Dominant Antibiotic Resistance Genes Research Articles

Occurrence and distribution of antibiotic resistance genes in Rivers entering the sea from the South bank of Laizhou Bay, China

The distribution of antibiotic resistance genes (ARGs) in Laizhou Bay affects the local socio-economic development. The study aimed to investigate the distribution of ARGs in the rivers that flow into the sea around Laizhou Bay’s southern shore. Water and sediment samples were collected from different typical sites of rivers entering the sea in Weifang, including Mi River, Bai Lang River, Yu River, Wei River, Jiaolai River, Xiaoqing River and Di River. The species and abundance of ARGs in the sediments were characterized and quantified by macro-genome high-throughput sequencing technology. The species distribution of ARGs was compared. In two sediment samples and seven water samples, 24 ARGs types and 1244 subtypes of ARGs were detected, in which multidrug-resistant class was the main ARGs type and FBJ murine osteosarcoma viral oncogene homolog B (fosB) was the dominant ARGs. The types of ARG in the top ten of these samples were the same, although the proportion was different. Dominant ARG subtypes accounted for more than 50% of all the nine samples. This article provides basic data support for pollution status and environmental risk assessment as well as remediation of ARGs in rivers entering the sea along the south coast of Laizhou Bay.

Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress

Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika’s intestine, and cold had no significant effect on the composition and structure of pika’s intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.

Distribution and community structure of antibiotic resistance genes in the Three Gorges Reservoir Area.

Antibiotic resistance genes (ARG) are widespread across various regions. While several studies have investigated the distribution of antibiotic resistance in natural environments, the occurrence and diversity of ARGs in the Three Gorges Reservoir have not been fully elucidated. In this study, we employed metagenomic sequencing techniques to investigate the abundance, diversity, and influencing factors of ARGs in the ecosystem of the Three Gorges Reservoir. A total of 874 ARGs, 20 antibiotic classes, and 6 resistance mechanisms were detected. The dominant ARG is the macB, the dominant antibiotic class is multidrug resistance (MDR), and the dominant resistance mechanism is antibiotic efflux. The microorganisms with the highest contribution to ARGs are Betaproteobacteria and Gammaproteobacteria. In this region, pH and NH4+ concentration were significantly negatively correlated with the relative abundance of most ARGs, while NO3- concentration and TN were significantly positively correlated with the relative abundance of most ARGs. The results indicate that the Three Gorges Reservoir constitutes a significant reservoir of ARGs. By studying the distribution of ARGs in the sediments of the Three Gorges Reservoir Area and the relationship between environmental factors and ARGs, we can more comprehensively understand the pollution status of ARGs in this area, and provide theoretical support for subsequent treatment.

Occurrence and distribution of antibiotic pollution and antibiotic resistance genes in seagrass meadow sediments based on metagenomics

Seagrass meadows are one of the most important coastal ecosystems that provide essential ecological and economic services. The contamination levels of antibiotic and antibiotic resistance genes (ARGs) in coastal ecosystems are severely elevated owing to anthropogenic disturbances, such as terrestrial input, aquaculture effluent, and sewage discharge. However, few studies have focused on the occurrence and distribution of antibiotics and their corresponding ARGs in this habitat. Thus, we investigated the antibiotic and ARGs profiles, microbial communities, and ARG-carrying host bacteria in typical seagrass meadow sediments collected from Swan Lake, Caofeidian shoal harbor, Qingdao Bay, and Sishili Bay in the Bohai Sea and northern Yellow Sea. The total concentrations of 30 detected antibiotics ranged from 99.35 to 478.02 μg/kg, tetracyclines were more prevalent than other antibiotics. Metagenomic analyses showed that 342 ARG subtypes associated with 22 ARG types were identified in the seagrass meadow sediments. Multidrug resistance genes and RanA were the most dominant ARG types and subtypes, respectively. Co-occurrence network analysis revealed that Halioglobus, Zeaxanthinibacter, and Aureitalea may be potential hosts at the genus level, and the relative abundances of these bacteria were higher in Sishili Bay than those in other areas. This study provided important insights into the pollution status of antibiotics and ARGs in typical seagrass meadow sediments. Effective management should be performed to control the potential ecological health risks in seagrass meadow ecosystems.

Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning

Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.

Linking bacterial life strategies with the distribution pattern of antibiotic resistance genes in soil aggregates after straw addition

Straw addition markedly affects the soil aggregates and microbial community structure. However, its influence on the profile of antibiotic resistance genes (ARGs), which are likely associated with changes in bacterial life strategies, remains unclear. To clarify this issue, a soil microcosm experiment was incubated under aerobic (WS) or anaerobic (AnWS) conditions after straw addition, and metagenomic sequencing was used to characterise ARGs and bacterial communities in soil aggregates. The results showed that straw addition shifted the bacterial life strategies from K- to r-strategists in all aggregates, and the aerobic and anaerobic conditions stimulated the growth of aerobic and anaerobic r-strategist bacteria, respectively. The WS decreased the relative abundances of dominant ARGs such as QnrS5, whereas the AnWS increased their abundance. After straw addition, the macroaggregates consistently exhibited a higher number of significantly altered bacteria and ARGs than the silt+clay fractions. Network analysis revealed that the WS increased the number of aerobic r-strategist bacterial nodes and fostered more interactions between r-and K-strategist bacteria, thus promoting ARGs prevalence, whereas AnWS exhibited an opposite trend. These findings provide a new perspective for understanding the fate of ARGs and their controlling factors in soil ecosystems after straw addition. Environmental implicationsStraw soil amendment has been recommended to mitigate soil fertility degradation, improve soil structure, and ultimately increase crop yields. However, our findings highlight the importance of the elevated prevalence of ARGs associated with r-strategist bacteria in macroaggregates following the addition of organic matter, particularly fresh substrates. In addition, when assessing the environmental risk posed by ARGs in soil that receives crop straw, it is essential to account for the soil moisture content. This is because the species of r-strategist bacteria that thrive under aerobic and anaerobic conditions play a dominant role in the dissemination and accumulation of ARG.

Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs

Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205–221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge (S) tanks. The greater abundance of mobile genetic elements (MGEs) in the S tank could significantly contribute to the greater abundance of ARGs there compared to the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.

Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

Characteristics of microbial communities and antibiotic resistance genes in typical rivers of the western Qinghai Lake basin

Environmental factors and anthropogenic activity are key factors that shape the distribution of bacteria and antibiotic resistance genes (ARGs) in natural environments. However, few studies have focused on the occurrence of bacteria and ARGs in remote and pristine environments. In this study, the distribution of bacteria and ARGs in two typical rivers of the western Qinghai Lake basin was investigated. Results showed that cold-resistant Planomicrobium sp. was the predominant genus due to the low temperature, followed by unclassified_f_Planococcaceae. High nitrogen nutrients increased the abundance and diversity of the bacteria community and denitrification was the dominant means of bacterial nitrate reduction. Tetracycline resistance genes including tetA, tetB, and tetC were the dominant ARGs in the western Qinghai Lake basin, ranging from 2.30 ​× ​103 to 1.91 ​× ​108 copies/L, while the low abundances of intI1, and ARGs such as sul1 indicated low anthropogenic activity in the western Qinghai Lake basin. Finally, the strong positive correlation between ARGs and intI1 highlights the potential transmission risk of ARGs through cross- or co-selection by horizontal gene transfer. Our study emphasized the adaptation of bacteria to the environment and the facilitation of anthropogenic activity in the propagation of ARGs in natural environments.

Concentrations, distribution, and key influencing factors of antibiotic resistance genes and bacterial community in water and reared fish tissues in a typical tilapia farm in South China

Although previous studies have investigated the occurrence of antibiotic resistance genes (ARGs) in aquaculture, few have monitored the concentrations and propagation of ARGs in biological tissues or investigated the key factors influencing their spread in aquaculture. This study investigated the concentration, propagation, and distribution of ARGs and bacterial communities in water sources, pond water, and tilapia tissues, and their key influencing factors, in a typical tilapia farm. ErmF, sul1, and sul2 were the dominant ARGs with high concentrations. The total concentrations of ARGs (TCAs) in tilapia tissues decreased in the following order: stomach > scales > intestine > gills (P < 0.05). Redundancy analysis and multiple linear regression revealed that suspended solids (SS) and chemical oxygen demand (COD) were positively correlated with the dominant ARGs ermF sul2, and the TCAs (P < 0.05); additionally, Chloroflexi and Bacteroidetes in tilapia aquaculture water were positively correlated with the dominant ARGs ermF and sul2, as well as the TCAs (P < 0.05). This study suggests that SS and COD were the key factors driving the distribution and spread of ARGs in tilapia aquaculture water. Additionally, Chloroflexi and Bacteroidetes were the key bacterial flora affecting the propagation of ARGs in tilapia aquaculture systems.

Analysis of Resistance Gene Diversity in the Intestinal Microbiome of Broilers from Two Types of Broiler Farms in Hebei Province, China.

The crucial reservoir of antibiotic resistance genes (ARGs) within the chicken intestinal microbiome poses a serious threat to both animal and human health. In China, the overuse of antibiotics has significantly contributed to the proliferation of ARGs in the chicken intestinal microbiome, which is a serious concern. However, there has been relatively little research on the diversity of resistance genes in the chicken intestinal microbiome since the implementation of the National Pilot Work Program for Action to Reduce the Use of Veterinary Antimicrobial Drugs in China. The objective of this study was to analyze the diversity of antibiotic resistance genes carried by the chicken intestinal microbiome in both standard farms (SFs), which implement antibiotic reduction and passed national acceptance, and nonstandard farms (NSFs), which do not implement antibiotic reductions, in Hebei Province. Fresh fecal samples of broiler chickens were collected from SFs (n = 4) and NSF (n = 1) and analyzed using high-throughput qPCR technology. Our findings revealed that all five farms exhibited a wide range of highly abundant ARGs, with a total of 201 ARGs and 7 MGEs detected in all fecal samples. The dominant ARGs identified conferred resistance to aminoglycosides, macrolide-lincosamide-streptomycin B (MLSB), and tetracycline antibiotics. Cellular protection mechanisms were found to be the primary resistance mechanism for these ARGs. The analysis of the co-occurrence network demonstrated a significant positive correlation between the abundance of MGEs and ARGs. The SF samples showed a significantly lower relative abundance of certain ARGs than the NSF samples (p < 0.05). The results of this study show that the abundance of ARGs demonstrated a downward trend after the implementation of the National Pilot Work Program for Action to Reduce the Usage of Veterinary Antimicrobial Drugs in Hebei Province, China.

Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime

BackgroundThe dissemination of antibiotic resistance genes (ARGs) poses a substantial threat to environmental safety and human health. Herein, we present a longitudinal paired study across the swine lifetime from birth to market, coupled with metagenomic sequencing to explore the dynamics of ARGs and their health risk in the swine fecal microbiome.ResultsWe systematically characterized the composition and distribution of ARGs among the different growth stages. In total, 829 ARG subtypes belonging to 21 different ARG types were detected, in which tetracycline, aminoglycoside, and MLS were the most abundant types. Indeed, 134 core ARG subtypes were shared in all stages and displayed a growth stage-associated pattern. Furthermore, the correlation between ARGs, gut microbiota and mobile genetic elements (MGEs) revealed Escherichia coli represented the main carrier of ARGs. We also found that in most cases, the dominant ARGs could be transmitted to progeny piglets, suggesting the potential ARGs generation transmission. Finally, the evaluation of the antibiotic resistance threats provides us some early warning of those high health risk ARGs.ConclusionsCollectively, this relatively more comprehensive study provides a primary overview of ARG profile in swine microbiome across the lifetime and highlights the health risk and the intergenerational spread of ARGs in pig farm.Graphical

Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting

Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and β-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.

High-risk antibiotics positively correlated with antibiotic resistance genes in five typical urban wastewater

Antibiotic resistance genes (ARGs) and antibiotic amount increased within close proximity to human dominated ecosystems. However, few studies assessed the distribution of antibiotics and ARGs in multiple ecosystems especially the different urban wastewater. In this study, the spatial distribution of ARGs and antibiotics across the urban wastewater included domestic, livestock, hospital, pharmaceutical wastewater, influent of the wastewater treatment plant (WWTP) in Northeast China. The q-PCR results showed that ARGs were most abundant in community wastewater and followed by WWTP influent, livestock wastewater, pharmaceutical wastewater and hospital wastewater. The ARG composition differed among the five ecotypes with qnrS was the dominant ARG subtypes in WWTP influent and community wastewater, while sul2 dominant in livestock, hospital, pharmaceutical wastewater. The concentration of antibiotics was closely related to the antibiotic usage and consumption data. In addition to the high concentration of azithromycin at all sampling points, more than half of the antibiotics in livestock wastewater were veterinary antibiotics. However, antibiotics that closely related to humankind such as roxithromycin and sulfamethoxazole accounted for a higher proportion in hospital wastewater (13.6%) and domestic sewage (33.6%), respectively. The ambiguous correlation between ARGs and their corresponding antibiotics was detected. However, antibiotics that exhibited high ecotoxic effects were closely and positively correlated with ARGs and the class 1 integrons (intI1), which indicated that high ecotoxic compounds might affect antimicrobial resistance of bacteria by mediating horizontal gene transfer of ARGs. The coupling mechanism between the ecological risk of antibiotics and bacterial resistance needed to be further studied, and thereby provided a new insight to study the impact of environmental pollutants on ARGs in various ecotypes.

Differential dose-response patterns of intracellular and extracellular antibiotic resistance genes under sub-lethal antibiotic exposure

Although antibiotics are one of the most significant factors contributing to the propagation of antibiotic resistance genes (ARGs), studies on the dose-response relationship at sub-lethal concentrations of antibiotics remain scarce, despite their importance for assessing the risks of antibiotics in the environment. In this study, we constructed a series of microcosms to investigate the propagation of intracellular (iARGs) and extracellular (eARGs) ARGs in both water and biofilms when exposed to antibiotics at various concentrations (1–100 μg/L) and frequencies. Results showed that eARGs were more abundant than iARGs in water, while iARGs were the dominant ARGs form in biofilms. eARGs showed differentiated dose-response relationships from iARGs. The abundance of iARGs increased with the concentration of antibiotics as enhanced selective pressure overcame the metabolic burden of antibiotic-resistant bacteria carrying ARGs. However, the abundance of eARGs decreased with increasing antibiotic concentrations because less ARGs were secreted from bacterial hosts at higher concentrations (100 μg/L). Furthermore, combined exposure to two antibiotics (tetracycline & imipenem) showed a synergistic effect on the propagation of iARGs, but an antagonistic effect on the propagation of eARGs compared to exposure to a single antibiotic. When exposed to antibiotic at a fixed total dose, one-time dosing (1 time/10 d) favored the propagation of iARGs, while fractional dosing (5 times /10 d) favored the propagation of eARGs. This study sheds light on the propagation of antibiotic resistance in the environment and can help in assessing the risks associated with the use of antibiotics.

Antibiotic resistance genes are closely linked with bacterial functions during anoxic-oxic treatment process of pig wastewater

The distribution of antibiotic resistance genes (ARGs) during the anoxic-oxic (A/O) treatment process of pig wastewater was studied by metagenomics. Subsequently, the relationships among bacterial communities, functions and ARGs were analyzed. During the A/O treatment processes, 314 ARG subtypes belonging to 15 ARG types were detected. The dominant ARG types were multidrug, MLS, peptide, glycopeptide, beta-lactam, aminoglycoside and tetracycline resistance genes. The resistance genes MexS, oleC, tetA(48), rphB, macB and smeS can be used as index factors to predict the total abundance of ARGs by a linear function. The functional bacterial genera and genes involved in C-, N- and S-cycling had significant positive correlations with some ARGs, suggesting that functional bacteria were potential ARG hosts. In addition, network analysis suggested that OprM was positively correlated with carbon and nitrogen metabolism. Presumably, functional bacteria containing ARGs may protect the removal process of pollutants in pig farm wastewater. This study highlighted the profiles of ARGs in pig farm wastewater A/O treatment processes and their complex interactions with bacterial functions, and provided an important reference for resolving the contradiction between pollutant removal and antibiotic resistance prevention and control in pig farm wastewater.

A global perspective on microbial risk factors in effluents of wastewater treatment plants

Effective monitoring and management of microbial risk factors in wastewater treatment plants (WWTPs) effluents require a comprehensive investigation of these risks. A global survey on microbial risk factors in WWTP effluents could reveal important insights into their risk features. This study aims to explore the abundance and types of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), the vector of ARG/VFG, and dominant pathogens in global WWTP effluents. We collected 113 metagenomes of WWTP effluents from the Sequence Read Archive of the National Center for Biotechnology Information and characterized the microbial risk factors. Our results showed that multidrug resistance was the dominant ARG type, while offensive virulence factors were the most abundant type of VFGs. The most dominant types of ARGs in the vector of plasmid and phage were both aminoglycoside resistance, which is concerning as aminoglycosides are often a last resort for treating multi-resistant infections. Acinetobacter baumannii was the most dominant pathogen, rather than Escherichia coli, and a weak negative correlation between Escherichia coli and two other dominant pathogens (Acinetobacter baumannii and Bacteroides uniformis) suggests that using Escherichia coli as a biological indicator for all pathogens in WWTP effluents may not be appropriate. The Getah virus was the most dominant virus found in global WWTP effluents. Our study presents a comprehensive global-scale investigation of microbial risk factors in WWTP effluents, providing valuable insights into the potential risks associated with WWTP effluents and contributing to the monitoring and control of these risks.

Distribution of Antibiotic Resistance Genes and Their Association with Microbes in Wastewater Treatment Plants: A Metagenomics Analysis

The extensive use of antibiotics has resulted in the generation and accumulation of antibiotic resistance genes (ARGs) in the environment, and domestic wastewater is one of the main reservoirs of ARGs and resistant bacteria. In this study, Illumina high-throughput sequencing and network analysis were used to study the microbial community characteristics, ARGs’ occurrence status, and resistance mechanism in the influent and effluent of a domestic sewage treatment plant in Changchun, China. A total of 29 phyla were found in the influent and effluent, including 23 bacterial phyla, 3 archaeal phyla, and 3 eukaryotic phyla. In total, 112 ARG subtypes were detected in the samples, and the dominant ARG subtypes were Erm(35) and tet(W/N/W). In this study, ARGs related to tetracycline and macrolide accounted for a high proportion, and the resistance mechanisms of ARGs detected in the samples were mainly antibiotic inactivation and antibiotic efflux pumps. Co-occurrence maps of ARGs and microbes demonstrated by network analysis indicated that the resistance genes kdpE, GES-5, and tetX may easily bind to microbes, potentially making them antibiotic-resistant bacteria. Fifty-seven bacteria in the genera Cupriavidus, Escherichia, and Collinsell are potential hosts of multiple ARGs. The findings can increase our understanding of the distribution of ARGs and their association with microbes in wastewater treatment plants, and also provide a research foundation for controlling the diffusion of ARGs in the environment.

Temporal variations, distribution, and dissemination of antibiotic resistance genes and changes of bacterial communities in a biofloc-based zero-water-exchange mariculture system

Antibiotic resistance genes (ARGs) have obtained an increasing number of global concerns for the severe risks they pose to food safety and public health. Studies have investigated the concentrations and distribution of ARGs in the environment. However, the distribution and dissemination of ARGs, the bacterial communities, and the key influencing factors during the entire rearing period in the biofloc-based zero-water-exchange mariculture system (BBZWEMS) remain unclear. The current study investigated the concentrations, temporal variations, distribution, and dissemination of ARGs, the changes in the bacterial communities, as well as the key influencing factors during the rearing period in the BBZWEMS. Sul1 and sul2 were dominant ARGs. Total concentrations of ARGs followed a trend of decrease in pond water, while they followed a trend of increase in source water, biofloc, and shrimp gut. Total concentrations of targeted ARGs in the water source were higher than those in the pond water and biofloc samples for each corresponding rearing stage by 2.25–122.97-fold (p < 0.05). The bacterial communities in biofloc and pond water did not change much, while they changed considerably in the shrimp gut samples during the rearing period. Pearson correlation, redundancy analysis, and multivariable linear regression analysis showed that suspended substances and Planctomycetes were positively correlated with the concentrations of ARGs (p < 0.05). The current study indicates that the water source may be a critical source of ARGs, and that suspended substances is a key factor influencing the distribution and dissemination of ARGs in the BBZWEMS. Early intervention measures on ARGs in water sources should be implemented to aid in the prevention and control of resistance genes in aquaculture industry, and reduce the potential risks of ARGs to public health and food safety.

Distribution and co-occurrence of antibiotic resistance genes and bacterial pathogens in the effluent of decentralized sewage treatment systems in China

Antibiotic resistance genes (ARGs) and bacterial pathogens (BPs) in wastewater have potential risks to human health, especially for decentralized wastewater treatment facilities (DWTFs) in rural areas where the effluent may directly expose to residents. In this study, ARGs and BPs were investigated in the effluent from five DWTFs having the Anaerobic-Oxic (AO) and AO-Membrane Bio-Reactor (AO-MBR) processes in rural areas of southeastern China. Totally 842 kinds of ARGs and 937 kinds of virulence factors (VFs) were identified. Most of the dominant ARG species (e.g., evgS, macB, and sav1866) were found to be multi-drug ARGs with antibiotic efflux pumping pathways. Most ARGs have higher relative abundances in the effluent of the AO process than the MBRs. Co-occurrence network analysis that explains the dominant pathogens (Pseudomonas, Neisseria, and Streptococcus) were supposed to carry multiple ARGs. Furthermore, typical ARGs and int1 in different ranges of particles were quantified and 51.54%–98.59% ARGs were identified in the samples filtrated in the 0.22–23 μm range, which were hard to be removed. Though AO-MBR processes were more efficient than standalone AO process, the maximum log removal value for the ARGs was only 1.9. Therefore, the results of this study might be referential for evaluating and controlling the risks of co-existed ARGs and pathogens in DWTFs.