The impact of municipal sewage sludge stabilization processes on the abundance, field persistence, and transmission of antibiotic resistant bacteria and antibiotic resistance genes to vegetables at harvest

Black soldier fly-based bioconversion of biosolids: Microbial community dynamics and fate of antibiotic resistance genes

Biosolids as by-products of wastewater treatment can contain a large spectrum of pathogens and antibiotic resistance genes (ARGs). Insect-based bioconversion using black soldier fly larvae (BSFL) is an emerging technology that has shown to reduce significant amounts of biosolids quickly and produce larvae biomass containing low heavy metal concentrations. However, to the best of our knowledge, this is the first study investigating the transfer of pathogens and ARGs from biosolids into the process' end-products, BSFL and frass. We hypothesized that BSF-based bioconversion can decrease the abundance of pathogenic bacteria and ARGs in biosolids. In this study, we performed BSFL feeding trials with biosolids blended or not blended with wheat bran, and wheat bran alone as a low bioburden diet (control). We conducted 16S rRNA amplicon sequencing to monitor changes of the BSFL-associated microbial community and the fate of biosolids-associated pathogens. A diverse set of ARGs (ermB, intl1, sul1, tetA, tetQ, tetW, and blaCTX-M-32) were quantified by qPCR and were linked to changes in substrate- and BSFL-associated microbiomes. BSF-based bioconversion of biosolids-containing substrates led to a significant reduction of the microbial diversity, the abundance of several pathogenic bacteria and the investigated ARGs (< 99 %). Feeding with a high bioburden biosolid diet resulted in a higher microbial diversity, and the accumulation of pathogenic bacteria and ARGs in the BSFL. Results of this study demonstrated that BSF-based bioconversion can be a suitable waste management technology to (1) reduce significant amounts of biosolids and (2) reduce the presence of pathogens and ARGs. However, the resulting larvae biomass would need to undergo further post-treatment to reduce the pathogenic load to allow them as animal feed.

A review of the influence of heat drying, alkaline treatment, and composting on biosolids characteristics and their impacts on nitrogen dynamics in biosolids-amended soils

Application of biosolids to agricultural land has gained increasing attention due to their rich nutrient content. There are a variety of treatment processes for converting sewage sludge to biosolids. Different treatment processes can change the physicochemical properties of the raw sewage sludge and affect the dynamics of nutrient release in biosolids-amended soils. This paper reviews heat drying, alkaline treatment, and composting as biosolids treatment processes and discusses the effects of these treatments on biosolid nitrogen (N) content and availability. Most N in the biosolids remain in organic forms, regardless of biosolids treatment type but considerable variation exists in the mean values of total N and mineralizable N across different types of biosolids. The highest mean total N content was recorded in heat-dried biosolids (HDB) (4.92%), followed by composted biosolids (CB) (2.25%) and alkaline-treated biosolids (ATB) (2.14%). The mean mineralizable N value was similar between HDB and ATB, with a broader range of mineralizable N in ATB. The lowest N availability was observed in CB. Although many models have been extensively studied for predicting potential N mineralization in soils amended with organic amendments, limited research has attempted to model soil N mineralization following biosolids application. With biosolids being a popular, economical, and eco-friendly alternative to chemical N-fertilizers, understanding biosolids treatment effects on biosolids properties is important for developing a sound biosolids management system. Moreover, modeling N mineralization in biosolids-amended soils is essential for the adoption of sustainable farming practices that maximize the agronomic value of all types of biosolids.

The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes

The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.

Residual effects of composted sewage sludge on nitrogen cycling and plant metabolism in a no-till common bean-palisade grass-soybean rotation

Introduction and aims

In the context of increasing population and decreasing soil fertility, food security is one of humanity's greatest challenges. Large amounts of waste, such as sewage sludge, are produced annually, with their final disposal causing environmental pollution and hazards to human health. Sludge has high amounts of nitrogen (N), and, when safely recycled by applying it into the soil as composted sewage sludge (CSS), its residual effect may provide gradual N release to crops. A field study was conducted in the Brazilian Cerrado. The aims were to investigate the residual effect of successive applications of CSS as a source of N in the common bean (Phaseolus vulgaris L. cv. BRS Estilo)-palisade grass (Urochloa brizantha (A.Rich.) R.D. Webster)-soybean (Glycine max L.) rotation under no-tillage. Additionally, N cycling was monitored through changes in N metabolism; the efficiency of biological N2 fixation (BNF) and its implications for plant nutrition, development, and productivity, was also assessed.

Methods

The experiment consisted of a randomized complete block design comparing four CSS rates (10, 15, 20, and 25 Mg ha-1, wet basis) to a control treatment (without adding mineral or organic fertilizer) over two crop years. Multiple plant and soil analyses (plant development and crop yield, Falker chlorophyll index (FCI), enzymatic, biochemical, 15N natural abundance, was evaluated, root and shoot N accumulation, etc.) were evaluated.

Results and discussion

Results showed that CSS: i) maintained adequate N levels for all crops, increasing their productivity; ii) promoted efficient BNF, due to the stability of ureide metabolism in plants and increased protein content; iii) increased the nitrate content and the nitrate reductase activity in soybean; iv) affected urease activity and ammonium content due to changes in the plant's urea metabolism; v) increased N accumulation in the aerial part of palisade grass. Composted sewage sludge can be used as an alternative source to meet crops' N requirements, promoting productivity gains and N cycling through forage and improving N metabolism.

Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework

Introduction

Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined.

Methods

To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region.

Results

A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km.

Discussion

Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.

Emerging environmental health risks associated with the land application of biosolids: a scoping review

BACKGROUND

Over 40% of the six million dry metric tons of sewage sludge, often referred to as biosolids, produced annually in the United States is land applied. Biosolids serve as a sink for emerging pollutants which can be toxic and persist in the environment, yet their fate after land application and their impacts on human health have not been well studied. These gaps in our understanding are exacerbated by the absence of systematic monitoring programs and defined standards for human health protection.

METHODS

The purpose of this paper is to call critical attention to the knowledge gaps that currently exist regarding emerging pollutants in biosolids and to underscore the need for evidence-based testing standards and regulatory frameworks for human health protection when biosolids are land applied. A scoping review methodology was used to identify research conducted within the last decade, current regulatory standards, and government publications regarding emerging pollutants in land applied biosolids.

RESULTS

Current research indicates that persistent organic compounds, or emerging pollutants, found in pharmaceuticals and personal care products, microplastics, and per- and polyfluoroalkyl substances (PFAS) have the potential to contaminate ground and surface water, and the uptake of these substances from soil amended by the land application of biosolids can result in contamination of food sources. Advanced technologies to remove these contaminants from wastewater treatment plant influent, effluent, and biosolids destined for land application along with tools to detect and quantify emerging pollutants are critical for human health protection.

CONCLUSIONS

To address these current risks, there needs to be a significant investment in ongoing research and infrastructure support for advancements in wastewater treatment; expanded manufacture and use of sustainable products; increased public communication of the risks associated with overuse of pharmaceuticals and plastics; and development and implementation of regulations that are protective of health and the environment.

Diversity of virulence and antibiotic resistance genes expressed in Class A biosolids and biosolids-amended soil as revealed by metatranscriptomic analysis

Class A biosolids is a treated sewage sludge, commonly applied to agricultural fields, home lawns/gardens, golf courses, forests, and remediation sites around the world. This practice is of public and agricultural concern due to the possibility that biosolids contain antibiotic-resistant bacteria and fungal pathogens that could persist for extended periods in soil. This possibility was determined by metatranscriptomic analysis of virulence, antibiotic resistance, and plasmid conjugation genes, a Class A biosolids, organically managed soil, and biosolids-amended soil under realistic conditions. Biosolids harbored numerous transcriptionally active pathogens, antibiotic resistance genes, and conjugative genes that annotated mostly to Gram-positive pathogens of animal hosts. Biosolids amendment to soil significantly increased the expression of virulence genes by numerous pathogens and antibiotic-resistant genes that were strongly associated with biosolids. Biosolids amendment also significantly increased the expression of virulence genes by native soil fungal pathogens of plant hosts, which suggests higher risks of crop damage by soil fungal pathogens in biosolids-amended soil. Although results are likely to be different in other soils, biosolids, and microbial growth conditions, they provide a more holistic, accurate view of potential health risks associated with biosolids and biosolids-amended soils than has been achievable with more selective cultivation and PCR-based techniques.

High prevalence and genomic characteristics of carbapenem-resistant Enterobacteriaceae and colistin-resistant Enterobacteriaceae from large-scale rivers in China

The widespread presence of carbapenem-resistant Enterobacteriaceae (CRE) and mcr-positive Escherichia coli (MCREC) poses a huge threat to both animal and human health. River water environments are vital reservoirs of antibiotic resistance genes, however, the prevalence and characteristics of CRE and MCREC from large-scale rivers in China have not been reported. In the current study, we sampled 86 rivers from four cities in Shandong Province, China in 2021 and analyzed the prevalence of CRE and MCREC. The bla_NDM/bla_KPC-2/mcr-positive isolates were characterized with methods including PCR, antimicrobial susceptibility testing, conjugation, replicon typing, whole-genome sequencing and phylogenetic analysis. We found that the prevalence of CRE and MCREC in 86 rivers was 16.3% (14/86) and 27.9% (24/86), respectively and eight rivers carried both mcr-1 and bla_NDM/bla_KPC-2. A total of 48 Enterobacteriaceae isolates (10 ST11 Klebsiella pneumoniae with bla_KPC-2, 12 bla_NDM-positive E. coli and 26 MCREC carrying only mcr-1) were obtained in this study and 47 displayed multidrug resistance (MDR). Notably, 10 of the 12 bla_NDM-positive E. coli isolates also harbored the mcr-1 gene. The bla_KPC-2 gene was located within mobile element ISKpn27-bla_KPC-2-ISKpn6 on novel F33:A-:B- non-conjugative MDR plasmids in ST11 K. pneumoniae. The dissemination of bla_NDM was mediated by transferable MDR IncB/O plasmids or IncX3 plasmids while mcr-1 was primarily disseminated by highly similar IncI2 plasmids. Notably, these waterborne IncB/O, IncX3 and IncI2 plasmids were all highly similar to previously identified plasmids from animal and human isolates. A phylogenomic analysis revealed that the CRE and MCREC isolates from water environments might be derived from animals and trigger infections in humans. The high prevalence of CRE and MCREC in large-scale environmental rivers is alarming and needs sustained surveillance due to the potential risk for transmission to humans via the food chain (irrigation) or direct contact.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

Does increasing the organic fertilizer application rate always boost the antibiotic resistance level in agricultural soils?

The amendment of organic fertilizer derived from livestock manure or biosolids is a significant driver of increasing antibiotic resistance in agricultural soils; however, it remains unclear whether increasing organic fertilizer application rates consistently enhances soil antibiotic resistance levels. Herein, we collected soils with long-term amendment with three types of organic fertilizers at four application rates (15, 30, 45, and 60 t/ha/y) and found that the higher the fertilization rate, the higher the antibiotic resistance gene (ARG) abundance. However, when the fertilization rate exceeded 45 t/ha/y, the ARG abundance ceased to significantly increase. Moreover, the soil ARG abundance was positively correlated with total nitrogen (TN) content and bacterial abundance, especially Firmicutes, and negatively affected by pH and bacterial diversity. Soil TN/bacterial abundance and pH/bacterial diversity reached maximum and minimum values at the 45 t/ha/y fertilization rate, respectively. Meanwhile, at this fertilization rate, Firmicutes enrichment peaked. Therefore, an organic fertilization rate of 45 t/ha/y appeared to represent the threshold for soil antibiotic resistance in this study. The underlying mechanism for this threshold was closely related to soil TN, pH, bacterial abundance, and diversity. Taken together, the findings of this study advance the current understanding regarding the soil resistome under different fertilization rates, while also providing novel insights into organic fertilizer management in agricultural practices.

Comparison of soil and grass microbiomes and resistomes reveals grass as a greater antimicrobial resistance reservoir than soil

Grasslands cover a large proportion of global agricultural landmass used to feed herbivores and ruminants and link the environment to the food chain via animals onto humans. However, most scientific studies of antimicrobial resistance and microbiomes at the environmental - animal nexus have focused on soil or vegetables rather than grasslands. Based on previous microbiome phyllosphere-soil studies we hypothesised that the microbiome and resistomes across soil and grass would have a core of shared taxa and antimicrobial resistance genes (ARGs), but that in addition each would also have a minority of unique signatures. Our data indicated grass contained a wider variety and higher relative abundance of ARGs and mobile genetic elements (MGEs) than soil with or without slurry amendments. The microbiomes of soil and grass were similar in content but varied in the composition proportionality. While there were commonalities across many of the ARGs present in soil and on grass their correlations with MGEs and bacteria differed, suggesting a source other than soil is also relevant for the resistome of grass. The variations in the relative abundances of ARGs in soil and on grass also indicated that either the MGEs or the bacteria carrying the ARGs comprised a higher relative abundance on grass than in soil. We conclude that while soil may be a source of some of these genes it cannot be the source for all ARGs and MGEs. Our data identifies grass as a more diverse and abundant reservoir of ARGs and MGEs in the environment than soil, which is significant to human and animal health when viewed in the context of grazing food animals.

Antibiotic resistant bacteria: A bibliometric review of literature

Antibiotic-resistant bacteria (ARB) are a serious threat to the health of people and the ecological environment. With this problem becoming more and more serious, more countries made research on the ARB, and the research number has been sharply increased particularly over the past decade. Therefore, it is quite necessary to globally retrace relevant researches on the ARB published from 2010 to 2020. This will help researchers to understand the current research situation, research trends and research hotspots in this field. This paper uses bibliometrics to examine publications in the field of ARB from 2010 to 2020 that were retrieved from the Web of Science (WOS). Our study performed a statistical analysis of the countries, institutions, journals, authors, research areas, author keywords, Essential Science Indicators (ESI) highly cited papers, and ESI hotspots papers to provide an overview of the ARB field as well as research trends, research hotspots, and future research directions in the field. The results showed that the number of related studies is increasing year by year; the USA is most published in the field of ARB; China is the most active in this field in the recent years; the Chinese Acad Sci published the most articles; Sci. Total Environ. published the greatest number of articles; CM Manaia has the most contributions; Environmental Sciences and Ecology is the most popular research area; and "antibiotic resistance," "antibiotics," and "antibiotic resistance genes" were the most frequently occurring author keywords. A citation analysis showed that aquatic environment-related antibiotic resistance is a key research area in this field, while antimicrobial nanomaterial-related research is a recent popular topic.

From Sewage Sludge to the Soil-Transfer of Pharmaceuticals: A Review

Sewage sludge, produced in the process of wastewater treatment and managed for agriculture, poses the risk of disseminating all the pollutants contained in it. It is tested for heavy metals or parasites, but the concentration of pharmaceuticals in the sludge is not controlled. The presence of these micropollutants in sludge is proven and there is no doubt about their negative impact on the environment. The fate of these micropollutants in the soil is a new and important issue that needs to be known to finally assess the safety of the agricultural use of sewage sludge. The article will discuss issues related to the presence of pharmaceuticals in sewage sludge and their physicochemical properties. The changes that pharmaceuticals undergo have a significant impact on living organisms. This is important for the implementation of a circular economy, which fits perfectly into the agricultural use of stabilized sewage sludge. Research should be undertaken that clearly shows that there is no risk from pharmaceuticals or vice versa: they contribute to the strict definition of maximum allowable concentrations in sludge, which will become an additional criterion in the legislation on municipal sewage sludge.

Improving the quality of organic compost of sewage sludge using grass cultivation followed by composting

Composting is one of the main processes of stabilization of sewage sludge and its association with cultivation in this residue has a great potential to produce stabilized organic fertilizer and, or substrate for plant development. The aim of this work was to evaluate the physical, chemical, and microbial attributes of sewage sludge (SS) aerated and cultivated with Pennisetum purpureum or Urochloa brizantha and, later, composted. The study was installed in a 2x2+2 factorial scheme, with four replications. The factors consisted of cultivation of P. purpureum or U. brizantha in SS for 90 days, with or without intermittent aeration for 60 days. The control treatments were SS without cultivation, with the presence or absence of aeration. After 90 days of cultivation, the grass was cut, crushed, and incorporated into the SS for composting for 60 days. The composted sewage sludge showed an increase of 26, 24, 17, 123, 19, 32, and 7.7% in the levels of P, Ca, Cu, Fe, Mn, Zn, and Pb; and a reduction of 22, 5.2, 26, 30, 8.8, and 70% in the levels of C, N, K, Mg, Ni, and Na, respectively. The levels of Cu, Ni, Zn, and Pb remained below the maximum limit allowed by environmental resolution. The degradation of SS decreased the particle diameter, increasing the bulk density and total porosity, improving the physical properties of the compost. The SS cultivation and composting, regardless of the grass, led to a reduction in pH, basal and accumulated respiration, nitrification index, and C/N ratio and an increase in the CEC/C ratio, showing adequate maturation of the compost produced. Thus, the SS cultivation and composting with grasses were effective for producing matured and quality organic compost with low risk of environmental contamination.

Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study

The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In order to help designing agricultural practices that minimize the spread of ARG, we fertilized, sown, and harvested lettuces and radish plants in experimental land plots for two consecutive agricultural cycles using four types of fertilizers: mineral fertilization, sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) identified a small, but significant overlap (<10%) between soil's and fertilizer microbiomes. Clinically relevant ARG were found in higher loads (up to 100 fold) in fertilized soils than in the initial soil, particularly in those treated with organic fertilizers, and their loads grossly correlated to the amount of antibiotic residues found in the corresponding fertilizer. Similarly, low, but measurable ARG loads were found in lettuce (tetM, sul1) and radish (sul1), corresponding the lowest values to samples collected from minerally fertilized fields. Comparison of soil samples collected along the total period of the experiment indicated a relatively year-round stability of soil microbiomes in amended soils, whereas ARG loads appeared as unstable and transient. The results indicate that ARG loads in soils and foodstuffs were likely linked to the contribution of bacteria from organic fertilizer to the soil microbiomes, suggesting that an adequate waste management and good pharmacological and veterinarian practices may significantly reduce the presence of these ARGs in agricultural soils and plant products.

Biosolids for safe land application: does wastewater treatment plant size matters when considering antibiotics, pollutants, microbiome, mobile genetic elements and associated resistance genes?

Soil fertilization with wastewater treatment plant (WWTP) biosolids is associated with the introduction of resistance genes (RGs), mobile genetic elements (MGEs) and potentially selective pollutants (antibiotics, heavy metals, disinfectants) into soil. Not much data are available on the parallel analysis of biosolid pollutant contents, RG/MGE abundances and microbial community composition. In the present study, DNA extracted from biosolids taken at 12 WWTPs (two large-scale, six middle-scale and four small-scale plants) was used to determine the abundance of RGs and MGEs via quantitative real-time PCR and the bacterial and archaeal community composition was assessed by 16S rRNA gene amplicon sequencing. Concentrations of heavy metals, antibiotics, the biocides triclosan, triclocarban and quaternary ammonium compounds (QACs) were measured. Strong and significant correlations were revealed between several target genes and concentrations of Cu, Zn, triclosan, several antibiotics and QACs. Interestingly, the size of the sewage treatment plant (inhabitant equivalents) was negatively correlated with antibiotic concentrations, RGs and MGEs abundances and had little influence on the load of metals and QACs or the microbial community composition. Biosolids from WWTPs with anaerobic treatment and hospitals in their catchment area were associated with a higher abundance of potential opportunistic pathogens and higher concentrations of QACs.

Contamination of hay and haylage with enteric bacteria and selected antibiotic resistance genes following fertilization with dairy manure or biosolids

The present study evaluated if enteric bacteria or antibiotic resistance genes carried in fecal amendments contaminate the hay at harvest, representing a potential route of exposure to ruminants that consume the hay. In field experiments, dairy manure was applied to a hay field for three successive growing seasons, and biosolids applied to a hay field for one growing season. Various enteric bacteria in the amendments were enumerated by viable plate count, and selected gene targets were quantified by qPCR. Key findings include the following: At harvest, hay receiving dairy manure or biosolids did not carry more viable enteric bacteria than did hay from unamended control plots. Fermentation of hay did not result in a detectable increase in viable enteric bacteria. The application of dairy manure or biosolids did result in a few gene targets being more abundant on hay at the first harvest. Fermentation of hay did result in an increase in the abundance of gene targets, but this occurred both with hay from amended and control plots. Overall, application of fecal amendments will result in an increase in the abundance of some gene targets associated with antibiotic resistance on first cut hay.

Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables

Treatment of manures prior to land application can potentially reduce the abundance of antibiotic resistance genes and thus the risk of contaminating crops or water resources. In this study, raw and composted chicken litter were applied to field plots that were cropped to carrots, lettuce and radishes. Vegetables were washed per normal culinary practice before downstream analysis. The impact of composting on manure microbial composition, persistence of antibiotic resistant bacteria in soil following application, and distribution of antibiotic resistance genes and bacteria on washed vegetables were determined. A subset of samples that were thought likely to reveal the most significant effects were chosen for shotgun sequencing. The absolute abundance of all target genes detected by qPCR decreased after composting except sul1, intI1, incW and erm(F) that remained stable. The shotgun sequencing revealed that some integron integrases were enriched by composting. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. Manure-amended soil showed significantly higher abundances of sul1, str(A), str(B), erm(B), aad(A), intI1 and incW compared to unmanured soil. At harvest, those genes that were detected in soil samples before the application of manure (intI1, sul1, strA and strB) were quantifiable by qPCR on vegetables, with a larger number of gene targets detected on the radishes than in the carrots or lettuce. Shotgun metagenomic sequencing suggested that the increase of antibiotic resistance genes on radishes produced in soil receiving raw manure may be due to changes to soil microbial communities following manure application, rather than transfer to the radishes of enteric bacteria. Overall, under field conditions there was limited evidence for transfer of antibiotic resistance genes from composted or raw manure to vegetables that then persisted through washing.

Environmental antibiotics and resistance genes as emerging contaminants: Methods of detection and bioremediation

In developing countries, the use of antibiotics has helped to reduce the mortality rate by minimizing the deaths caused by pathogenic infections, but the costs of antibiotic contamination remain a major concern. Antibiotics are released into the environment, creating a complicated environmental problem. Antibiotics are used in human, livestock and agriculture, contributing to its escalation in the environment. Environmental antibiotics pose a range of risks and have significant effects on human and animal health. Nevertheless, this is the result of the development of antibiotic-resistant and multi-drug-resistant bacteria. In the area of health care, animal husbandry and crop processing, the imprudent use of antibiotic drugs produces antibiotic-resistant bacteria. This threat is the deepest in the developing world, with an estimated 700,000 people suffering from antibiotic-resistant infections each year. The study explores how bacteria use a wide variety of antibiotic resistance mechanism and how these approaches have an impact on the environment and on our health. The paper focuses on the processes by which antibiotics degrade, the health effects of these emerging contaminants, and the tolerance of bacteria to antibiotics.

A Review on Occurrence and Spread of Antibiotic Resistance in Wastewaters and in Wastewater Treatment Plants: Mechanisms and Perspectives

This paper reviews current knowledge on sources, spread and removal mechanisms of antibiotic resistance genes (ARGs) in microbial communities of wastewaters, treatment plants and downstream recipients. Antibiotic is the most important tool to cure bacterial infections in humans and animals. The over- and misuse of antibiotics have played a major role in the development, spread, and prevalence of antibiotic resistance (AR) in the microbiomes of humans and animals, and microbial ecosystems worldwide. AR can be transferred and spread amongst bacteria via intra- and interspecies horizontal gene transfer (HGT). Wastewater treatment plants (WWTPs) receive wastewater containing an enormous variety of pollutants, including antibiotics, and chemicals from different sources. They contain large and diverse communities of microorganisms and provide a favorable environment for the spread and reproduction of AR. Existing WWTPs are not designed to remove micropollutants, antibiotic resistant bacteria (ARB) and ARGs, which therefore remain present in the effluent. Studies have shown that raw and treated wastewaters carry a higher amount of ARB in comparison to surface water, and such reports have led to further studies on more advanced treatment processes. This review summarizes what is known about AR removal efficiencies of different wastewater treatment methods, and it shows the variations among different methods. Results vary, but the trend is that conventional activated sludge treatment, with aerobic and/or anaerobic reactors alone or in series, followed by advanced post treatment methods like UV, ozonation, and oxidation removes considerably more ARGs and ARB than activated sludge treatment alone. In addition to AR levels in treated wastewater, it examines AR levels in biosolids, settled by-product from wastewater treatment, and discusses AR removal efficiency of different biosolids treatment procedures. Finally, it puts forward key-points and suggestions for dealing with and preventing further increase of AR in WWTPs and other aquatic environments, together with a discussion on the use of mathematical models to quantify and simulate the spread of ARGs in WWTPs. Mathematical models already play a role in the analysis and development of WWTPs, but they do not consider AR and challenges remain before models can be used to reliably study the dynamics and reduction of AR in such systems.

Effect of copper and zinc as sulfate or nitrate salts on soil microbiome dynamics and blaVIM-positive Pseudomonas aeruginosa survival

The exposure of soil to metals and to antibiotic resistant bacteria may lead to the progressive deterioration of soil quality. The persistence of antibiotic resistant bacteria or antibiotic resistance genes in soil can be influenced by the microbial community or by soil amendments with metal salts. This work assessed the effect of soil amendment with copper and zinc, as sulfate or nitrate salts, on the fate of a carbapenem-resistant (bla_VIM⁺) hospital effluent isolate of Pseudomonas aeruginosa (strain H1FC49) and on the variations of the microbial community composition. Microcosms with soil aged or not with copper and zinc salts (20 mM), and inoculated with P. aeruginosa H1FC49 were monitored at 0, 7, 14 and/or 30 days, for community composition (16S rRNA gene amplicon) and strain H1FC49 persistence. Data on culturable P. aeruginosa, quantitative PCR of the housekeeping gene ecf, and the presumably acquired genes bla_VIM⁺ and integrase (intI1), and community composition were interpreted based on descriptive statistics and multivariate analysis. P. aeruginosa and the presumably acquired genes, were quantifiable in soil for up to one month, in both metal-amended and non-amended soil. Metal amendments were associated with a significant decrease of bacterial community diversity and richness. The persistence of P. aeruginosa and acquired genes in soils, combined with the adverse effect of metals on the bacterial community, highlight the vulnerability of soil to both types of exogenous contamination.

Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species

Antibiotic resistance genes (ARGs) in the endophytes of vegetables represent a potential route of human exposure to the soil resistome. However, the effect of vegetable species on the endophytic ARG profiles is unclear, hampering our understanding of how ARGs migrate into the soil-vegetable system and their potential health risks. Here, we planted four leafy vegetables (cilantro, endive, lettuce, and pak choi), which are commonly eaten raw, and analyzed the resistomes and microbiomes in three sample types (rhizosphere soil, root, and leaf endophytes). A total of 150 ARG subtypes were detected using high-throughput quantitative PCR. Vegetable species had a significant effect on ARG diversity and abundance, and pak choi accumulated more ARGs in its associated microbiome than the other three vegetables. The bacterial community was the primary factor shaping ARG profiles and was significantly correlated with ARG subtypes. We identified aadE, tet(34), and vanSB as shared ARGs among leaves of the four vegetables; the bacterial families correlated with tet(34) and vanSB were also shared across the vegetables and belonged to Proteobacteria. This study deepens our understanding of how endophytic ARG profiles vary among different vegetables and highlights the potential health risk associated with consuming these vegetables raw.

Azithromycin and Ciprofloxacin Can Promote Antibiotic Resistance in Biosolids and Biosolids-Amended Soils

Spread of biosolids-borne antibiotic resistance is a growing public and environmental health concern. Herein, we conducted incubation experiments involving biosolids, which are byproducts of sewage treatment processes, and biosolids-amended soil. Quantitative reverse transcription-PCR (RT-qPCR) was employed to assess responses of select antibiotic resistance genes (ARGs) and mobile elements to environmentally relevant concentrations of two biosolids-borne antibiotics, azithromycin (AZ) and ciprofloxacin (CIP). Additionally, we examined sequence distribution of gyrA (encoding DNA gyrase; site of action of CIP) to assess potential shifts in genotype. Increasing antibiotic concentrations generally increased the transcriptional activities of qnrS (encoding CIP resistance) and ermB and mefE (encoding AZ resistance). The transcriptional activity of intl1, a marker of class 1 integrons, was unaffected by CIP or AZ concentrations, but biosolids amendment increased intl1 activity in the soil by 4 to 5 times, which persisted throughout incubation. While the dominant gyrA sequences found herein were unrelated to known CIP-resistant genotypes, the increasing CIP concentrations significantly decreased the diversity of genes encoding the DNA gyrase A subunit, suggesting changes in microbial community structures. This study suggests that biosolids harbor transcriptionally active ARGs and mobile elements that could survive and spread in biosolids-amended soils. However, more research is warranted to investigate these trends under field conditions. IMPORTANCE Although previous studies have indicated that biosolids may be important spreaders of antibiotics and antibiotic resistance genes (ARGs) in environments, the potential activities of ARGs or their responses to environmental parameters have been understudied. This study highlights that certain biosolids-borne antibiotics can induce transcriptional activities of ARGs and mobile genetic elements in biosolids and biosolids-amended soil, even when present at environmentally relevant concentrations. Furthermore, these antibiotics can alter the structure of microbial populations expressing ARGs. Our findings indicate the bioavailability of the antibiotics in biosolids and provide evidence that biosolids can promote the activities and dissemination of ARGs and mobile genes in biosolids and soils that receive contaminated biosolids, thus, underscoring the importance of investigating anthropogenically induced antibiotic resistance in the environment under real-world scenarios.

Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.

Elimination of antibiotic resistance genes from excess activated sludge added for effective treatment of fruit and vegetable waste in a novel vermireactor

Elimination of antibiotic resistance genes (ARGs) from excess activated sludge (EAS) mixed for effective treatment of different fruit and vegetable waste (FVW) by using a novel vermireactor consisted of substrate and bed compartments was investigated. ARGs (tet G, tet M and sul 1) and mobile genetic element gene (intl 1) were targeted and, through quantitative analysis of their abundances in both the compartments and the fresh cast of earthworms, significant reductions in substrate compartments were confirmed for the treatments for FVW added with EAS and EAS alone even if the reduction extents differed among the types of FVW. Apparent reductions were not found in the bed compartment where the final products accumulated. For the fresh cast, the relative abundances of ARGs and intl 1 against to the total bacterial 16S rDNA decreased markedly. The present study provided an insight for proper controlling of ARGs during vermicomposting of FVW and EAS.

Antibiotics and Antibiotic Resistance Genes in Animal Manure - Consequences of Its Application in Agriculture

Antibiotic resistance genes (ARGs) are a relatively new type of pollutant. The rise in antibiotic resistance observed recently is closely correlated with the uncontrolled and widespread use of antibiotics in agriculture and the treatment of humans and animals. Resistant bacteria have been identified in soil, animal feces, animal housing (e.g., pens, barns, or pastures), the areas around farms, manure storage facilities, and the guts of farm animals. The selection pressure caused by the irrational use of antibiotics in animal production sectors not only promotes the survival of existing antibiotic-resistant bacteria but also the development of new resistant forms. One of the most critical hot-spots related to the development and dissemination of ARGs is livestock and poultry production. Manure is widely used as a fertilizer thanks to its rich nutrient and organic matter content. However, research indicates that its application may pose a severe threat to human and animal health by facilitating the dissemination of ARGs to arable soil and edible crops. This review examines the pathogens, potentially pathogenic microorganisms and ARGs which may be found in animal manure, and evaluates their effect on human health through their exposure to soil and plant resistomes. It takes a broader view than previous studies of this topic, discussing recent data on antibiotic use in farm animals and the effect of these practices on the composition of animal manure; it also examines how fertilization with animal manure may alter soil and crop microbiomes, and proposes the drivers of such changes and their consequences for human health.

Microbial Safety of Smoothie Drinks from Fresh Bars Collected in Slovakia

Among the many consumers in Slovakia, smoothies are nowadays gaining popularity. Smoothie drinks are prepared from raw fruits and vegetables. Therefore, their microbiological safety depends on hygiene standards. The aim of this work was to monitor and quantify selected sensitive and antibiotic-resistant microorganisms present in collected smoothies. Twenty analyzed smoothie samples were collected from six food service establishments (fresh bars) in the capital city of Slovakia, Bratislava. Antibiotic-resistant bacteria were found in at least one of each fresh bar. Antibiotic-resistant coliform bacteria prevailed, especially in green smoothies or juices containing more vegetable ingredients. Resistance to ampicillin, ciprofloxacin, tetracycline, chloramphenicol, and gentamicin was observed in the case of coliform bacteria. More than half of the smoothie drink samples did not contain resistant enterococci. On the other hand, vancomycin-resistant enterococci were detected in 20% of samples. The most frequently isolated antibiotic-resistant strains belonged to the Enterobacter spp. or Klebsiella spp. genus. In the last part of the work, the pretreatment effect of smoothie components on the selected microorganisms' counts in the final product was investigated. Washing ingredients with an aqueous solution of a biocide agent containing silver and hydrogen peroxide proved to be the most effective way to decrease bacterial counts.

Microbiological safety and antibiotic resistance risks at a sustainable farm under large-scale open-air composting and composting toilet systems

This study evaluated the microbial safety and antibiotic resistance risks of a sustainable ecological farm under large-scale open-air composting (OC) and green composting toilet systems (CT). Samples of livestock manure, compost, soil, vegetables, and rainwater were analysed to determine the best treatment of wastes and risk assessment of land application. Results showed that pathogenic bacteria (PB) in livestock manure was significantly greater than that in the surrounding topsoil, while the distribution of bacteria resistant to amoxicillin (AMX), tetracycline (TC), and amoxicillin-tetracycline (AMX- TC) was the opposite through long-term resistance selection pressure. E. coli and Enterococcus were the dominant pathogens in feces and surrounding soil, respectively, and AMX-resistant bacteria dominated soil, compost, and vegetable samples. Overall, while OC may significantly increase antibiotic resistance and effectively remove fecal PB, CT offers faster consumption with greater antibiotic resistant bacteria (ARB) removal but more PB. Moreover, PB and ARB were concentrated in mature compost, soil in planting areas, vegetables, and rainwater. In farm soil and vegetables, AMX-resistant and AMX-TC-resistant bacterial communities displayed similar composition. These findings may explain the main pathways of PB transmission, migration and accumulation of ARB in farms, and the potential risks to human health through the food chain.

Dose effect of Zn and Cu in sludge-amended soils on vegetable uptake of trace elements, antibiotics, and antibiotic resistance genes: Human health implications

The application of sewage sludge to agricultural fields reduces the need for mineral fertilizers by increasing soil organic matter, but may also increase soil pollution. Previous studies indicate that zinc and copper, as the most abundant elements in sewage sludge, affect plant uptake of other contaminants. This paper aims to investigate and compare the effect of increasing amounts of Zn and Cu in sludge-amended soils on the accumulation of trace elements (TEs), antibiotics (ABs), and antibiotic resistance genes (ARGs) in lettuce and radish. The vegetables were grown under controlled conditions, and the influence on plant physiology and human health were also evaluated. The results show that the addition of Zn and Cu significantly increased the concentration of TEs in the edible tissue of both vegetables. According to the hazard quotient (HQ) of the TEs, the human health risk increased 2 to 3 times and was 3-4 times greater in lettuce than in radish. In contrast to the TEs, the occurrence of ABs and most of the ARGs was higher in radish roots than lettuce leaves. ABs were not detected in lettuce leaves, and the amount of all ARGs except bla_TEM was 10 times lower than in radish roots. On the other hand, the addition of Zn and Cu had no significant effect on the occurrence of ABs and ARGs in the edible part of the vegetables, and no damage was found to plant productivity or physiology. The results show that the consumption of lettuce and radish grown in sewage-sludge-amended soils under tested doses of Cu and Zn does not pose an adverse human health effect, as the total HQ value was always less than 1, and the presence of ABs and ARGs was not found to have any potential impact. Nevertheless, further studies are needed to estimate the long-term effect on human health of crops grown under frequent application of biosolids in arable soil.

Residuals, sludge, and biosolids: Advancements in the field

Advancements in the field of residuals, sludge, and biosolids have been made in 2019. This review outlines the major contributions of researchers that have been published in peer-reviewed journals and conference proceedings throughout 2019 and includes brief summaries from over 125 articles. The review is organized in sections including life cycle and risk assessments; characteristics, quality, and measurement including micropollutants, nanoparticles, pathogens, and metals; sludge treatment technologies including dewatering, digestion, composting, and wetlands; disposal and reuse including adsorbents, land application and agricultural uses, nutrient recovery, and innovative uses; odor and air emissions; and energy issues.

Study of Evolution of Microbiological Properties in Sewage Sludge-Amended Soils: A Pilot Experience

Large amounts of sewage sludge are generated in urban wastewater treatment plants and used as fertilizer in agriculture due to its characteristics. They can contain contaminants such as heavy metals and pathogenic microorganisms. The objective of this research work is to study, in real conditions, the evolution of microbial concentration in agricultural soils fertilized by biologically treated sewage sludge. The sludge (6.25 tons Ha⁻¹) was applied in two agricultural soils with different textures and crops. A microbiological (total coliforms, Escherichia coli, Staphylococcus aureus, Enterococcus sp., Pseudomonas sp., Salmonella sp. and total mesophylls) and physical-chemical characterization of the sludge, soils and irrigation water were carried out. The evolution of these parameters during sowing, growth and harvesting of crops was studied. Initially, sewage sludge had a higher concentration of microorganisms than soils. Irrigation water also contained microorganisms, fewer than sewage sludge amendment but not negligible. After amendment, there were no differences in the microbiological evolution in the two types of soil. In general, bacterial concentrations after crop harvest were lower than bacterial concentrations detected before sewage sludge amendment. Consequently, the application of sludge from water treatment processes did not worsen the microbiological quality of agricultural soil in this study at real conditions.

Insights into factors driving the transmission of antibiotic resistance from sludge compost-amended soil to vegetables under cadmium stress

Sludge compost is often used as a fertilizer for crops, although it might be enriched with antibiotic resistance genes (ARGs) and heavy metals that cannot be removed through composting. A robust understanding of the factors affecting the transmission of ARGs to vegetables grown in soils treated with sludge products is lacking. In this study, target ARGs in the bulk and rhizosphere soils and endophytes of shallots under heavy metal stress (i.e., Cd) were assessed, and the factors driving the transmission of ARGs were identified. Cd stress resulted in an increase in the relative abundances of target ARGs in the bulk and rhizosphere soils and endophytes. The driving factors were different in soils and plants under different degrees of Cd stress. The fungal community composition was the main driving factor of ARG variation in both bulk and rhizosphere soils. Moreover, endophytic bacteria played a crucial role in transferring ARGs to plants. Higher Cd stress promoted the transfer of most target ARGs from the below-ground plant parts to the above-ground parts. These findings indicate that application of sludge contaminated with heavy metals, such as Cd, can facilitate the dissemination of ARGs into vegetables, which must be considered while assessing the risks to public health.

Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome

The widespread practice of applying sewage sludge to arable land makes use of nutrients indispensable for crops and reduces the need for inorganic fertilizer, however this application also provides a potential route for human exposure to chemical contaminants and microbial pathogens in the sludge. A recent concern is that such practice could promote environmental selection and dissemination of antibiotic resistant bacteria or resistance genes. Understanding the risks of sludge amendment in relation to antibiotic resistance development is important for sustainable agriculture, waste treatment and infectious disease management. To assess such risks, we took advantage of an agricultural field trial in southern Sweden, where land used for growing different crops has been amended with sludge every four years since 1981. We sampled raw, semi-digested and digested and stored sludge together with soils from the experimental plots before and two weeks after the most recent amendment in 2017. Levels of selected antimicrobials and bioavailable metals were determined and microbial effects were evaluated using both culture-independent metagenome sequencing and conventional culturing. Antimicrobials or bioavailable metals (Cu and Zn) did not accumulate to levels of concern for environmental selection of antibiotic resistance, and no coherent signs, neither on short or long time scales, of enrichment of antibiotic-resistant bacteria or resistance genes were found in soils amended with digested and stored sewage sludge in doses up to 12 metric tons per hectare. Likewise, only very few and slight differences in microbial community composition were observed after sludge amendment. Taken together, the current study does not indicate risks of sludge amendment related to antibiotic resistance development under the given conditions. Extrapolations should however be done with care as sludge quality and application practices vary between regions. Hence, the antibiotic concentrations and resistance load of the sludge are likely to be higher in regions with larger antibiotic consumption and resistance burden than Sweden.

Manure Application Did Not Enrich Antibiotic Resistance Genes in Root Endophytic Bacterial Microbiota of Cherry Radish Plants

Growing evidence suggests that livestock manure used as organic fertilizer in agriculture may lead to the potential propagation of antibiotic resistance genes (ARGs) from "farm to fork." However, little is known about the impacts of manure fertilization on the incidence of ARGs in the plant-associated microbiomes (including rhizosphere, endosphere, and phyllosphere), which hampers our ability to assess the dissemination of antibiotic resistance in the soil-plant system. Here, we constructed a pot experiment to explore the effects of poultry and cattle manure applications on the shifts in the resistome in the plant microbiome of harvested cherry radish. A total of 144 ARGs conferring resistance to eight major classes of antibiotics were detected among all the samples. Rhizosphere and phyllosphere microbiomes harbored significantly higher diversity and abundance of ARGs than did root endophytic microbiomes of cherry radish. Manure application significantly increased the abundance of ARGs in the rhizosphere and phyllosphere but not in the endophytes of the root, which is the edible part of cherry radish. Soil and plant microbiomes changed dramatically after manure applications and clustered separately according to different sample types and treatments. Structural equation modeling revealed that bacterial abundance was the most important factor modulating the distribution patterns of soil and plant resistomes after accounting for multiple drivers. Taken together, we provide evidence that enrichment of the resistome in the rhizosphere and phyllosphere of cherry radish is more obvious than with the endosphere after manure application, suggesting that manure amendment might not enhance the dissemination of ARGs into the root of vegetables in the pot experiment.IMPORTANCE Our study provides important evidence that manure application increased the occurrence of ARGs in the rhizosphere and phyllosphere of cherry radish, compared with that in the endophytic bacterial microbiota of root, which is the edible part of cherry radish. Our findings suggest that although manure amendment is a significant route of ARGs entering agricultural soils, these manure-derived ARGs may be at low risk of migrating into the endophytes of root vegetables.

Occurrence and distribution of antibiotics and antibiotic resistant genes in water and sediments of urban rivers with black-odor water in Guangzhou, South China

Urban rivers in some countries have been heavily polluted and the water became black and odor. Nevertheless, only few studies reported the occurrence of antibiotics and their corresponding antibiotic resistant genes (ARGs) in urban rivers with black-odor water with and without remediation. In this study, nine antibiotics (belonging to sulfonamides, tetracyclines, quinolones, and macrolides) and their corresponding ARGs in water and sediments of six urban rivers in Guangzhou, South China were analyzed to investigate their spatial distribution and the influence of water remediation. The concentrations of individual antibiotics varied from ND (not detectable) to 2702 ng/L and ND to 449 μg/kg in surface water and sediments, respectively. Norfloxacin displayed the highest average concentrations, followed by ciprofloxacin. The relative abundance of quinolone-resistance gene qnrA (~10³ ARGs/16S rRNA) was the highest, followed by tetracyclines-resistance genes tetC (~10^-2 ARGs/16S rRNA). The antibiotics and ARGs in sediments from various rivers exhibited distinct spatial distribution with large variation from upstream to downstream. Generally, levels of antibiotics and tetracyclines-resistance genes (tetA, tetC and tetM) in urban rivers with black-odor water (affected by industrial and domestic sewage) were higher than those in remediated urban rivers. Significant positive correlations were observed only between the relative abundances of tetA (or tetC) with the concentrations of some antibiotics (e.g., ciprofloxacin and norfloxacin). TetA was also significantly positively correlated with the concentrations of Ni, Cr, and As in sediments. This study found that urban rivers remediated with dredging might lower antibiotic levels in sediment, but high relative abundance of certain ARGs (e.g., tetB, qnrA) may still exist.