tet genes as indicators of changes in the water environment: relationships between culture-dependent and culture-independent approaches

Seasonal and spatial variations of antibiotic resistance genes and bacterial biodiversity in biofilms covering the equipment at successive stages of drinking water purification

The presence of ARGs (antibiotic resistance genes) in the aquatic environment is a serious threat to public health especially in environmental biofilms as natural reservoirs of ARGs in water treatment plants (WTP). It has been shown that the treatment technology and source of water have a significant impact on the abundance and type of genes determining antibiotic resistance. The following indicator genes were proposed that should absolutely be controlled in environmental biofilms: intl1, sul2, sul1, tetA, blaOXA, and blaTEM. In both studied WTPs, the highest number of copies was determined for the intI1 gene. Among the tested ARGs, the highest values were obtained for genes sul1 and tetA. The qPCR analysis also revealed that the amounts of determined ARGs decreased in the following order: sulphonamides>carbapenems >tetracyclines > β-lactams >macrolides. The dominant bacterial types in all analysed samples were Proteobacteria and Bacteroidetes. Both ARGs and bacterial biodiversity was determined rather by sampling site (spatial variation) than seasonality. The obtained results show that biofilms are reservoirs of ARGs. This may affect the microbiological quality of water entering the water system. It is therefore necessary to include their analysis in the classical studies of water quality.

The reasons for the spatial and media distribution variations of ARGs in a typical semi-enclosed bay

Antibiotic resistance genes (ARGs) are considered a newly emerging contaminant. This study aimed to investigate the spatial and media distribution patterns of ARGs in Jiaozhou Bay, as well as the reasons behind these patterns. The results revealed that aminoglycoside and MLSB resistant genes predominated in all samples, and the relative abundance of ARGs ranging from 10^-6 to 10^-2, 10^-6 to 10^-3 and 10^-5 to 10^-2 copies/16S rRNA in coastal water, bay water, and sediments, respectively. The significant spatial variation of ARGs was explained by the fact that the coastal water was more susceptible to human activities, whereas environmental physicochemical factors played a crucial role in the bay water. The intrinsic reason for the media distribution variation was the different assembly processes in the two media, while the external reason was that the ARGs in the water and sediments were mainly influenced by environmental physicochemical factors and heavy metals, respectively.

Fate of antibiotic resistance genes (ARGs) in wastewater treatment plant: Preliminary study on identification before and after ultrasonication

This study collected sludge samples from four different sections of a local wastewater treatment plant in Mikkeli, Finland, for antibiotic resistance genes (ARGs) analysis. Here, we examine the seven representative ARGs in sludge, encoding erythromycin (ermB), tetracycline (tetA, tetC, tetQ, tetW) and sulphonamide (sul1) to check abundance before and after ultrasonication. The class 1 integron (intl1) was also observed as an indicator of antibiotic resistance and horizontal gene transmission. The pre-treatment condition included 10 min of ultrasonication (US) for the sludge sample before freeze-drying. The droplet digital PCR system was used to assess the ARGs from the samples, and it was found that ARGs were not effectively eliminated by pre-treatment. After ultrasonication, tetA, tetC and tetQ did not show any variation but tetW showed 20 copies/ng of lower abundance in digested sludge than raw sludge, and a similar abundance was found in dewatered sludge. For MBR sludge, only ermB showed 1000 copies/ng higher abundance compared to the raw sample and surprisingly it did not show the presence of any other types of ARG. This study provides an overview of the appearance of ARGs in regional municipal sludge for further research reflection.

Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms

The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.

Metagenomic insights into resistome coalescence in an urban sewage treatment plant-river system

The effluents of sewage treatment plants (eSTP) are one of the critical contributors of antibiotic resistiome in rivers. Recently, community coalescence has been focused as the entire microbiome interchanges with one another. While works have reported the prevalence of antibiotic resistance genes (ARGs) in eSTP and their effects on river resistome, little research has investigated the extent of resistome coalescence in the environment. In the study, we have addressed the issue and focused on the resistome coalescence of eSTP in an urban river with a typical effluent/river coalescence model, by utilizing high-throughput sequencing (HTS)-based metagenomic assembly analysis. In all, a total of 609 ARGs were found in the eSTP-river system, conferring resistance to 30 antibiotic classes and including some emerging ARGs such as mcr-type, tetX and carbapenemase genes. Statistical analyses including linear discriminant analysis effect size (LEfSe) showed the coalescence of STP effluents increased the diversity and abundance of river resistome, indicating its low resistance to disturb the invasion of resistome community in eSTP. After coalescence in the river, the imprints of STP-derived ARGs presented a temporary increase and gradually decreased trend along the flow path. Further, an innovative fast expectation-maximization microbial source tracking (FEAST) method was used to quantitatively apportion the coalescence event, and demonstrated the contribution of eSTP on river resistome and its attenuation dynamics in the downstream. Notably, correlation-based network analysis and contig-based co-occurrence analysis showed the coalesced resistome in the downstream river co-occurred with human bacterial pathogens, mobile genetic elements and virulence factor genes, indicating potential resistome dissemination risk in the environment. This study provides more profound understanding of resistome coalescence between engineered and natural contexts, which is helpful for optimizing strategies to prevent and control resistome risk in aquatic environment.

Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes

Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.

An improved selective/differential medium for culturing the Bacteroides fragilis group from wastewater

The aim of this study was to develop an effective selective/differential medium for culturing environmental strains of the Bacteroides fragilis group (BFG). This goal was achieved by modifying standard commercial Bacteroides Bile Esculin Agar (BBE Agar). Bacteroides Bile Esculin Agar was combined with substances that inhibit the growth of non-BFG bacteria, mostly Klebsiella pneumoniae and Fusobacterium mortiferum. The strains isolated from standard and modified BBE Agar were identified as BFG strains by PCR and 16S rRNA gene sequencing. The supplementation of standard BBE Agar with colistin (40 mg L^-1), kanamycin (400 mg L^-1) and vancomycin (7.5 mg L^-1) increases the effectiveness of BFG bacteria isolation from <10% to 35%, and additional Gram staining improves the effectiveness of bacterial isolation five-fold relative to standard BBE Agar. The results of the present study also suggest that the presence of the bfr gene is not a reliable indicator for the identification of BFG strains.

Antibiotic resistance genes and mobile genetic elements in a rural river in Southeast China: Occurrence, seasonal variation and association with the antibiotics

Human activities in rural areas, such as livestock farming, aquaculture, and rural domestic sewage discharge, may result in antibiotic resistance genes (ARGs) pollution in rural rivers. A systematic monitoring in different seasons was conducted in a typical agriculture-polluted river with Real-Time Quantitative PCR. A total of 11 ARGs and 2 related mobile genetic elements (MGEs) were detected at all sites with relative abundances of 6.9 × 10^-10-0.2 copies/16S rRNA copies. Among them, sul1, sul2 and int1 were the dominant target genes in water samples. tetW, ermB, and floR were more abundant in November (the dry season), while other ARGs, MGEs and 16s rRNA were at a higher absolute abundance in warm seasons. There was less spatial variation of ARGs in the dry season than in the other two seasons. Furthermore, the relative abundance of ARGs was higher at sampling sites adjoining pollution sources. In addition, cluster analysis implied that ARGs in upstream sediments may be released into surface water and migrate downstream in the direction of river flow. There was no significant correlation between ARGs and their corresponding antibiotics. However, the total concentration of tetracycline was significantly correlated with the non-paired ARGs, including sul3, floR, and ermB. At the same time, heavy metals (Zn, Pb, Cd, Cr⁶⁺, As) and other environmental parameters (permanganate index, pH, DO) may apply selective pressure on the spread of ARGs, according to redundancy and Pearson's correlation analysis.

Tetracycline and Sulfonamide Antibiotics in Soils: Presence, Fate and Environmental Risks

Veterinary antibiotics are widely used worldwide to treat and prevent infectious diseases, as well as (in countries where allowed) to promote growth and improve feeding efficiency of food-producing animals in livestock activities. Among the different antibiotic classes, tetracyclines and sulfonamides are two of the most used for veterinary proposals. Due to the fact that these compounds are poorly absorbed in the gut of animals, a significant proportion (up to ~90%) of them are excreted unchanged, thus reaching the environment mainly through the application of manures and slurries as fertilizers in agricultural fields. Once in the soil, antibiotics are subjected to a series of physicochemical and biological processes, which depend both on the antibiotic nature and soil characteristics. Adsorption/desorption to soil particles and degradation are the main processes that will affect the persistence, bioavailability, and environmental fate of these pollutants, thus determining their potential impacts and risks on human and ecological health. Taking all this into account, a literature review was conducted in order to shed light on the current knowledge about the occurrence of tetracycline and sulfonamide antibiotics in manures/slurries and agricultural soils, as well as on their fate in the environment. For that, the adsorption/desorption and the degradation (both abiotic and biotic) processes of these pollutants in soils were deeply discussed. Finally, the potential risks of deleterious effects on human and ecological health associated with the presence of these antibiotic residues were assessed. This review contributes to a deeper understanding of the lifecycle of tetracycline and sulfonamide antibiotics in the environment, thus facilitating decision-making for the application of preventive and mitigation measures to reduce its negative impacts and risks to public health.

Prevalence and pollution characteristics of antibiotic resistant genes in one high anthropogenically-impacted river

The objectives of this study were to comprehensively investigate the occurrence, distribution, and mobility of antibiotic resistant genes (ARGs) in the biofilm, water, and sediment from a section of the Weihe-river, in the northern Henan province, China. The abundances of nine ARGs belonging to four commonly used antibiotic classes (tetracyclines, sulfonamides, fluoroquinolones, and multidrug) and class 1 integron-integrase gene (intI1) were quantified. Sulfonamides gene (sulI) accounted for the highest percentage of detected ARGs in most sampling sites, including in water, biofilm, and sediment. Among the resistance genes, IntI1 and sul1 were significantly correlated (r>0.800, p<0.01) with a fecal coliform (FC) detected in the biofilm, and there was also a significantly positive correlation between the abundances of 16SrRNA and intI1 in the biofilms. Compared with the sediment and water samples, the biofilms contained sufficient nutrients to promote bacterial reproduction. Under sufficient total nitrogen and phosphorus concentrations, the horizontal gene transfer due to intI1 plays a key role in the formation and migration of ARGs within biofilms.

Antibiotic resistance genes identified in wastewater treatment plant systems - A review

The intensive use of antibiotics for human, veterinary and agricultural purposes, results in their continuous release into the environment. Together with antibiotics, antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are introduced into wastewater. Wastewater treatment plants (WWTPs) are believed to be probable hotspots for antibiotic resistance dissemination in the environment as they offer convenient conditions for ARB proliferation as well as for horizontal transfer of ARGs among different microorganisms. In fact, genes conferring resistance to all classes of antibiotics together with mobile genetic elements (MGEs) like plasmids, transposons, bacteriophages, integrons are detected in WWTPs in different countries. It seems that WWTPs with conventional treatment processes are capable of significant reduction of ARB but are not efficient in ARG removal. Implementation of advanced wastewater cleaning processes in addition to a conventional wastewater treatment is an important step to protect the aquatic environment. Growing interest in presence and fate of ARB and ARGs in WWTP systems resulted in the fact that knowledge in this area has increased staggeringly in the past few years. The main aim of the article is to collect and organize available data on ARGs, that are commonly detected in raw sewage, treated wastewater or activated sludge. Resistance to the antibiotics usually used in antibacterial therapy belonging to main classes like beta-lactams, macrolides, quinolones, sulfonamides, trimethoprim and tetracyclines was taken into account. The presence of multidrug efflux genes is also included in this paper. The occurrence of antibiotics may promote the selection of ARB and ARGs. As it is important to discuss the problem considering all aspects that influence it, the levels of antibiotics detected in influent and effluent of WWTPs were also presented.

Evolution of Antibiotic Resistance and the Relationship between the Antibiotic Resistance Genes and Microbial Compositions under Long-Term Exposure to Tetracycline and Sulfamethoxazole

The removal of antibiotics and widespread of antibiotic resistance genes (ARGs) have received continuous attention due to the possible threats to environment. However, little information is available on the evolution of antibiotic resistance and the relationship between ARGs and microbial communities under long-term exposure to sub-inhibitory concentrations of antibiotics. In our study, two laboratory-scale anoxic-aerobic wastewater treatment systems were established and operated for 420 days to investigate the evolution of antibiotic resistance under exposure of 5 mg·L⁻¹ tetracycline (TC) or 5 mg·L⁻¹ TC and 1 mg·L⁻¹ sulfamethoxazole (SMX). The average removal rates of TC and SMX were about 59% and 72%, respectively. The abundance of the main ARGs responsible for resistance to TC and SMX increased obviously after antibiotics addition, especially when TC and SMX in combination (increased 3.20-fold). The tetC and sul1 genes were the predominant genes in the development of TC and SMX resistance, in which gene sul1 had the highest abundance among all the detected ARGs. Network analysis revealed that under antibiotic pressure, the core bacterial groups carrying multiple ARGs formed and concentrated in about 20 genera such as Dechloromonas, Candidatus Accumulibacter, Aeromonas, Rubrivivax, in which intI1 played important roles in transferring various ARGs except sul3.

Antimicrobial pharmaceuticals in the aquatic environment - occurrence and environmental implications

The environmental occurrence of antimicrobial pharmaceuticals and antibiotic resistant bacteria and antibiotic resistant genes has become a global phenomenon and a multifaceted threat. Integrated actions of many parties are needed to prevent further aggravation of the problem. Well-directed actions require clear understanding of the problem, which can be ensured by frequent revaluation of the existing knowledge and disseminating it among relevant audiences. The goal of this review paper is to discuss the occurrence and abundance of antimicrobial pharmaceuticals in the aquatic environment in context of adverse effects caused directly by these substances and the threat associated with the antibiotics resistance phenomenon. Several classes of antimicrobial pharmaceuticals (aminoglycosides, β-lactams, glycopeptides, macrolides, fluoroquinolones, sulfonamides and trimethoprim, tetracyclines) have been selected to illustrate their sources, environmental abundance, degradation routes (transformation products) and environmental implications including their ecotoxic effect and the spread of antibiotic resistance within the compartments of the aquatic environment and wastewater treatment plants. Wastewater treatment plants are indeed the main source responsible for the prevalence of these factors in the aquatic environment, since predominantly the plants have not been designed to retain antimicrobial pharmaceuticals. In order to limit the prevalence of these impurities into the environment, better source control is recommended as well as the establishment of stricter environmental quality standards. Counteracting all the above-mentioned threats requires to undertake integrated activities based on cooperation of professionals and scientists from various fields of science or industry, such as environmental sciences, medicine, veterinary, pharmacology, chemical engineering and others.

The presence of antibiotic resistance genes in coastal soil and sediment samples from the eastern seaboard of the USA

Infections from antibiotic resistant microorganisms are considered to be one of the greatest global public health challenges that result in huge annual economic losses. While genes that impart resistance to antibiotics (AbR) existed long before the discovery and use of antibiotics, anthropogenic uses of antibiotics in agriculture, domesticated animals, and humans are known to influence the prevalence of these genes in pathogenic microorganisms. It is critical to understand the role that natural and anthropogenic processes have on the occurrence and distribution of antibiotic resistance in microbial populations to minimize health risks associated with exposures. As part of this research, 15 antibiotic resistance genes were analyzed in coastal sediments and soils along the eastern seaboard of the USA using presence/absence quantitative and digital polymerase chain reaction assays. Samples (53 soil and 192 sediment samples including 54 replicates) were collected from a variety of coastal settings where human and wildlife exposure is likely. At least one of the antibiotic resistance genes was detected in 76.4% of the samples. Samples that contained at least five or more antibiotic resistance genes (5.7%) where typically hydrologically down gradient of watersheds influenced by combined sewer outfalls (CSO). The most frequently detected antibiotic resistance target genes were found in 33.2%, 34.4%, and 42.2% of samples (target genes bla_SHV, tetO, and aadA2, respectively). These data provide unique insight into potential exposure of AbR genes over a large geographical region of the eastern seaboard of the USA.

Mercury/silver resistance genes and their association with antibiotic resistance genes and microbial community in a municipal wastewater treatment plant

Municipal wastewater treatment plants (WWTPs) are an important reservoir for heavy metal (e.g., Hg and Ag) resistance genes and antibiotic resistance genes (ARGs). However, current knowledge on Hg/Ag resistance genes and their association with ARGs in WWTPs remains largely unknown. In this study, the fates of five Hg/Ag resistance genes (merB, merD, merR, silE, and silR), five ARGs (sulI, sulII, tetO, tetQ, tetW), and class 1 integrase (intI1) in a WWTP were investigated. Results show that the absolute abundances of all target genes were greatly reduced through the treatment systems. The dynamics of merB, merD and silE were significantly correlated with tetW and sulII. Based on network analysis, Hg/Ag resistance genes might share the same microbial hosts with tetQ and tetW, implying the potential importance of Hg/Ag in ARGs evolution and spread. These findings advanced our understanding of the occurrence of Hg/Ag resistance genes and ARGs in WWTPs.

The emergence of antimicrobial resistance in environmental strains of the Bacteroides fragilis group

Anaerobic bacteria of the genus Bacteroides are a large group of commensal microorganisms that colonize the human and animal digestive tract. The genus Bacteroides and the closely related genus Parabacteroides include the Bacteroides fragilis group (BFG) of potentially pathogenic bacteria which are frequently isolated from patients with anaerobic infections. The aim of this study was to assess the antimicrobial resistance of environmental strains of the Bacteroides fragilis group. Strains were isolated from human feces, hospital wastewater, influent (UWW) and effluent (TWW) wastewater from a wastewater treatment plant (WWTP), and from the feces of lab rats as a negative control to monitor the entire route of transmission of BFG strains from humans to the environment. The resistance of 123 environmental BFG strains to six antibiotic groups was analyzed with the use of culture-dependent methods. Additionally, the presence of 25 genes encoding antibiotic resistance was determined by PCR. The analyzed environmental BFG strains were highly resistant to the tested antibiotics. The percentage of resistant strains differed between the analyzed antibiotics and was determined at 97.56% for ciprofloxacin, 49.59% for erythromycin, 44.71% for ampicillin, 35.77% for tetracycline, 32.52% for amoxicillin/clavulanic acid, 26.83% for chloramphenicol, 26.01% for clindamycin, 11.38% for moxifloxacin, and 8.94% for metronidazole. The highest drug-resistance levels were observed in the strains isolated from UWW and TWW samples. The mechanisms of antibiotic-resistance were determined in phenotypically resistant strains of BFG. Research has demonstrated the widespread presence of genes encoding resistance to chloramphenicol (100% of all chloramphenicol-resistant strains), tetracyclines (97.78% of all tetracycline-resistant strains), macrolides, lincosamides and streptogramins (81.97% of all erythromycin-resistant strains). Genes encoding resistance to β-lactams and fluoroquinolones were less prevalent. None of the metronidazole-resistant strains harbored the gene encoding resistance to nitroimidazoles. BFG strains isolated from UWW and TWW samples were characterized by the highest diversity of antibiotic-resistance genes and were most often drug-resistant and multidrug-resistant. The present study examines the potential negative consequences of drug-resistant and multidrug-resistant BFG strains that are evacuated with treated wastewater into the environment. The transmission of these bacteria to surface water bodies can pose potential health threats for humans and animals; therefore, the quality of treated wastewater should be strictly monitored.

Antibiotic-Resistant Bacteria in Greywater and Greywater-Irrigated Soils

This study represents the first systematic attempt to evaluate antibiotic-resistant bacteria (ARB) occurrence in treated greywater and the potential spread of these bacteria from the greywater to greywater-irrigated soil. Treated greywater from three recirculating vertical flow constructed wetlands, each located in a household in the central Negev Desert, Israel, was surveyed. The presence of antibiotic-resistant bacteria in raw and treated greywater was investigated with culture and molecular methods, as well as their presence in the corresponding treated-greywater-irrigated soils. Additionally, the effectiveness of chlorination to prevent the spread of ARB was tested. The total count of tetracycline-resistant bacteria significantly increased in the treated greywater, likely due to their concentration on the filter matrix of the treatment systems. Twenty-four strains of tetracycline-resistant bacteria were isolated and identified at the genus level by 16Sr RNA gene sequencing. All the tetracycline-resistant bacteria showed high resistance traits, and some of them presented multiple antibiotic resistances. Six tetracycline resistance genes (coding for efflux and ribosomal resistance mechanisms) and five β-lactamase genes were detected. In 14 of the isolated strains, the gene tet39, which is phylogenetically related to both environmental and clinical strains, was identified. All the tet39 resistant bacteria were positive to at least one of the β-lactamase genes tested. Chlorination was found to be an efficient method to reduce ARB in treated greywater. We concluded that disinfection of treated greywater may reduce the risks not only from the potential presence of pathogens but also from the presence of ARB and antibiotic resistance genes.

Relationship between modification of activated sludge wastewater treatment and changes in antibiotic resistance of bacteria

Biological treatment processes at wastewater treatment plants (WWTPs), which are the most common methods of sewage treatment, could cause selective elimination and/or changes in the proportions of phenotypes/genotypes within bacterial populations in effluent. Therefore, WWTPs based on activated sludge used in sewage treatment constitute an important reservoir of enteric bacteria which harbour potentially transferable resistance genes. Together with treated wastewater, these microorganisms can penetrate the soil, surface water, rural groundwater supplies and drinking water. Because of this, the aim of this study was to determine the impact of various modification of sewage treatment (the conventional anaerobic/anoxic/oxic (A2/O) process, mechanical-biological (MB) system, sequencing batch reactors (SBR), mechanical-biological system with elevated removal of nutrients (MB-ERN)) on the amount of antibiotic resistant bacteria (ARB) (including E. coli) and antibiotic resistance genes (ARGs) in sewage flowing out of the 13 treatment plants using activated sludge technology. There were no significant differences in ARB and ARGs regardless of time of sampling and type of treated wastewater (p > 0.05). The highest percentage of reduction (up to 99.9%) in the amount of ARB and ARGs was observed in WWTPs with MB and MB-ERN systems. The lowest reduction was detected in WWTPs with SBR. A significant increase (p < 0.05) in the percentage of bacteria resistant to the new generation antibiotics (CTX and DOX) in total counts of microorganisms was observed in effluents (EFF) from WWTPs with A2/O system and with SBR. Among all ARGs analyzed, the highest prevalence of ARGs copies in EFF samples was observed for sul1, tet(A) and qepA, the lowest for bla_TEM and bla_SHV. Although, the results of presented study demonstrate high efficiency of ARB and ARGs removal during the wastewater treatment processes, especially by WWTPs with MB and MB-ERN systems, EFF is still an important reservoir of ARGs which can be transferred to other microorganisms.

Antibiotic resistance genes in China: occurrence, risk, and correlation among different parameters

Antibiotic resistance has become a widely concerned issue due to the huge risk on the ecological environment and human health. China has the highest production and consumption of antibiotics than other countries. Thus, antibiotic resistance genes (ARGs) have been detected in various environmental settings (e.g., surface water, wastewater, sediment) in China. The occurrence of ARGs in these matrixes was summarized and discussed in this review. Sulfonamide resistance genes and tetracycline resistance genes were the most frequently detected ARGs in China. According to the abundance of these two classes of ARGs in the natural environment, sulfonamide resistance genes seem to be more stable than tetracycline resistance genes. Furthermore, the relationships between ARGs and antibiotics, antibiotic resistance bacteria (ARB), heavy metals, and environmental parameters (e.g., pH, organics) were also investigated. Specifically, relative abundance of total ARGs was found to correlate well with concentration of total antibiotics in aqueous phase but not in the solid phase (soil, sediment, sludge, and manure). As for relationship between ARGs and ARB, metals, and environmental parameters in different media, due to complex and variable environment, some exhibit positive correlation, some negative, while others no correlation at all. Three potential risks are discussed in the text: transmission to human, synergistic effect of different ARGs, and variability of ARGs. However, due to the complexity of the environment, more work is needed to establish a quantitative approach of ARG risk assessment, which can provide a theoretical support for the management of antibiotics and the protection of human health.

The prevalence of multidrug-resistant Aeromonas spp. in the municipal wastewater system and their dissemination in the environment

The objective of this study was to identify the determinants of antibiotic resistance and virulence of Aeromonas spp. isolated from treated wastewater (WW) and from samples of river water collected upstream (URW) and downstream (DRW) from the effluent discharge point. The resistance of Aeromonas spp. to antibiotics that are widely used in human and veterinary medicine, including beta-lactams, tetracyclines, glycylcyclines, fluoroquinolones, aminoglycosides and sulfamethoxazole-trimethoprim, was analyzed by disk diffusion method. The prevalence of hemolysins, aerolysins (virulence factors) and integrase genes was determined. A total of 83 Aeromonas spp. strains were selected from the isolates obtained from river water and wastewater samples. The highest percentage (81.8%) of multidrug-resistant isolates was noted in DRW samples. The analyzed isolates were most frequently resistant to beta-lactams, tetracyclines and aminoglycosides, whereas resistance to glycylcyclines was least common. Isolates resistant to beta-lactams most frequently harbored bla_TEM and bla_OXA genes. The group of genes encoding resistance to tetracyclines was most frequently represented by tet(E) and tet(O). Genes encoding virulence ahh1 (heat-labile hemolysin) or integrase intI1 occurred more frequently in the strains isolated from DRW than URW. An analysis of genetic relatedness revealed two main clusters - one with closely related WW and DRW isolates and one with less related isolates from all analyzed samples. The results of this study indicate that regardless of the applied treatment, municipal sewage may be a reservoir of antibiotic-resistant bacteria, antibiotic resistance and virulence genes and that treated water can contaminate other environmental domains.

Occurrence of intracellular and extracellular antibiotic resistance genes in coastal areas of Bohai Bay (China) and the factors affecting them

Coastal areas are the transition zones between ocean and land where intracellular antibiotic resistance genes (iARGs) and extracellular antibiotic resistance genes (eARGs) could spread among marine organisms, and between humans and marine organisms. However, little attention has been paid to the combined research on iARGs and eARGs in marine environment. In this context, we collected water and sediment samples from the coastal areas of the Bohai Bay in China and performed molecular and chemical analyses. The results of quantitative real-time PCR (qPCR) showed that the relative abundance of eARGs was up to 4.3 ± 1.3 × 10^-1 gene copies/16S rRNA copies in the water samples and 2.6 ± 0.3 × 10^-3 gene copies/16S rRNA copies in the sediment samples. Also, the abundance of eARGs was significantly higher than that of iARGs. Furthermore, the average abundances of antibiotic resistance genes (ARGs, include iARGs and eARGs) were the highest in both the water and sediment samples from the estuaries. The results of liquid chromatography-mass spectrometry showed that the concentrations of antibiotics in estuaries and areas near the mariculture site were higher than that in the other sites. The class 1 integron gene (int1) and sul1 in the intracellular DNA were significantly correlated in the water samples. Moreover, significant correlation between int1 and sul2 in the extracellular DNA was also found in the sediment samples. The combination of sulfamerazine and tetracycline as well as the combination of sulfamethazine and dissolved oxygen can both explain the abundance of ARGs, implying the combined effects of multiple stresses on ARGs.

Prevalence of quinolone resistance genes, copper resistance genes, and the bacterial communities in a soil-ryegrass system co-polluted with copper and ciprofloxacin

The presence of high concentrations of residual antibiotics and antibiotic resistance genes (ARGs) in soil may pose potential health and environmental risks. This study investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) genes, copper resistance genes (CRGs), and the bacterial communities in a soil-ryegrass pot system co-polluted with copper and ciprofloxacin (CIP; 0, 20, or 80 mg kg^-1 dry soil). Compared with the samples on day 0, the total relative abundances of the PMQR genes and mobile genetic elements (MGEs) were reduced significantly by 80-89% in the ryegrass and soil by the cutting stage (after 75 days). The abundances of PMQR genes and MGEs were reduced by 63-81% in soil treated with 20 mg kg^-1 CIP compared with the other treatments, but the abundances of CRGs increased by 18-42%. The presence of 80 mg kg^-1 CIP affected the microbial community structure in the soil by increasing the abundances of Acidobacteria and Thaumarchaeota, but decreasing those of Firmicutes. Redundancy analysis indicated that the pH and microbial composition were the main factors that affected the variations in PMQR genes, MGEs, and CRGs, where they could explain 42.2% and 33.3% of the variation, respectively. Furthermore, intI2 may play an important role in the transfer of ARGs. We found that 80 mg kg^-1 CIP could increase the abundances of ARGs and CRGs in a soil-ryegrass pot system.

Fate of antimicrobial resistance genes in response to application of poultry and swine manure in simulated manure-soil microcosms and manure-pond microcosms

This study aimed to determine the occurrence, abundance, and fate of nine important antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, and Intl1) in the simulated soil and pond microcosms following poultry and swine manure application. Absolute quantitative PCR method was used to determine the gene copies. The results were modeled as a logarithmic regression (N = mlnt + b) to explore the fate of target genes. Genes sul1, Intl1, sul2, and tetM had the highest abundance following the application of the two manure types. The logarithmic regression model fitted the results well (R ² values up to 0.99). The reduction rate of all genes (except for the genes fexA and cfr) in manure-pond microcosms was faster than those in manure-soil microcosms. Importantly, sul1, intl1, sul2, and tetM had the lowest reduction rates in all the samples and the low reduction rates of tetM was the first time to be reported. These results indicated that ARG management should focus on using technologies for the ARG elimination before the manure applications rather than waiting for subsequent attenuation in soil or water, particularly the ARGs (such as sul1, intl1, sul2, and tetM investigated in this study) that had high abundance and low reduction rate in the soil and water after application of manure.

Distribution of tetracycline resistance genes and AmpC β-lactamase genes in representative non-urban sewage plants and correlations with treatment processes and heavy metals

The mixed development of livestock breeding and industry in non-urban zones is a very general phenomenon in China. Distribution of antibiotic resistance genes (ARGs) in non-urban sewage treatment systems has not been paid enough attentions. In this study, eleven tetracycline resistance genes (tetA, tetB, tetC, tetE, tetG, tetL, tetM, tetO, tetQ, tetS and tetX), four AmpC β-lactamase genes (EBC, MOX, FOX and CIT) and four heavy metals (Cu, Zn, Cd and Pb) were detected and analyzed in four non-urban sewage plants with different sewage sources and different treatment processes in Guangzhou. The results showed that tetA and tetC were the most prevalent tetracycline resistance genes with the same detection frequency of 85% and EBC was the most prevalent AmpC β-lactamase gene with a detection frequency of 75%. The relative abundance of tetracycline resistance genes was approximately 1.6 orders of magnitudes higher than that of AmpC β-lactamase genes in all samples. A/O was the most effective process for the non-urban sewage plant receiving industrial or agricultural wastewater. Sedimentation was the most key process to eliminate ARGs from liquid phase. Most ARGs were carried in excess sludge rather than effluent. Significant correlation was found between the tet gene and Zn (r = 0.881, p < 0.01), followed by the AmpC gene and Cu (r = 0.847, p < 0.01), the tet gene and Cu (r = 0.714, p < 0.05). Therefore, the pollution of ARGs in the sewage treatment systems of non-urban zones co-polluted by heavy metals should be paid more attentions.

Antibiotic pollution in the Katari subcatchment of the Titicaca Lake: Major transformation products and occurrence of resistance genes

An increasing number of studies pointed out the ubiquitous presence of medical residues in surface and ground water as well as in soil compartments. Not only antibiotics can be found in the environment but also their transformation products about which little information is generally available. The development of bacterial resistance to antibiotics is particularly worrying as it can lead to sanitary and health problems. Studies about the dissemination of antibiotics and associated resistances in the Bolivian Altiplano are scarce. We provide baseline information on the occurrence of Sulfamethoxazole (SMX) and Trimethoprim (TMP) antibiotics as well as on the most common human SMX transformation products (TP) and on the occurrence of sulfonamide resistance genes. The studied water and soil compartments presented high levels of antibiotic pollution. This situation was shown to be mainly linked with uncontrolled discharges of treated and untreated wastewaters, resulting on the presence of antibiotics in the Titicaca Lake. SMX TPs were detected in surface waters and on soil sampled next to the wastewater treatment plant (WWTP). SMX resistance genes sulI and sulII were widely detected in the basin hydrological network, even in areas unpolluted with antibiotics. Mechanisms of co-selection of antibiotic- and metal- resistance may be involved in the prevalence of ARG's in pristine areas with no anthropogenic activity and free of antibiotic pollution.

The prevalence and characterization of antibiotic-resistant and virulent Escherichia coli strains in the municipal wastewater system and their environmental fate

Antibiotics are widely used in human and veterinary medicine and in animal production, which increases their concentrations in aquatic ecosystems and contributes to selective pressure on environmental microorganisms. The objective of this study was to identify antibiotic resistance determinants in Escherichia coli strains isolated from untreated and treated wastewater (UWW and TWW) and from river water sampled downstream and upstream (URW and DRW) from the effluent discharge point. The analyzed antibiotic groups were beta-lactams, tetracyclines and fluoroquinolones which are widely used in human and veterinary medicine. The virulence of the isolated E. coli strains was also analyzed, and their clonal relatedness was determined by ERIC (enterobacterial repetitive intergenic consensus sequence) PCR. The highest counts of bacteria resistant to beta-lactams, tetracyclines and fluoroquinolones were noted in UWW at 6.4×10⁴, 4.2×10⁴ and 3.1×10³CFU/mL, respectively. A total of 317 E. coli isolates resistant to at least one group of antibiotics were selected among bacterial isolates from river water and wastewater samples. Nearly 38% of those isolates were resistant to all of the tested antibiotics. The highest percent (43%) of multidrug-resistant isolates was noted in UWW samples. Isolates resistant to beta-lactams most frequently harbored bla_TEM and bla_OXA genes. The group of genes encoding resistance to tetracyclines was most frequently represented by tetA, tetB and tetK, whereas the qnrS gene was noted in isolates resistant to fluoroquinolones. Virulence genes bfpA (65%), ST (56%) and eae (39%) were most widely distributed in all isolates, regardless of their origin. The results of this experiment reveal the dangers associated with environmental contamination by drug-resistant and virulent E. coli strains distributed with treated wastewater. Multidrug resistance was determined more frequently in strains isolated from DRW than in isolates from URW samples. Our findings provide valuable inputs for evaluating public health hazards associated with bacterial contamination.

Presence and distribution of Macrolides-Lincosamide-Streptogramin resistance genes and potential indicator ARGs in the university ponds in Guangzhou, China

This study aimed to determine the occurrence, abundance, and variation of seven Macrolides-Lincosamide-Streptogramin (MLS) resistance genes (ereB, ermA, ermB, ermF, mefA, vatB, mphA) and six potential indicator ARGs (tet (B), sul1, qnrS, fexA, IntI1, ermB) from three ponds at university by quantitative PCR and assess the impacts on the surroundings. Solid samples (fish feces, soil and sediment) and water samples were tested. All the genes were found at low levels in soil samples. For the MLS resistance genes, only two MLS genes (ermB, ermF) were detected in all samples and significant correlations between ermB and Σ MLS (R = 0.91 in solid samples; R = 0.86 in water samples, p < 0.01) were found. For the potential indicators, intl1 and sul1 were present at high levels in the three different ponds while the other genes showed varying levels. These findings show that the ermB gene can probably be served as an indicator to evaluate the overall level of MLS resistance genes. The fairly low abundance of all the tested resistance genes in soil samples and the moderate levels in other samples suggests that the university ponds kept a good state and did not have a significant impact on their surroundings.

Prevalence of plasmid-mediated multidrug resistance determinants in fluoroquinolone-resistant bacteria isolated from sewage and surface water

Fluoroquinolones (FQs) are fully synthetic broad-spectrum antibacterial agents that are becoming increasingly popular in the treatment of clinical and veterinary infections. Being excreted during treatment, mostly as active compounds, their biological action is not limited to the therapeutic site, but it is moved further as resistance selection pressure into the environment. Water environment is an ideal medium for the aggregation and dissemination of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs), which can pose a serious threat to human health. Because of this, the aim of this study was to determine the number of fluoroquinolone-resistant bacteria (FQRB) and their share in total heterotrophic plate counts (HPC) in treated wastewater (TWW), and upstream and downstream river water (URW, DRW) samples where TWW is discharged. The spread of plasmid-mediated quinolone resistance (PMQR) determinants and the presence/absence of resistance genes to other most popular antibiotic groups (against tetracyclines and beta-lactams) in selected 116 multiresistant isolates were investigated. The share of FQRB in total HPC in all samples was rather small and ranged from 0.7 % in URW samples to 7.5 % in TWW. Bacteria from Escherichia (25.0 %), Acinetobacter (25.0 %), and Aeromonas (6.9 %) genera were predominant in the FQRB group. Fluoroquinolone resistance was mostly caused by the presence of the gene aac(6')-1b-cr (91.4 %). More rarely reported was the occurrence of qnrS, qnrD, as well as oqxA, but qnrA, qnrB, qepA, and oqxB were extremely rarely or never noted in FQRB. The most prevalent bacterial genes connected with beta-lactams' resistance in FQRB were bla TEM, bla OXA, and bla CTX-M. The bla SHV was less common in the community of FQRB. The occurrence of bla genes was reported in almost 29.3 % of FQRB. The most abundant tet genes in FQRB were tet(A), tet(L), tet(K), and tet(S). The prevalence of tet genes was observed in 41.4 % of FQRB. The highest prevalence of multidrug-resistant (MDR) microorganisms was detected in TWW and DRW samples. It indicates that discharged TWW harbors multiresistant bacterial strains and that mobile PMQR and ARGs elements may have a selective pressure for species affiliated to bacteria in the river water.

Tetracycline and Phenicol Resistance Genes and Mechanisms: Importance for Agriculture, the Environment, and Humans

Recent reports have speculated on the future impact that antibiotic-resistant bacteria will have on food production, human health, and global economics. This review examines microbial resistance to tetracyclines and phenicols, antibiotics that are widely used in global food production. The mechanisms of resistance, mode of spread between agriculturally and human-impacted environments and ecosystems, distribution among bacteria, and the genes most likely to be associated with agricultural and environmental settings are included. Forty-six different tetracycline resistance () genes have been identified in 126 genera, with (M) having the broadest taxonomic distribution among all bacteria and (B) having the broadest coverage among the Gram-negative genera. Phenicol resistance genes are organized into 37 groups and have been identified in 70 bacterial genera. The review provides the latest information on tetracycline and phenicol resistance genes, including their association with mobile genetic elements in bacteria of environmental, medical, and veterinary relevance. Knowing what specific antibiotic-resistance genes (ARGs) are found in specific bacterial species and/or genera is critical when using a selective suite of ARGs for detection or surveillance studies. As detection methods move to molecular techniques, our knowledge about which type of bacteria carry which resistance gene(s) will become more important to ensure that the whole spectrum of bacteria are included in future surveillance studies. This review provides information needed to integrate the biology, taxonomy, and ecology of tetracycline- and phenicol-resistant bacteria and their resistance genes so that informative surveillance strategies can be developed and the correct genes selected.

Class 1 integrase, sulfonamide and tetracycline resistance genes in wastewater treatment plant and surface water

Wastewater treatment plants are considered hot spots for multiplication and dissemination of antibiotic-resistant bacteria and resistance genes. In this study, we determined the presence of class 1 integron integrase and genes conferring resistance to tetracyclines and sulfonamides in the genomes of culturable bacteria isolated from a wastewater treatment plant and the river that receives the treated wastewater. Moreover, using PCR-based metagenomic approach, we quantified intI1, tet and sul genes. Wastewater treatment caused the decrease in the total number of culturable heterotrophs and bacteria resistant to tetracycline and sulfonamides, along with the decrease in the number of intI1, sul and tet gene copies per ml, with significant reduction of tet(B). On the other hand, the treatment process increased both the frequency of tetracycline- and sulfonamide-resistant bacteria and intI1-positive strains, and the relative abundance of all quantified antibiotic resistance genes (ARGs) and intI1 gene; in the case of tet(A) and sul2 significantly. The discharge of treated wastewater increased the number of intI1, tet and sul genes in the receiving river water both in terms of copy number per ml and relative abundance. Hence, despite the reduction of the number of ARGs and ARBs, wastewater treatment selects for bacteria with ARGs in effluent.

The impact of a freshwater fish farm on the community of tetracycline-resistant bacteria and the structure of tetracycline resistance genes in river water

The aim of this study was to assess the impact of a fish farm on the structure of antibiotic resistant bacteria and antibiotic resistance genes in water of Drwęca River. Samples of upstream river waters; post-production waters and treated post-production waters from fish farm; as well as downstream river waters were monitored for tetracycline resistant bacteria, tetracycline resistant genes, basic physico-chemical parameters and tetracyclines concentration. The river waters was characterized by low levels of pollution, which was determined based on water temperature, pH and concentrations of dissolved oxygen and tetracycline antibiotics. Culture-dependent (heterotrophic plate counts, counts of bacteria resistant to oxytetracycline (OTC(R)) and doxycycline (DOX(R)), minimum inhibitory concentrations for oxytetracycline and doxycycline, multidrug resistance of OTC(R) and DOX(R), qualitative composition of OTC(R) and DOX(R), prevalence of tet genes in resistant isolates) and culture-independent surveys (quantity of tet gene copies) revealed no significant differences in the abundance of antibiotic-resistant bacteria and antibiotic resistance genes between the studied samples. The only way in which the fish farm influenced water quality in the Drwęca River was by increasing the diversity of tetracycline-resistance genes. However, it should also be noted that the bacteria of the genera Aeromonas sp. and Acinetobacter sp. were able to transfer 6 out of 13 tested tet genes into Escherichiacoli, which can promote the spread of antibiotic resistance in the environment.