Transfer of antibiotic resistance plasmids in pure and activated sludge cultures in the presence of environmentally representative micro-contaminant concentrations

Deciphering antibiotic resistance gene transfer in activated sludge systems for piggery wastewater: behaviors, hosts and drivers

Understanding the transfer and driving mechanisms of antibiotic resistance genes (ARGs) in activated sludge is essential for mitigating environmental risks, particularly during real wastewater treatment where these processes remain poorly characterized. This study investigated the prevalence of ARGs in a sequencing batch reactor (SBR) - up-flow microaerobic sludge reactor (UMSR) system treating high-risk piggery wastewater and revealed critical pathways for resistance propagation. Ten prevalent ARG subtypes, categorized into three types, were selected as target genes, exhibiting a total relative abundance of 0.52 copies per 16S rRNA in raw wastewater. The SBR-UMSR system reduced total ARGs by 0.04 log in wastewater, with half of subtypes decreasing 0.14-1.30 log, despite 0.23-0.58 log enrichment in sludge. By integrating correlation analysis with partial least-squares path modeling, this study identified Burkholderiaceae as the primary potential host of ARGs and pinpointed other high-risk hosts. It further revealed two crucial mechanisms: i) conjugation-mediated horizontal gene transfer dominated ARG propagation, and ii) bacterial community succession served as the main driving force for ARG transfer. This study advances mechanistic understanding of ARG transmission in real wastewater systems, providing critical insights for optimizing sludge management to mitigate antibiotic resistance risks.

Co-contaminant risks in water reuse and biosolids application for agriculture

Agriculture made the shift toward resource reuse years ago, incorporating materials such as treated wastewater and biosolids. Since then, research has documented the widespread presence of contaminants of emerging concern in agricultural systems. Chemicals such as pesticides, pharmaceuticals and poly- and -perfluoroalkyl substances (PFASs); particulate matter such as nanomaterials and microplastics; and biological agents such as antibiotic resistance genes (ARGs) and bacteria (ARB) are inadvertently introduced into arable soils where they can be taken up by crops and introduced to the food-web. Thus, concern about the presence of contaminants in agricultural environments has grown in recent years with evidence emerging linking agricultural exposure and accumulation in crops to ecosystem and human health effects. Our current assessment of risk is siloed by working within disciplines (i.e., chemistry and microbiology) and mostly focused on individual chemical classes. By not acknowledging the fact that contaminants are mostly introduced as a mixture, with the potential for interactions, with each other and with environmental factors, we are limiting our current approach to evaluate the real potential for ecosystem and human health effects. By uniting expertise across disciplines to integrate recent understanding regarding the risks posed by a range of chemically diverse contaminants in resources destined for reuse, this review provides a holistic perspective on the current regulatory challenges to ensure safe and sustainable reuse of wastewater and biosolids to support a sanitation-agriculture circular economy.

Antibiotic Resistance Dissemination and Mapping in the Environment Through Surveillance of Wastewater

Antibiotic resistance is one of the major health threat for humans, animals, and the environment, according to the World Health Organization (WHO) and the Global Antibiotic-Resistance Surveillance System (GLASS). In the last several years, wastewater/sewage has been identified as potential hotspots for the dissemination of antibiotic resistance and transfer of resistance genes. However, systematic approaches for mapping the antibiotic resistance situation in sewage are limited and underdeveloped. The present review has highlighted all possible perspectives by which the dynamics of ARBs/ARGs in the environment may be tracked, quantified and assessed spatio-temporally through surveillance of wastewater. Moreover, application of advanced methods like wastewater metagenomics for determining the community distribution of resistance at large has appeared to be promising. In addition, monitoring wastewater for antibiotic pollution at various levels, may serve as an early warning system and enable policymakers to take timely measures and build infrastructure to mitigate health crises. Thus, by understanding the alarming presence of antibiotic resistance in wastewater, effective action plans may be developed to address this global health challenge and its associated environmental risks.

Cyanobacteria mediate the dissemination of bacterial antibiotic resistance through conjugal transfer

Cyanobacterial blooms are expanding world-wide in freshwater and marine environments, and can cause serious ecological and environmental issues, which also contribute to the spread of antibiotic resistance genes (ARGs). However, the mechanistic understanding of cyanobacteria-mediated resistance dynamics is not fully elucidated yet. We selected Microcystis aeruginosa as a model cyanobacteria to illustrate how cyanobacteria mediate the evolution and transfer processes of bacterial antibiotic resistance. The results show that the presence of cyanobacteria significantly decreased the abundance of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) by 3%-99% and 2%-18%, respectively. In addition, it clearly altered bacterial community structure, with the dominant genera evolving from Acinetobacter (27%) and Enterobacter (42%) to Porphyrobacter (59%). The abundance of ARGs positively correlated with Proteobacteria and Firmicutes, rather than Cyanobacteria, and Bacteroidetes. In the presence of cyanobacteria, the transfer events of bacterial resistance genes via conjugation were found to decrease by 10%-89% (p < 0.05). Surprisingly, we found an extradentary high transfer frequency (about 0.1) for the ARGs via plasmid conjugation from the bacteria into M. aeruginosa population. It confirmed the role of cyanobacterial population as the competent hosts to facilitate ARGs spreading. Our findings provide valuable information on the risk evaluation of ARGs caused by cyanobacterial blooms in aquatic environments, key for the protection and assessment of aquatic environmental quality.

Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring

It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.

Making waves: The NORMAN antibiotic resistant bacteria and resistance genes database (NORMAN ARB&ARG)-An invitation for collaboration to tackle antibiotic resistance

With the global concerns on antibiotic resistance (AR) as a public health issue, it is pivotal to have data exchange platforms for studies on antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. For this purpose, the NORMAN Association is hosting the NORMAN ARB&ARG database, which was developed within the European project ANSWER. The present article provides an overview on the database functionalities, the extraction and the contribution of data to the database. In this study, AR data from three studies from China and Nepal were extracted and imported into the NORMAN ARB&ARG in addition to the existing AR data from 11 studies (mainly European studies) on the database. This feasibility study demonstrates how the scientific community can share their data on AR to generate an international evidence base to inform AR mitigation strategies. The open and FAIR data are of high potential relevance for regulatory applications, including the development of emission limit values / environmental quality standards in relation to AR. The growth in sharing of data and analytical methods will foster collaboration on risk management of AR worldwide, and facilitate the harmonization in the effort for identification and surveillance of critical hotspots of AR. The NORMAN ARB&ARG database is publicly available at: https://www.norman-network.com/nds/bacteria/.

Structural effects of sulfonamides on the proliferation dynamics of sulfonamide resistance genes in the sequencing batch reactors and the mechanism

Antibiotic resistance genes (ARGs) can be easily promoted by antibiotics, however, the structural effects of antibiotics on the proliferation of ARGs dynamic and the associated mechanisms remain obscure in, especially, activated sludge sequencing batch reactors. In the present study, the effects of 9 sulfonamides (SAs) with different structures on the proliferation dynamic of sulfonamide resistance genes (Suls) in the activated sludge sequencing batch reactors and the corresponding mechanisms were determined (30 days), and the results showed that the largest proliferation value (∆AR) of Suls dynamic for SAs (sulfachloropyridazine) was approximately 2.9 times than that of the smallest one (sulfadiazine). The proliferation of Suls was significantly related to the structural features (minHBint6, SssNH, SHBd and SpMax2_Bhm) that represent the biological activity of SAs. To interpret the phenomenon, a mechanistic model was developed and the results indicated that the biodegradation of SAs (T1/2) rather than conjugative transfer frequency or mutation frequency tends to be the key process for affecting Suls proliferation. T1/2 was proved to be dependent on the interactions between SAs and receptors (Ebinding), the cleavage mode (bond dissociation energy), and the site of nucleophilic assault. Besides, the metagenomic analysis showed that SAs posed significant effect on antibiotic resistome and Tnp31 played a vital role in the proliferation of Suls. Overall, our findings provide important insight into a theoretical basis for understanding the structural effects of SAs on the proliferation of ARGs in SBR systems.

Synergistic removal of pharmaceuticals and antibiotic resistance from ultrafiltered WWTP effluent: Free-floating ARGs exceptionally susceptible to degradation

To protect the environment and human health, antibiotic resistance genes (ARGs) and persistent pharmaceuticals need to be removed from WWTP effluent prior to its reuse. However, an efficient process for removing free-floating extracellular DNA (exDNA) in combination with a wide range of pharmaceuticals is yet to be reported for real process conditions. As a possible solution, we treated real ultrafiltered WWTP effluent with UV/H₂O₂ and combined GAC and zeolite sorption. In terms of exDNA, sequencing and high-throughput quantitative PCR (HT-qPCR) showed that exDNA is a potent carrier of numerous ARGs in ultrafiltered WWTP effluent (123 ARGs), including multi-drug efflux pump mexF that became the dominant exARG in GAC effluent over time. Due to the exposure to degradation agents, exDNA was reduced more efficiently than intracellular DNA, and overall levels of ARGs were substantially lowered. Moreover, GAC sorption was particularly effective in the removal of almost all the 85 detected pharmaceutical residues, with fresh GAC demonstrating an efficiency of up to 100%. However, zeolite (Si/Al 0.8) addition was needed to enhance the removal of persistent pollutants such as gabapentin and diclofenac to 57% and up to 100%, respectively. Our combined approach eminently decreases the hazardous effects of pharmaceuticals and antibiotic resistance in the ultrafiltered WWTP effluent, producing effluent suitable for multiple reuse options according to the latest legislation. In addition, we provided similarly promising but less extensive data for surface water and treated greywater.

Occurrence and prevalence of antibiotic resistance genes and pathogens in an industrial park wastewater treatment plant

Antibiotic resistance genes (ARGs) and pathogens are emerging environmental pollutants that pose a threat to human health and ecosystem. Industrial park wastewater treatment plants (WWTPs) treat large amounts of comprehensive wastewater derived from industrial production and park human activity, which is possible a source of ARGs and pathogens. Therefore, this study investigated the occurrence and prevalence of ARGs, ARGs hosts and pathogens and assesses the ARGs health risk in the biological treatment process in a large-sale industrial park WWTP using metagenomic analysis and omics-based framework, respectively. Results show that the major ARG subtypes are multidrug resistance genes (MDRGs), macB, tetA(58), evgS, novA, msbA and bcrA and the ARGs main hosts were genus Acidovorax, Pseudomonas, Mesorhizobium. In particular, all determined ARGs genus level hosts are pathogens. The total removal percentage of ARGs, MDRGs and pathogens were 12.77 %, 12.96 % and 25.71 % respectively, suggesting that the present treatment could not efficiently remove these pollutants. The relative abundance of ARGs, MDRGs and pathogens varied along biological treatment process that ARGs and MDRGs were enriched in activated sludge and pathogens were enriched in both secondary sedimentation tank and activated sludge. Among 980 known ARGs, 23 ARGs (e.g., ermB, gadX and tetM) were assigned into risk Rank I with characters of enrichment in the human-associated environment, gene mobility and pathogenicity. The results indicate that industrial park WWTPs might serve as an important source of ARGs, MDRGs, and pathogens. These observations invite further study of the origination, development, dissemination and risk assessment of industrial park WWTPs ARGs and pathogens.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

Induced development of oxytetracycline tolerance in bacterial communities from soil amended with well-aged cow manure

The use of animal manure as organic fertilizer is a common agricultural practice that can improve soil health and crop yield. However, antibiotics and their metabolites are often present in animal manure and, hence, in manure-amended soil. The aim of this study was to assess the induced development of oxytetracycline (OTC) tolerance in soil bacterial communities as a result of the addition of OTC to soil amended with well-aged cow manure. To this purpose, soil amended with well-aged cow manure was repeatedly - three times - spiked with different OTC concentrations (0, 2, 20, 60, 150, and 500 mg OTC kg^-1 dry weight soil, each time) according to a pollution-induced community tolerance (PICT) assay. The PICT detection phase was conducted in Biolog EcoPlates^TM in the presence of the following OTC concentration gradient in the wells: 0, 5, 20, 40, 60, and 100 mg L^-1. For all treatments, the application of OTC in the PICT selection phase resulted in lower values of bacterial metabolic activity (i.e., lower values of average well color development) in the PICT detection phase. A significant increase in OTC tolerance was observed in soil bacterial communities that had been exposed three times to ≥ 20 mg OTC kg^-1 DW soil during the PICT selection phase. In general, higher levels of OTC exposure during the PICT selection phase resulted in bacterial tolerance to higher OTC concentrations during the PICT detection phase, pointing to a dose-dependent induced tolerance. It is important to (i) rationalize the amount of antibiotics administered to livestock, and (ii) treat properly the antibiotic-containing manure before its application to agricultural soil as fertilizer.

Stimulants and donors promote megaplasmid pND6-2 horizontal gene transfer in activated sludge

The activated sludge process is characterized by high microbial density and diversity, both of which facilitate antibiotic resistance gene transfer. Many studies have suggested that antibiotic and non-antibiotic drugs at sub-inhibitory concentrations are major inducers of conjugative gene transfer. The self-transmissible plasmid pND6-2 is one of the endogenous plasmids harbored in Pseudomonas putida ND6, which can trigger the transfer of another co-occurring naphthalene-degrading plasmid pND6-1. Therefore, to illustrate the potential influence of stimulants on conjugative transfer of pND6-2, we evaluated the effects of four antibiotics (ampicillin, gentamycin, kanamycin, and tetracycline) and naphthalene, on the conjugal transfer efficiency of pND6-2 by filter-mating experiment. Our findings demonstrated that all stimulants within an optimal dose promoted conjugative transfer of pND6-2 from Pseudomonas putida GKND6 to P. putida KT2440, with tetracycline being the most effective (100 µg/L and 10 µg/L), as it enhanced pND6-2-mediated intra-genera transfer by approximately one hundred-fold. Subsequently, seven AS reactors were constructed with the addition of donors and different stimulants to further elucidate the conjugative behavior of pND6-2 in natural environment. The stimulants positively affected the conjugal process of pND6-2, while donors reshaped the host abundance in the sludge. This was likely because stimulant addition enhanced the expression levels of conjugation transfer-related genes. Furthermore, Blastocatella and Chitinimonas were identified as the potential receptors of plasmid pND6-2, which was not affected by donor types. These findings demonstrate the positive role of sub-inhibitory stimulant treatment on pND6-2 conjugal transfer and the function of donors in re-shaping the host spectrum of pND6-2.

Emerging technologies for enhanced removal of residual antibiotics from source-separated urine and wastewaters: A review

Antibiotic residues are of significant concern in the ecosystem because of their capacity to mediate antibiotic resistance development among environmental microbes. This paper reviews recent technologies for the abatement of antibiotics from human urine and wastewaters. Antibiotics are widely distributed in the aquatic environment as a result of the discharge of municipal sewage. Their existence is a cause for worry due to the potential ecological impact (for instance, antibiotic resistance) on bacteria in the background. Numerous contaminants that enter wastewater treatment facilities and the aquatic environment, as a result, go undetected. Sludge can act as a medium for some chemicals to concentrate while being treated as wastewater. The most sewage sludge that has undergone treatment is spread on agricultural land without being properly checked for pollutants. The fate of antibiotic residues in soils is hence poorly understood. The idea of the Separation of urine at the source has recently been propagated as a measure to control the flow of pharmaceutical residues into centralized wastewater treatment plants (WWTPs). With the ever increasing acceptance of urine source separation practices, visibility and awareness on dedicated treatement technologies is needed. Human urine, as well as conventional WWTPs, are point sources of pharmaceutical micropollutants contributing to the ubiquitous detection of pharmaceutical residues in the receiving water bodies. Focused post-treatment of source-separated urine includes distillation and nitrification, ammonia stripping, and adsorption processes. Other reviewed methods include physical and biological treatment methods, advanced oxidation processes, and a host of combination treatment methods. All these are aimed at ensuring minimized risk products are returned to the environment.

Subinhibitory antibiotic concentrations promote the horizontal transfer of plasmid-borne resistance genes from Klebsiellae pneumoniae to Escherichia coli

Horizontal gene transfer plays an important role in the spread of antibiotic resistance, in which plasmid-mediated conjugation transfer is the most important mechanism. While sub-minimal inhibitory concentrations (sub-MIC) of antibiotics could promote conjugation frequency, the mechanism by which sub-MIC levels of antibiotics affect conjugation frequency is not clear. Here, we used Klebsiella pneumoniae SW1780 carrying the multi-drug resistance plasmid pSW1780-KPC as the donor strain, to investigate the effects of sub-MICs of meropenem (MEM), ciprofloxacin (CIP), cefotaxime (CTX), and amikacin (AK) on conjugational transfer of pSW1780-KPC from SW1780 to Escherichia coli J53. Our results showed that the transfer frequencies increased significantly by treating SW1780 strain with sub-MIC levels of MEM, CIP, CTX and AK. Transfer frequencies at sub-MIC conditions in a Galleria mellonella were significantly higher than in vitro. To investigate gene expression and metabolic effects, RT-qPCR and LC-MS-based metabolome sequencing were performed. Transcript levels of T4SS genes virB1, virB2, virB4, virB8, and conjugation-related genes traB, traK, traE, and traL were significantly upregulated by exposure to sub-MICs of MEM, CIP, CTX, and AK. Metabolome sequencing revealed nine differentially regulated metabolites. Our findings are an early warning for a wide assessment of the roles of sub-MIC levels of antibiotics in the spread of antibiotic resistance.

Triclosan Promotes Conjugative Transfer of Antibiotic Resistance Genes to Opportunistic Pathogens in Environmental Microbiome

Although triclosan, as a widely used antiseptic chemical, is known to promote the transmission of antibiotic resistance to diverse hosts in pure culture, it is still unclear whether and how triclosan could affect the transmission of broad-host-range plasmids among complex microbial communities. Here, bacterial culturing, fluorescence-based cell sorting, and high-throughput 16S rRNA gene amplicon sequencing were combined to investigate contributions of triclosan on the transfer rate and range of an IncP-type plasmid from a proteobacterial donor to an activated sludge microbiome. Our results demonstrate that triclosan significantly enhances the conjugative transfer of the RP4 plasmid among activated sludge communities at environmentally relevant concentrations. High-throughput 16S rRNA gene sequencing on sorted transconjugants demonstrates that triclosan not only promoted the intergenera transfer but also the intragenera transfer of the RP4 plasmid among activated sludge communities. Moreover, triclosan mediated the transfer of the RP4 plasmid to opportunistic human pathogens, for example, Legionella spp. The mechanism of triclosan-mediated conjugative transfer is primarily associated with excessive oxidative stress, followed by increased membrane permeability and provoked SOS response. Our findings offer insights into the impacts of triclosan on the dissemination of antibiotic resistance in the aquatic environmental microbiome.

How heavy metal stress promotes dissemination of antibiotic resistance genes in the activated sludge process

Heavy metals have been recently revealed as promoters to antibiotic resistance gene (ARG) dissemination in water environment, but their influence on ARG transfer in the activated sludge process has not been clear. In this study, a set of sequencing batch reactors (SBRs) and micro-scale microfluidic chips were established to quantify the impacts of heavy metals (0.5 mM of Pb, 0.1 mM of As, and 0.005 mM of Hg) on the ARG spreading in the activated sludge consortium. Under heavy metal stress, transfer frequencies were 1.7-3.6 folds increase compared to the control. Gram-negative bacteria increased significantly after heavy metal added, which were more prone to receiving resistant plasmid from donors. Meanwhile, the relative expression of genes related to conjugation changed in activated sludge, especially the expression of outer membrane protein and oxidative stress regulatory genes increased by 2.9-7.4 folds and 7.8-13.1 folds, respectively. Furthermore, using microfluidic chips, the dynamics of ARG transfer was observed at single cell level under heavy metal pressure. Heavy metals firstly promoted conjugation and then vertical gene transfer played an important part for ARG spreading. The results provided in-depth understanding of the influence of heavy metals on ARG behavior in the environment.

Increase of antibiotic resistance genes via horizontal transfer in single- and two-chamber microbial electrolysis cells

Microbial electrolysis cells (MECs) have been applied for antibiotic degradation but simultaneously induced antibiotic resistance genes (ARGs), thus representing a risk to disseminate antibiotic resistance. However, few studies were on the potential and risk of ARGs transmission in the MECs. This work assessed conjugative transfer of ARGs under three tested conditions (voltages, cell concentration, and donor/recipient ratio) in both single- and two-chamber MECs. The results indicated that voltages (> 0.9 V) facilitated the horizontal frequency of ARGs in the single-chamber MECs and anode chamber of two-chamber MECs. The donor cell number (donor/recipient ratio was 2:1) increased the transfer frequency of ARGs. Furthermore, voltages ranged from 0.9 to 2.5 V increased reactive oxygen species (ROS) production and cell membrane permeability in MECs. These findings offer new insights into the roles of ARG transfer under different applied voltages in the MECs, which should not be ignored for horizontal transfer of antibiotic resistance.

Gentamicin at sub-inhibitory concentrations selects for antibiotic resistance in the environment

Antibiotics released into the environment at low (sub-inhibitory) concentrations could select for antibiotic resistance that might disseminate to the human microbiome. In this case, low-level anthropogenic sources of antibiotics would have a significant impact on human health risk. In order to provide data necessary for the evaluation of this risk, we implemented river water microcosms at both sub-inhibitory and inhibitory concentrations of gentamicin as determined previously based on bacterial growth in enriched media. Using metagenomic sequencing and qPCR/RT-qPCR, we assessed the effects of gentamicin on water bacterial communities and their resistome. A change in the composition of total and active communities, as well as a gentamicin resistance gene selection identified via mobile genetic elements, was observed during a two-day exposure. We demonstrated the effects of sub-inhibitory concentrations of gentamicin on bacterial communities and their associated resistome in microcosms (simulating in situ conditions). In addition, we established relationships between antibiotic dose and the magnitude of the community response in the environment. The scope of resistance selection under sub-inhibitory concentrations of antibiotics and the mechanisms underlying this process might provide the basis for understanding resistance dispersion and associated risks in relatively low impacted ecosystems.

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.

Do microplastic biofilms promote the evolution and co-selection of antibiotic and metal resistance genes and their associations with bacterial communities under antibiotic and metal pressures?

Microplastic (MP) biofilms with heterogeneous bacterial compositions and structure have become a hotspot of antibiotic resistance genes (ARGs) in aquatic environments. The evolutionary features of ARGs and their related factors including class 1 integron (intI1), metal resistance genes (MRGs), and bacterial communities in MP biofilms under exogenous pressures and how they compared with natural substrates (NS) are unclear. The individual and combined pressures of sulfamethoxazole, tetracycline, and zinc were used to drive the dynamic evolution of ARGs, intI1, MRGs, and bacterial communities in the MP and NS biofilms. The exogenous pressures from the combined selection of sulfamethoxazole, tetracycline, and zinc and their increasing concentrations both significantly enhanced the abundances of ARGs on the MP compared to the NS. Meanwhile, the selective pressures resulted in obvious dissimilarities between the MP and NS bacterial communities. The core bacterial taxa and the co-occurrence patterns of ARGs and bacterial genera in the biofilms of MP and NS were obviously different, and more potential ARG host bacteria selectively colonized the MP. Metal pressure also enhanced the enrichment of ARGs in the MP biofilms by promoting the spread of intI1 via the co-selection mechanism.

Effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of antibiotic resistance genes in water environments: A review

Antibiotic resistance has created obstacles in the treatment of infectious diseases with antibiotics. The horizontal transfer of antibiotic resistance genes (ARGs) can exacerbate the dissemination of antibiotic resistance in water environments. In addition to antibiotic selective pressure, multiple non-antibiotic factors can affect the horizontal transfer of ARGs. Herein, we seek to comprehensively review the effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of ARGs in water environments, especially contaminants from human activities and water treatment processes. Four pathways have been identified to accomplish horizontal gene transfer (HGT), i.e., conjugation, transformation, transduction, and vesiduction. Changes in conjugative frequencies by non-antibiotic factors are mainly related to their concentrations, which conform to hormesis. Relevant mechanisms involve the alteration in cell membrane permeability, reactive oxygen species, SOS response, pilus, and mRNA expression of relevant genes. Transformation induced by extracellular DNA may be more vulnerable to non-antibiotic factors than other pathways. Except bacteriophage infection, the effects of non-antibiotic factors on transduction exhibit many similarities with that of conjugation. Given the secretion of membrane vesicles stimulated by non-antibiotic factors, their effects on vesiduction can be inferred. Furthermore, contaminants from human activities at sub-inhibitory or environmentally relevant concentrations usually promote HGT, resulting in further dissemination of antibiotic resistance. The horizontal transfer of ARGs is difficult to be inhibited by individual water treatment processes (e.g., chlorination, UV treatment, and photocatalysis) unless they attain sufficient intensity. Accordingly, the synergistic application containing two or more water treatment processes is recommended. Overall, we believe this review can elucidate the significance for risk assessments of contaminants from human activities and provide insights into the development of environment-friendly and cost-efficient water treatment processes to inhibit the horizontal transfer of ARGs.

Toxicity impact of hydrogen peroxide on the fate of zebrafish and antibiotic resistant bacteria

Hydrogen peroxide (H₂O₂) is applied in various environments. It could be present at concentrations ranging from nanomolar to micromolar in a water system. It is produced through pollutants and natural activities. Since few studies have been conducted about the impact of naturally produced H₂O₂ on aquatic organisms, the objective of the present study was to monitor changes in responses of aquatic model organisms such as zebrafish and antibiotic-resistant bacteria to different exogenous H₂O₂ exposure. Increases in exposure concentration and time induced decreases in the perception of zebrafish larvae (up to 69%) and movement of adult zebrafish (average speed, average acceleration, movement distance, and activity time) compared to the control (non-exposed group). In addition, as a function of H₂O₂ exposure concentration (0-100,000 nM) and time, up to 20-fold increase (p = 5.00*10^-6) of lipid peroxidation compared to control was observed. For microorganisms, biofilm, an indirect indicator of resistance to external stressors, was increased up to 68% and gene transfer was increased (p = 2.00*10^-6) by more than 30% after H₂O₂ exposure. These results imply that naturally generated H₂O₂ could adversely affect aquatic environment organisms and public health. Thus, more careful attention is needed for H₂O₂ production in an aquatic system.

Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review

The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.

Enhanced removal of sulfamethoxazole and tetracycline in bioretention cells amended with activated carbon and zero-valent iron: System performance and microbial community

Antibiotics, heavily used as medicine, enter the environment inevitably and raise concerns of the risk to the ecosystems. In this study, we explored the removal efficiency and mechanism of sulfamethoxazole (SMX) and tetracycline (TC) in activated carbon (AC) and AC-zero-valent iron amended bioretention cells (AC-BRC and AC-Fe-BRC) compared with a conventional bioretention cell (BRC). Moreover, the system performance of BRCs, the shifts of the microbial community, as well as the fate of corresponding antibiotic resistance genes (ARGs) were comprehensively investigated. The results showed that, exposed to antibiotics notwithstanding, AC-BRC and AC-Fe-BRC significantly outperformed BRC on total nitrogen (TN) removal (BRC: 70.36 ± 13.61%; AC-BRC: 91.43 ± 6.41%; AC-Fe-BRC: 83.44 ± 12.13%). Greater than 97% of the total phosphorous (TP) was removed in AC-Fe-BRC, remaining unimpacted despite of the selective pressure from SMX/TC. Excellent removals of antibiotics (above 99%) were achieved in AC-BRC and AC-Fe-BRC regardless of the types and initial concentrations (0.8 mg/L, 1.2 mg/L and 1.6 mg/L) of antibiotics, dwarfing the removal performance of BRC (12.2 ± 4.4%-64.2 ± 5.5%). The illumina high throughput sequencing analysis demonstrated the concomitant variations of microbial communities as SMX/TC was loaded. AC layers tended to alleviate the adverse effect of SMX/TC on microbial biodiversity. Proteobacteria (34.55-68.47%), Chloroflexi (7.13-33.54%), and Bacteroidetes (6.20-21.03%) were the top three dominant phyla in the anaerobic zone of the BRCs. The abundance of antibiotic resistance genes (ARGs) sulI, sulII and tetA genes were dramatically higher in AC-BRC and AC-Fe-BRC when exposed to 0.8 mg/L SMX/TC, which indicated that relatively low concentrations of SMX/TC induced the production of these three ARGs in the presence of AC. Although the amendment of AC led to highly efficient SMX/TC removals, further investigation is still required to improve the retention of ARGs in BRCs.

Abundance and Dynamic Distribution of Antibiotic Resistance Genes in the Environment Surrounding a Veterinary Antibiotic Manufacturing Site

Background: Antibiotics releasing from the manufacturing sites to the surrounding environment has been identified as a risk factor for the development of antibiotic resistance of bacterial pathogens. However, the knowledge of the abundance and distribution of antibiotic resistance genes (ARGs) influenced by antibiotic pollution is still limited. Methods: In this work, the contamination by resistance genes of the environmental media including an urban river and soil along the river located near the sewage outlet of a veterinary antibiotic manufacturing site in Shijiazhuang, China, was assessed. The abundance and dynamic distribution of ARGs in different sampling points and during different seasons were analyzed using fluorescent quantitative PCR method (qPCR). Results: A total of 11 resistance genes, one integron and one transposon were detected in water and soils around the pharmaceutical factory, and among which, the sulfonamide resistance genes sul1 and β-lactam resistance genes blaSHV were the most abundant genes. The relative abundance of ARGs in both river water and soil samples collected at the downstream of the sewage outlet was higher than that of samples collected at the upstream, non-polluted areas (p < 0.05). The mobile genetic elements (MGEs) integron in river was significantly correlated (p < 0.05) with the relative abundance of ARGs. Conclusions: The results indicate that the discharge of waste from antibiotic manufacturing site may pose a risk of horizontal transfer of ARGs.

Functionalized magnetite nanoparticles with Moringa oleifera with potent antibacterial action in wastewater

Contaminations by Staphylococcus aureus in food industry environments have been extended to industrial Effluent Treatment Plant (ETP). The methodologies used in ETP for bacterial removals and quality parameters adjustment commonly use products toxic to the environment, being mostly inefficient against virulent bacteria such as S. aureus. Seeds of Moringa oleifera Lam. (MO) have potential to be used in ETP as an alternative to harmful products, as it has both the ability to regulate the physicochemical parameters of water and has antibacterial action. Functionalization of MO with magnetite magnetic nano particles (Fe₃O₄) at nano scale focusing on coagulation and flocculation of wastewater has been gaining prominence. Therefore, the present study evaluated the potential use of the magnetic coagulant MO-Fe₃O₄ in the elimination of S. aureus in synthetic dairy effluent; concomitantly sought to adjust the quality levels of physicochemical parameters. MO-Fe₃O₄ added to synthetic dairy effluent at different concentrations amounted to 16 treatments, which were evaluated for removal of color, turbidity, UV_254nm and S. aureus on the effluent surface and sludge after 30 min of sedimentation. The results confirmed the efficient elimination of S. aureus simultaneously with a significant reduction of the physicochemical values, with constant efficiency up to 30 min. Scanning electron microscopy images confirm the removal of S. aureus on the effluent surface and sludge. Thus, this study was able to present a natural coagulant capable of remove bacteria and adjust the quality levels of the effluent after 10 min of sedimentation, making this biotechnological innovation highly applicable to ETP.

Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges

Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in molecular biology has revealed new and significant challenges for AMR mitigation given the immense diversity of antibiotic resistance genes (ARGs), the complexity of ARG transfer, and the broad range of omnipresent factors contributing to AMR. Municipal, hospital and abattoir wastewater are collected and treated in wastewater treatment plants (WWTPs), where the presence of diverse selection pressures together with a highly concentrated consortium of pathogenic/commensal microbes create favourable conditions for the transfer of ARGs and proliferation of antibiotic resistant bacteria (ARB). The rapid emergence of antibiotic resistant pathogens of clinical and veterinary significance over the past 80 years has re-defined the role of WWTPs as a focal point in the fight against AMR. By reviewing the occurrence of ARGs in wastewater and sludge and the current technologies used to quantify ARGs and identify ARB, this paper provides a research roadmap to address existing challenges in AMR control via wastewater treatment. Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. State of the art ARB identification technologies, such as metagenomic sequencing and fluorescence-activated cell sorting, have enriched ARG/ARB databases, unveiled keystone species in AMR networks, and improved the resolution of AMR dissemination models. Data and information provided in this review highlight significant knowledge gaps. These include inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment. This is due to a lack of standard monitoring targets and agreed threshold values, and paucity of information on the ARG-pathogen host relationship and risk management. These research gaps need to be addressed and research findings need to be transformed into practical guidance for WWTP operators to enable effective progress towards mitigating the evolution and spread of AMR.

Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

Background

Klebsiella pneumoniae, as a global priority pathogen, is well known for its capability of acquiring mobile genetic elements that carry resistance and/or virulence genes. Its virulence plasmid, previously deemed nonconjugative and restricted within hypervirulent K. pneumoniae (hvKP), has disseminated into classic K. pneumoniae (cKP), particularly carbapenem-resistant K. pneumoniae (CRKP), which poses alarming challenges to public health. However, the mechanism underlying its transfer from hvKP to CRKP is unclear.

Methods

A total of 28 sequence type (ST) 11 bloodstream infection-causing CRKP strains were collected from Ruijin Hospital in Shanghai, China, and used as recipients in conjugation assays. Transconjugants obtained from conjugation assays were confirmed by XbaI and S1 nuclease pulsed-field gel electrophoresis, PCR detection and/or whole-genome sequencing. The plasmid stability of the transconjugants was evaluated by serial culture. Genetically modified strains and constructed mimic virulence plasmids were employed to investigate the mechanisms underlying mobilization. The level of extracellular polysaccharides was measured by mucoviscosity assays and uronic acid quantification. An in silico analysis of 2608 plasmids derived from 814 completely sequenced K. pneumoniae strains available in GenBank was performed to investigate the distribution of putative helper plasmids and mobilizable virulence plasmids.

Results

A nonconjugative virulence plasmid was mobilized by the conjugative plasmid belonging to incompatibility group F (IncF) from the hvKP strain into ST11 CRKP strains under low extracellular polysaccharide-producing conditions or by employing intermediate E. coli strains. The virulence plasmid was mobilized via four modes: transfer alone, cotransfer with the conjugative IncF plasmid, hybrid plasmid formation due to two rounds of single-strand exchanges at specific 28-bp fusion sites or homologous recombination. According to the in silico analysis, 31.8% (242) of the putative helper plasmids and 98.8% (84/85) of the virulence plasmids carry the 28-bp fusion site. All virulence plasmids carry the origin of the transfer site.

Conclusions

The nonconjugative virulence plasmid in ST11 CRKP strains is putatively mobilized from hvKP or E. coli intermediates with the help of conjugative IncF plasmids. Our findings emphasize the importance of raising public awareness of the rapid dissemination of virulence plasmids and the consistent emergence of hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) strains.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00936-5.

Evaluation of Metagenomic-Enabled Antibiotic Resistance Surveillance at a Conventional Wastewater Treatment Plant

Wastewater treatment plants (WWTPs) receive a confluence of sewage containing antimicrobials, antibiotic resistant bacteria, antibiotic resistance genes (ARGs), and pathogens and thus are a key point of interest for antibiotic resistance surveillance. WWTP monitoring has the potential to inform with respect to the antibiotic resistance status of the community served as well as the potential for ARGs to escape treatment. However, there is lack of agreement regarding suitable sampling frequencies and monitoring targets to facilitate comparison within and among individual WWTPs. The objective of this study was to comprehensively evaluate patterns in metagenomic-derived indicators of antibiotic resistance through various stages of treatment at a conventional WWTP for the purpose of informing local monitoring approaches that are also informative for global comparison. Relative abundance of total ARGs decreased by ∼50% from the influent to the effluent, with each sampling location defined by a unique resistome (i.e., total ARG) composition. However, 90% of the ARGs found in the effluent were also detected in the influent, while the effluent ARG-pathogen taxonomic linkage patterns identified in assembled metagenomes were more similar to patterns in regional clinical surveillance data than the patterns identified in the influent. Analysis of core and discriminatory resistomes and general ARG trends across the eight sampling events (i.e., tendency to be removed, increase, decrease, or be found in the effluent only), along with quantification of ARGs of clinical concern, aided in identifying candidate ARGs for surveillance. Relative resistome risk characterization further provided a comprehensive metric for predicting the relative mobility of ARGs and likelihood of being carried in pathogens and can help to prioritize where to focus future monitoring and mitigation. Most antibiotics that were subject to regional resistance testing were also found in the WWTP, with the total antibiotic load decreasing by ∼40–50%, but no strong correlations were found between antibiotics and corresponding ARGs. Overall, this study provides insight into how metagenomic data can be collected and analyzed for surveillance of antibiotic resistance at WWTPs, suggesting that effluent is a beneficial monitoring point with relevance both to the local clinical condition and for assessing efficacy of wastewater treatment in reducing risk of disseminating antibiotic resistance.

Understanding of the mechanism of extracellular polymeric substances of aerobic granular sludge against tetracycline from the perspective of fluorescence properties

Aerobic granular sludge (AGS) exhibited an excellent removal efficiency and a high tolerance in the treatment of antibiotics wastewater. Extracellular polymeric substances (EPS) of AGS with abundant binding sites might serve as the first barrier to prevent the direct contact of antibiotics and cells, thereby keeping the stability of AGS. In this study, the investigations in the fluorescence properties and the molecular weight of AGS-EPS after interaction with tetracycline (TC) were combined to reveal the resistance mechanism of AGS-EPS against TC. The two-dimensional correlation spectroscopy (2D-COS) was utilized to analyze the interaction priority of the AGS-EPS components with TC. Results showed that TC interacted with proteins and humic acid in AGS-EPS by forming a complex through hydrogen bond and van der Waals force. Compared with humic acid, TC could preferentially interact with proteins and form more stable complexes. Moreover, the components with the larger molecular weight in AGS-EPS interact with TC prior to which with smaller molecular weight. Significantly, TC exhibited the potential of binding with the divalent cation of AGS-EPS and caused the conformation changes of the protein. Therefore, AGS-EPS could resist the TC at a certain concentration range by trapping antibiotics, while over-loaded TC would cause the instability of AGS due to the limited interaction site of AGS-EPS and the destructive effect of antibiotics on AGS-EPS. This study provided a theoretical basis for understanding the interaction mechanism between antibiotics and AGS-EPS and offered a reference for AGS to maintain the stability of granules under the threat of antibiotics.

Selection of Resistant Bacteria in Mallards Exposed to Subinhibitory Concentrations of Ciprofloxacin in Their Water Environment

Emergence and selection of antibiotic resistance following exposure to high antibiotic concentrations have been repeatedly shown in clinical and agricultural settings, whereas the role of the weak selective pressures exerted by antibiotic levels below the MIC (sub-MIC) in aquatic environments due to anthropogenic contamination remains unclear. Here, we studied how exposure to sub-MIC levels of ciprofloxacin enriches for Escherichia coli with reduced susceptibility to ciprofloxacin using a mallard colonization model. Mallards were inoculated with two isogenic extended-spectrum-β-lactamase (ESBL)-encoding E. coli strains, differing only by a gyrA mutation that results in increased MICs of ciprofloxacin, and exposed to different levels of ciprofloxacin in their swimming water. Changes in the ratios of mutant to parental strains excreted in feces over time and ESBL plasmid spread within the gut microbiota from individual birds were investigated. Results show that in vivo selection of gyrA mutants occurred in mallards during exposure to ciprofloxacin at concentrations previously found in aquatic environments. During colonization, resistance plasmids were readily transferred between strains in the intestines of the mallards, but conjugation frequencies were not affected by ciprofloxacin exposure. Our results highlight the potential for enrichment of resistant bacteria in wildlife and underline the importance of reducing antibiotic pollution in the environment.

Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level

Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.

Adding a complex microbial agent twice to the composting of laying-hen manure promoted doxycycline degradation with a low risk on spreading tetracycline resistance genes

Poultry manure is a reservoir for antibiotics and antibiotic resistance genes and composting is an effective biological treatment for manure. This study explored the effect of using two methods of adding a complex microbial agent to the composting of laying-hen manure on doxycycline degradation and tetracycline resistance genes elimination. The results showed that incorporating a complex microbial agent at 0.8% (w/w) on the 0^th and 11th day (group MT2) effectively degraded doxycycline with a final degradation rate of 46.83 ± 0.55%. The half-life of doxycycline in this group was 21.90 ± 0.00 days and was significantly lower than that of group MT1 (1.6% (w/w) complex microbial agent added on the 0^th day) and group DT (compost without complex microbial agent). But there was no significant difference in the final degradation rate of doxycycline between group DT and group MT1. The addictive with the complex microbial agent changed the microbial community structure. Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla during composting. Aerococcus, Desemzia, Facklamia, Lactobacillus, Streptococcus, and Trichococcus were the bacteria related to the degradation of doxycycline. Moreover, the incorporation of a complex microbial agent could decrease the risk on spreading tetracycline resistance genes. The single addition promoted the elimination of tetM, whose possible hosts were Enterococcus, Lactobacillus, Staphylococcus, and Trichococcus. Adding the complex microbial agent twice promoted the elimination of tetX, which was related to the low abundance of Chryseobacterium, Flavobacterium and Neptunomonas in group MT2. Redundancy analysis showed that the bacterial community, residual doxycycline and physiochemical properties have a potential effect on the variation in tetracycline resistance genes levels. Overall, adding the complex microbial agent twice is an effective measure to degrade doxycycline.

Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland)

As small, mobilizable replicons with a broad host range, IncQ plasmids are widely distributed among clinical and environmental bacteria. They carry antibiotic resistance genes, and it has been shown that they confer resistance to β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, sulphonamides, and tetracycline. The previously proposed classification system divides the plasmid group into four subgroups, i.e., IncQ-1, IncQ-2, IncQ-3, and IncQ-4. The last two subgroups have been poorly described so far. The aim of this study was to analyze five newly identified IncQ-3 plasmids isolated from a wastewater treatment plant in Poland and to compare them with all known plasmids belonging to the IncQ-3 subgroup whose sequences were retrieved from the NCBI database. The complete nucleotide sequences of the novel plasmids were annotated and bioinformatic analyses were performed, including identification of core genes and auxiliary genetic load. Furthermore, functional experiments testing plasmid mobility were carried out. Phylogenetic analysis based on three core genes (repA, mobA/repB, and mobC) revealed the presence of three main clusters of IncQ-3 replicons. Apart from having a highly conserved core, the analyzed IncQ-3 plasmids were vectors of antibiotic resistance genes, including (I) the qnrS2 gene that encodes fluoroquinolone resistance and (II) β-lactam, trimethoprim, and aminoglycoside resistance genes within integron cassettes.

New parameters for the quantitative assessment of the proliferation of antibiotic resistance genes dynamic in the environment and its application: A case of sulfonamides and sulfonamide resistance genes

Antibiotic resistance genes (ARGs) have been widely detected around the world and are generally viewed as emerging pollutants with environmental persistence. The proliferation of ARGs can be easily promoted by antibiotics. However, the dynamics of ARGs in the environment are still unable to be quantified using a single parameter, which is vital to evaluating the ability of ARGs to spread by antibiotics and effectively controlling ARGs. A new parameter, termed the relative area ratio of sample to control (ΔA^R), was developed based on the quantitative features determined by ARG-time curves in soils contaminated with sulfonamides (SAs) and verified by quantitative structure-activity relationships (QSARs) models. The results showed that ΔA^R can not only be used to accurately quantify the characteristics of SAs resistance genes (Suls) over time but also be applied to reveal the relationships between the proliferation of Suls and important factors (i.e., concentrations and chemical structures). Moreover, the ΔA^R-based QSARs model indicated that bioavailability and the frequency of conjugative transfer, rather than the ability of induced mutations in bacteria, tend to be key processes of the characteristics of the proliferation of Suls. Therefore, ΔA^R is a useful parameter to perform environmental risk assessments of ARG proliferation in the environment.

Removal of antibiotic resistance genes in an algal-based wastewater treatment system employing Galdieria sulphuraria: A comparative study

In this study, we compared removal of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in two wastewater treatment systems fed with the same primary effluent: a conventional wastewater treatment system (consisting of a trickling filter followed by an activated sludge process) versus an algal-based system, employing an extremophilic alga, Galdieria sulphuraria. Our results demonstrated that the algal system can reduce concentrations of erythromycin- and sulfamethoxazole-resistant bacteria in the effluent more effectively than the conventional treatment system. A decreasing trend of total bacteria and ARGs was observed in both the treatment systems. However, the relative ratio of most ARGs (qnrA, qnrB, qnrS, sul1) and intI1 in the surviving bacteria increased in the conventional system; whereas, the algal system reduced more of the relative abundance of qnrA, qnrS, tetW and intⅠ1 in the surviving bacteria. The role of bacteriophages in horizontal gene transfer (HGT) of ARGs in the two systems was indicated by a positive correlation between ARG absolute abundance in bacteriophage and ARG relative abundance in the bacteria. Four of the five detectable genes (qnrS, tetW, sul1 and intI1) were significantly reduced in the algal system in bacteriophage phase which signified a decrease in phage-mediated ARG transfer in the algal system. Results of this study demonstrate the feasibility of the algal-based wastewater treatment system in decreasing ARGs and ARB and in minimizing the spread of antibiotic resistance to the environment.

Constructed Wetland Revealed Efficient Sulfamethoxazole Removal but Enhanced the Spread of Antibiotic Resistance Genes

Constructed wetlands (CWs) could achieve high removal efficiency of antibiotics, but probably stimulate the spread of antibiotic resistance genes (ARGs). In this study, four CWs were established to treat synthetic wastewater containing sulfamethoxazole (SMX). SMX elimination efficiencies, SMX degradation mechanisms, dynamic fates of ARGs, and bacterial communities were evaluated during the treatment period (360 day). Throughout the whole study, the concentration of SMX in the effluent gradually increased (p < 0.05), but in general, the removal efficiency of SMX remained at a very high level (>98%). In addition, the concentration of SMX in the bottom layer was higher compared with that in the surface layer. The main byproducts of SMX degradation were found to be 4-amino benzene sulfinic acid, 3-amino-5-methylisoxazole, benzenethiol, and 3-hydroxybutan-1-aminium. Temporally speaking, an obvious increase of sul genes was observed, along with the increase of SMX concentration in the bottom and middle layers of CWs. Spatially speaking, the concentration of sul genes increased from the surface layer to the bottom layer.

Antibiotics and their alternatives in Artificial Breeding in livestock

Antibiotics are mandatory components of semen extenders for the control of bacterial contamination and growth. The increasing rate of worldwide resistance to conventional antibiotics in semen preservation media requires the development of new antimicrobial alternatives. This review provides an update on this topic and also highlights the improvement of hygiene in Artificial Insemination centers in order to prevent the development of bacterial resistance. Ideas are shared on future diagnostic tools for bacterial contamination in Artificial Breeding. Finally, new methods to remove or reduce bacteria in semen will be discussed.

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant

This study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr-1) and integron (intI) through a distributed swine wastewater purification facility and the effluent-receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs' prevalence. 3.1 × 10⁴ -7.1 × 10⁸  copies/L were present after purification, and 4%-57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co-occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs' abundance, but negatively correlated to their relative abundance. PRACTITIONER POINTS: Fate of five ARGs and intI was studied in a swine wastewater treatment system. The treatment process could not effectively reduce ARGs' abundance. ARGs and pathogens in wastewater were transferred to the receiving creek and soil. The network analysis found wide co-occurrence among ARGs, metal resistance genes, and pathogens. Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.

Dissecting horizontal and vertical gene transfer of antibiotic resistance plasmid in bacterial community using microfluidics

The spread of antibiotic resistance genes (ARGs) has become an emerging threat to the global health. Although horizontal gene transfer (HGT) is regarded as one of the major pathways, more evidence has shown the significant involvement of vertical gene transfer (VGT). However, traditional cultivation-based methods cannot distinguish HGT and VGT, resulting in often contradictory conclusions. Here, single-cell microfluidics with time-lapse imaging has been successfully employed to dissect the contribution of plasmid-mediated HGT and VGT to ARG transmission in an environmental community. Using Escherichia coli with an ARG-coded plasmid pKJK5 with trimethoprim resistance as the donor, we quantified the effects of three representative antibiotics (trimethoprim, tetracycline and amoxicillin) on the ARG transfer process in an activated sludge bacterial community. It was found that HGT was influenced by the inhibitory mechanism of an antibiotic and its targets (donor, recipient alone or together), whereas VGT contributes significantly to the formation of transconjugants and consequently ARG spreading. Trimethoprim is highly resisted by the donor and transconjugants, and its presence significantly increased both the HGT and VGT rates. Although tetracycline and amoxicillin both inhibit the donor, they showed different effects on HGT rate as a result of different inhibitory mechanisms. Furthermore, we show the kinetics of HGT in a community can be described using an epidemic infection model, which in combination with quantitative measure of HGT and VGT on chip provides a promising tool to study and predict the dynamics of ARG spread in real-world communities.

Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments

High antibiotic releases from manufacturing facilities have been identified as a risk factor for antibiotic resistance development in bacterial pathogens. However, the role of antibiotic pollution in selection and transferability of antibiotic resistance genes (ARGs) is still limited. In this study, we analyzed effluents from azithromycin-synthesis and veterinary-drug formulation facilities as well as sediments from receiving river and creek taken at the effluent discharge sites, upstream and downstream of discharge. Culturing showed that the effluent discharge significantly increased the proportion of antibiotic resistant bacteria in exposed sediments compared to the upstream ones. Quantitative real-time PCR revealed that effluents from both industries contained high and similar relative abundances of resistance genes [sul1, sul2, qacE/qacEΔ1, tet(A)], class 1 integrons (intI1) and IncP-1 plasmids (korB). Consequently, these genes significantly increased in relative abundances in receiving sediments, with more pronounced effects being observed for river than for creek sediments due to lower background levels of the investigated genes in the river. In addition, effluent discharge considerably increased transfer frequencies of captured ARGs from exposed sediments into Escherichia coli CV601 recipient as shown by biparental mating experiments. Most plasmids exogenously captured from effluent and polluted sediments belonged to the broad host range IncP-1ε plasmid group, conferred multiple antibiotic resistance and harbored class 1 integrons. Discharge of pharmaceutical waste from antibiotic manufacturing sites thus poses a risk for development and dissemination of multi-resistant bacteria, including pathogens.

Inhibition of methanogens decreased sulfadiazine removal and increased antibiotic resistance gene development in microbial fuel cells

The aim of this work was to study sulfadiazine (SDZ) biodegradation efficiency, antibiotic resistance genes (ARGs) development and shift of microbial communities under conditions of limited methanogens activity in Microbial fuel cells (MFCs). The results indicated that the removal performance of SDZ was decreased with the suppression of methanogens in both MFCs and open-circuit controls. The relative abundances of ARGs were even enhanced by the inhibition of methanogens. The biodegradation mechanism of SDZ was obtained, in which SDZ was initially divided into aniline and pyrimidin-2ylsulfamic acid, then converted into small molecules. Geobacter was found as the dominant microorganism, indicating its potential to degrade SDZ in the MFCs. These findings suggest there is a trade-off between electricity production and SDZ removal and ARG development by the mean of methanogen inhibition in MFCs.

A novel microfluidic system enables visualization and analysis of antibiotic resistance gene transfer to activated sludge bacteria in biofilm

Antibiotic resistance genes (ARGs) in environment have become a growing public concern, due to their potential to be obtained by pathogens and their duplication along cell division. Horizontal gene transfer (HGT) was reported to be responsible for ARGs dissemination in microbes, but the HGT feature in environmental biofilm was still unclear due to insufficient assay tools. To address this challenge, we applied a novel microfluidic system to cultivate thin biofilm by continuous supply of nutrients and close contact between cells. Resembling the living state of biofilm in open environment, this chip visualized the transfer of ARG-encoded plasmids RP4 and pKJK5 to the receptors, e.g., activated sludge bacteria. The average plasmid transfer frequency per receptor (T/R) from RP4-hosted Pseudomonas putida KT2440 to activated sludge bacteria was quantified to be 2.5 × 10^-3 via flow cytometry, and T/R for pKJK5-hosted Escherichia coli MG1655 was 8.9 × 10^-3, while the corresponding average frequencies per donor (T/D) were diverse for the two host strains as 4.3 × 10^-3 and 1.4 × 10^-1 respectively. The difference between T/R and T/D was explained by the plasmid transfer kinetics, implying specific purposes of the two calculations. Finally, we collected the transconjugants by fluorescent activated cell sorting and further sequenced their 16S rDNA. Bacteria from phyla Proteobacteria and Firmicutes were found more susceptible to be transconjugants than those from Bacteroidetes. Our work demonstrated that microfluidic system was advantageous in biofilm HGT study, which can provide more insights into environmental ARG control.

Antibiotic resistance genes and intI1 prevalence in a swine wastewater treatment plant and correlation with metal resistance, bacterial community and wastewater parameters

The livestock wastewater treatment plant represents an important reservoir of antibiotic resistance determinants in the environment. The study explored the prevalence of five antibiotic resistance genes (ARGs, including sulI, tetA, qnrD, mphB and mcr-1) and class 1 integron (intI1) in a typical livestock wastewater treatment plant, and analyzed their integrated association with two metal resistance genes (copA and czcA), two pathogens genes (Staphylococcus and Campylobacter), bacterial community and wastewater properties. Results indicated that all investigated genes were detected in the plant. The treatment plant could not completely remove ARGs abundances, with up to 2.2 × 10⁴~3.7 × 10⁸ copies/L of them remaining in the effluent. Mcr-1 was further enriched by 27-fold in the subsequent pond. The correlation analysis showed that mphB significantly correlateed with tetA and intI. Mcr-1 strongly correlated with copA. MphB and intI significantly correlated with czcA. The correlations implied a potential co-selection risk of bacterial resistant to antibiotics and metals. Redundancy analyses indicated that qnrD and mcr-1 strongly correlated with 13 and 14 bacterial genera, respectively. Most ARGs positively correlated to wastewater nutrients, indicating that an efficient reduction of wastewater nutrients would contribute to the antibiotic resistance control. The study will provide useful implications on fates and reductions of ARGs in livestock facilities and receiving environments.

Physicochemical Factors That Favor Conjugation of an Antibiotic Resistant Plasmid in Non-growing Bacterial Cultures in the Absence and Presence of Antibiotics

Horizontal gene transfer (HGT) of antibiotic resistance genes has received increased scrutiny from the scientific community in recent years owing to the public health threat associated with antibiotic resistant bacteria. Most studies have examined HGT in growing cultures. We examined conjugation in growing and non-growing cultures of E. coli using a conjugative multi antibiotic and metal resistant plasmid to determine physiochemical parameters that favor horizontal gene transfer. The conjugation frequency in growing and non-growing cultures was generally greater under shaken than non-shaken conditions, presumably due to increased frequency of cell collisions. Non-growing cultures in 9.1 mM NaCl had a similar conjugation frequency to that of growing cultures in Luria-Bertaini broth, whereas those in 1 mM or 90.1 mM NaCl were much lower. This salinity effect on conjugation was attributed to differences in cell-cell interactions and conformational changes in cell surface macromolecules. In the presence of antibiotics, the conjugation frequencies of growing cultures did not increase, but in non-growing cultures of 9.1 mM NaCl supplemented with Cefotaxime the conjugation frequency was as much as nine times greater than that of growing cultures. The mechanism responsible for the increased conjugation in non-growing bacteria was attributed to the likely lack of penicillin-binding protein 3 (the target of Cefotaxime), in non-growing cells that enabled Cefotaxime to interact with the plasmid and induce conjugation. Our results suggests that more attention may be owed to HGT in non-growing bacteria as most bacteria in the environment are likely not growing and the proposed mechanism for increased conjugation may not be unique to the bacteria/plasmid system we studied.

Effect of UVA/LED/TiO2 photocatalysis treated sulfamethoxazole and trimethoprim containing wastewater on antibiotic resistance development in sequencing batch reactors

Controlling of antibiotics is the crucial step for preventing antibiotic resistance genes (ARGs) dissemination; UV photocatalysis has been identified as a promising pre-treatment technology for antibiotics removal. However, information about the effects of intermediates present in the treated antibiotics wastewater on the downstream biological treatment processes or ARGs development is very limited. In the present study, continuous UVA/LED/TiO₂ photocatalysis removed more than 90% of 100 ppb sulfamethoxazole (SMX)/trimethoprim (TMP), the treated wastewater was fed into SBR systems for over one year monitoring. Residual SMX/TMP (2-3 ppb) and intermediates present in the treated wastewater did not adversely affect SBR performance in terms of TOC and TN removal. SMX and TMP resistance genes (sulI, sulII, sulIII, dfrII, dfrV and dfr13) were also quantified in SBRs microbial consortia. Results suggested that continuous feeding of treated SMX/TMP containing wastewaters did not trigger any ARGs promotion during the one year operation. By stopping the input of 100 ppb SMX/TMP, abundance of sulII and dfrV genes were reduced by 83% and 100%, respectively. sulI gene was identified as the most persistence ARG, and controlling of 100 ppb SMX input did not achieve significant removal of sulI gene. A significant correlation between sulI gene and class 1 integrons was found at the level of p = 1.4E-10 (r = 0.94), and sulII gene positively correlated with the plasmid transfer efficiency (r = 2.442E-10, r = 0.87). Continuous input of 100 ppb SMX enhanced plasmid transfer efficiency in the SBR system, resulting in sulII gene abundance increasing more than 40 times.

Seasonal Changes in Antibiotic Resistance Genes in Rivers and Reservoirs in South Korea

The fate of antibiotic resistance genes (ARGs) in aquatic environments, especially in rivers and reservoirs, is receiving growing attention in South Korea because reservoirs are an important source of drinking water in this country. Seasonal changes in the abundance of 11 ARGs and a mobile genetic element () in two reservoirs in South Korea, located near drinking water treatment plants in Cheonan and Cheongju cities, were monitored for 6 mo. In these drinking water sources, total ARG concentrations reached 2.5 × 10 copies mL, which is one order of magnitude higher than in influents of some wastewater treatment plants in South Korea. During the sampling periods in August, October, and November 2016 and January 2017, sulfonamides (), β-lactam antibiotics (), and tetracycline () resistance genes were the most abundant genes at the two sites. The ARG abundance consistently increased in January relative to 16S ribosomal ribonucleic acid (rRNA) counts. General stress responses to oxidative stress and other environmental factors associated with the cold season could be significant drivers of ARG horizontal gene transfer in the environment. Accordingly, removal of ARGs as a key step in water treatment warrants more attention.

The occurrence, maintenance, and proliferation of antibiotic resistance genes (ARGs) in the environment: influencing factors, mechanisms, and elimination strategies

Here, we review the possible reasons responsible for the occurrence, maintenance and proliferation of antibiotic resistance genes (ARGs) in the environment, as well as the corresponding mechanisms of their development, diffusion and transfer. Additionally, elimination strategies are also discussed. The factors that influence the development of ARGs are selection pressure, including that from antibiotics, metal and multiple other factors, co-resistance and cross-resistance, microbial consortium structure, nutrients in the environment and oxidative stress responses. Process parameters, transport pathways, and elimination strategies to reduce the health risk caused by ARGs are also reviewed in detail. Moreover, knowledge gaps and future opportunities of ARGs are addressed.

Vertical up-flow constructed wetlands exhibited efficient antibiotic removal but induced antibiotic resistance genes in effluent

The intensive use of antibiotics results in their continuous release into the environment and the subsequent widespread dissemination of antibiotic resistance genes (ARGs), thus posing potential risks for public health. Although vertical up-flow constructed wetlands (VUF-CWs) have been widely used to treat wastewater in remote or rural regions, few studies have assessed the potential risks of ARG dissemination when VUF-CWs are applied to treat wastewaters containing antibiotics. In this study, the removal performance of two typical antibiotics (sulfamethoxazole (SMX) and tetracycline (TC)) and the fate of ARGs were evaluated in three lab-scale VUF-CWs. The results indicated that high removal efficiencies (>98%) could be achieved for both SMX and TC. However, the exposure of antibiotics resulted in harboring abundant ARGs (mainly sul- and tet-related genes), even with increasing abundances with operation time. The abundances of ARGs had a positive correlation with the accumulation of SMX and TC in different layers of VUF-CWs, where the tet and sul genes have the highest abundance in the bottom layer due to the highest antibiotic exposure concentration. Positive correlations were observed between the abundance of tet gene and antibiotic concentration in effluent. Although the effluent had lower abundances of the ARGs than that in the wetland media, the occurrence of ARGs in effluent might still pose risk for public health. Further studies are required to explore effective control strategies to eliminate ARGs from VUF-CWs.