initial OTC concentration of 50 mg/L. During the co-adsorption process, Cr(VI) removal proceeded mainly by reduction and the formation of chromite complex, and OTC removal involved oxidation degradation, adsorption, and complexation. Laboratory incubation experiments were conducted to study the effects of Fe0/FeSx@BFS amendment on Cr immobilization, antibiotic resistance genes (ARGs) distribution, and microbial community in Cr(VI) and OTC co-contaminated soil. Results showed that 3% Fe0/FeSx@BFS treatment could efficiently remove 60% of bio-available Cr and 42.14% of total ARGs copies in the contaminated soil after 49 days incubation. Additionally, Fe0/FeSx@BFS amendment significantly reduced the abundance of ARGs-source bacteria, Firmicutes. The results suggested that Fe0/FeSx@BFS amendment was a feasible method to remediate the Cr(VI) and OTC co-contaminated groundwater and saturated soil.

Plastisphere enrich antibiotic resistance genes and potential pathogenic bacteria in sewage with pharmaceuticals

Microplastics (MPs) and pharmaceuticals are common emerging pollutants in sewage, and their coexistence may have more negative effects on the environments. This study chose tetracycline (TC), ampicillin (AMP) and triclosan (TCS) to investigate the responses of antibiotic resistance genes (ARGs) and microbial communities on different MPs (polyvinyl chloride (PVC), polyethylene (PE)) biofilms (plastisphere). The adsorption capacity of three pharmaceuticals on PVC and PE decreased in the order of AMP > TC > TCS. PE was more conducive to microbial attachment than PVC. MPs led to the increase of the total copies of ARGs and mobile genetic elements (MGEs) in the sewage. Importantly, multidrug ARGs and MGEs were enriched on plastisphere. Furthermore, the co-occurrence of TC and MPs led to higher risks of spreading ARGs and MGEs. In addition, potential pathogenic bacteria Legionella, Mycobacterium, Neisseria and Arcobacter were more abundant on plastisphere than those in sewage, and these bacteria might be the hosts for ARGs and MGEs. This study showed that plastisphere could be repositories of ARGs and MGEs in sewage and accumulated potential pathogenic bacteria.

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China

Ready-to-eat (RTE) foods have been considered to be reservoirs of antibiotic resistance bacteria, which constitute direct threat to human health, but the potential microbiological risks of RTE foods remain largely unexplored. In this study, the metagenomic approach was employed to characterize the comprehensive profiles of bacterial community and antibiotic resistance gene (ARG) in 18 RTE food samples (8 RTE meat, 7 RTE vegetables and 3 RTE fruit) in southern China. In total, the most abundant phyla in RTE foods were Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes and Actinobacteria. 204 ARG subtypes belonging to 18 ARG types were detected with an abundance range between 2.81 × 10−5 and 7.7 × 10−1 copy of ARG per copy of 16S rRNA gene. Multidrug-resistant genes were the most predominant ARG type in the RTE foods. Chloramphenicol, macrolide-lincosamide-streptogramin, multidrug resistance, aminoglycoside, bacitracin, tetracycline and β-lactam resistance genes were dominant, which were also associated with antibiotics used extensively in human medicine or veterinary medicine/promoters. Variation partitioning analysis indicated that the join effect of bacterial community and mobile genetic elements (MGEs) played an important role in the resistome alteration. This study further deepens the comprehensive understanding of antibiotic resistome and the correlations among the antibiotic resistome, microbiota, and MGEs in the RTE foods.