Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant

Use of reclaimed municipal wastewater in agriculture: Comparison of present practice versus an emerging paradigm of anaerobic membrane bioreactor treatment coupled with hydroponic controlled environment agriculture

Advancements in anaerobic membrane bioreactor (AnMBR) technology have opened up exciting possibilities for sustaining precise water quality control in wastewater treatment and reuse. This approach not only presents an opportunity for energy generation and recovery but also produces an effluent that can serve as a valuable nutrient source for crop cultivation in hydroponic controlled environment agriculture (CEA). In this perspective article, we undertake a comparative analysis of two approaches to municipal wastewater utilization in agriculture. The conventional method, rooted in established practices of conventional activated sludge (CAS) wastewater treatment for soil/land-based agriculture, is contrasted with a new paradigm that integrates AnMBR technology with hydroponic (soilless) CEA. This work encompasses various facets, including wastewater treatment efficiency, effluent quality, resource recovery, and sustainability metrics. By juxtaposing the established methodologies with this emerging synergistic model, this work aims to shed light on the transformative potential of the integration of AnMBR and hydroponic-CEA for enhanced agricultural sustainability and resource utilization.

Presence and Persistence of ESKAPEE Bacteria before and after Hospital Wastewater Treatment

The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February to March 2020. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize bacterial abundance and antimicrobial resistance gene analysis. The main bacterial phyla found in all the samples were as follows: Proteobacteria, Bacteroides, Firmicutes, and Actinobacteria. At the species level, ESKAPEE bacteria such as E. coli relative abundance decreased between raw and treated wastewater, but S. aureus, A. baumannii, and P. aeruginosa increased, as did the persistence of K. pneumoniae in both raw and treated wastewater. A total of 172 different ARGs were detected; blaOXA, blaVEB, blaKPC, blaGES, mphE, mef, erm, msrE, AAC(6'), ant(3″), aadS, lnu, PBP-2, dfrA, vanA-G, tet, and sul were found at the highest abundance and persistence. This study demonstrates the ability of ESKAPEE bacteria to survive tertiary treatment processes of hospital wastewater, as well as the persistence of clinically important antimicrobial resistance genes that are spreading in the environment.

A review focusing on mechanisms and ecological risks of enrichment and propagation of antibiotic resistance genes and mobile genetic elements by microplastic biofilms

Microplastics (MPs) are emerging ubiquitous pollutants in aquatic environment and have received extensive global attention. In addition to the traditional studies related to the toxicity of MPs and their carrier effects, their unique surface-induced biofilm formation also increases the ecotoxicity potential of MPs from multiple perspectives. In this review, the ecological risks of MPs biofilms were summarized and assessed in detail from several aspects, including the formation and factors affecting the development of MPs biofilms, the selective enrichment and propagation mechanisms of current pollution status of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in MPs biofilms, the dominant bacterial communities in MPs biofilms, as well as the potential risks of ARGs and MGEs transferring from MPs biofilms to aquatic organisms. On this basis, this paper also put forward the inadequacy and prospects of the current research and revealed that the MGEs-mediated ARG propagation on MPs under actual environmental conditions and the ecological risk of the transmission of ARGs and MGEs to aquatic organisms and human beings are hot spots for future research. Relevant research from the perspective of MPs biofilm should be carried out as soon as possible to provide support for the ecological pollution prevention and control of MPs.

Prevalence of antibiotics, antibiotic resistance genes, and their associations in municipal wastewater treatment plants along the Yangtze River basin, China

The overuse and misuse of antibiotics have resulted in the pollution of antibiotics and antibiotic resistance genes (ARGs) in municipal wastewater treatment plants (WWTPs), posing threats to ecological security and human health. Thus, a comprehensive investigation was conducted to assess the occurrence, removal efficiency, and ecological risk of antibiotics, along with the diversity, abundance, and co-occurrence of ARGs, and their correlations in 13 WWTPs along the Yangtze River Basin. Among 35 target antibiotics, 23 antibiotics within 6 categories were detected in all the samples. Amoxicillin (AMO), ofloxacin (OFL), and pefloxacin (PEF) were predominant in influents, while AMO exhibited dominance with the highest concentration of 1409 ng/L in effluents. Although antibiotic removal performance varied among different WWTPs, a significant decrease in each antibiotic category and overall antibiotics was observed in effluents compared with that in influents (p < 0.05). Remarkably, ecological risk assessment revealed high risks associated with AMO and ciprofloxacin (CIP) and medium risks linked to several antibiotics, notably including OFL, roxithromycin (ROX), clarithromycin (CLA), and tetracycline (TC). Furthermore, 96 ARG subtypes within 12 resistance types were detected in this study, and the total absolute abundance and diversity of ARGs were significantly decreased from influents to effluents (p < 0.05). Enrichment of 38 ARGs (e.g., blaNDM, ermA, vatA, mexA, and dfrA25) in effluents indicated potential health risks. Various mobile genetic elements (MGEs), exhibited significant correlations with a majority of ARGs in both influents and effluents, such as intⅠ1, tnpA1, tnpA5, and tp614, underscoring the important role of MGEs in contributing to the ARG dissemination. Many antibiotics displayed lower correlations with corresponding ARGs, but exhibited higher correlations with other ARGs, suggesting complex selective pressures influencing ARG propagation. Overall, the incomplete elimination of antibiotics and ARGs in WWTPs is likely to pose adverse impacts on aquatic ecosystems in the Yangtze River Basin.

Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater

Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.

Metagenome sequencing to unveil the occurrence and distribution of antibiotic resistome and in a wastewater treatment plant

The emergence and persistence of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs) has aroused growing public concern for its risk to human health and ecological safety. Moreover, heavy metals concentrated in sewage and sludge could potentially favour co-selection of ARGs and heavy metal resistance genes (HMRGs). In this study, the profile and abundance of antibiotic and metal resistance genes in influent, sludge and effluent were characterized based on the Structured ARG Datebase (SARG) and Antibacterial Biocide and Metal Resistance Gene Datebase (BacMet) by metagenomic analysis. Sequences were aligning against the INTEGRALL, ISFinder, ICEberg and NCBI RefSeq databases to obtain the diversity and abundance of mobile genetic elements (MGEs, e.g.plasmid and transposon). Among them, 20 types of ARGs and 16 types of HMRG were detected in all samples, the influent metagenomes contained many more resistance genes (both ARGs and HMRGs) than the sludge and the influent sample, large reductions in the relatively abundance and diversity of ARG were achieved by biological treatment. ARGs and HMRGs cannot be completely eliminated during the oxidation ditch. A total of 32 species of the potential pathogens were detected, relative abundances of pathogens had no obvious changes. It is suggested that more specific treatments are required to limit their proliferation in the environment. This study can be helpful for further understanding the removal of antibiotic resistance genes in the sewage treatment process via metagenomic sequencing.

Removal of intI1, ARGs, and SARS-CoV-2 and changes in bacterial communities in four sewage treatment facilities

Currently, discharge regulations for wastewater treatment plants (WWTPs) are based on conventional parameters, but more is needed to ensure safe water reuse. In particular, emerging pollutants, as antimicrobials and antibiotic resistance genes (ARGs), are not considered. This research focuses on the fate of emerging biological contaminants during wastewater treatment in Mexico City. intI1 and the ARGs cphA-02, OXA-10 and sul1 were analyzed by qPCR; pathogenic bacteria species were characterized by high throughput sequencing of complete 16S rRNA gene, and fragments of SARS-CoV-2 were quantified by RT-qPCR. Conventional parameters (chemical oxygen demand and coliform bacteria) were also determined. Two sampling campaigns (rainy and dry seasons) were carried out in four municipal WWTPs in Mexico City, representing five biological treatment processes: conventional activated sludge, extended aeration activated sludge, membrane bioreactor, direct anaerobic digestion, and constructed wetland, followed by ultraviolet light or chlorine disinfection. In most cases, gene fragments of SARS-CoV-2 were eliminated below the detection limit of RT-qPCR. The abundance of intI1 positively correlated with the sul1, OXA-10, and cphA-02 abundances; intI1 and the ARGs here studied were partially removed in the WWTPs, and in most cases, the number of copies per second discarded in the sludge were higher those in the effluent. The treatment processes decreased the abundance of dominant bacterial groups in the raw wastewater, while enriching bacterial groups in the effluent and the biological sludge, with possible pollutant removal capabilities. Bacterial communities in the raw wastewater showed the predominance of the genus Arcobacter (from 62.4 to 86.0 %) containing potentially pathogenic species. Additionally, DNA of some species persisted after the treatment processes: A. johnsonii, A. junii, A. caviae, A. hydrophila, A. veronii, A. butzleri, A. cryaerophilus, Chryseobacterium indologenes, Hafnia paralvei, M. osloensis, Pseudomonas putida and Vibrio cholerae, which deserves special attention in future regulation for safe water reuse.

Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent

The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.

Water Quality, Heavy Metals, and Antifungal Susceptibility to Fluconazole of Yeasts from Water Systems

Aquatic environments could be reservoirs of pathogenic yeasts with acquired antifungal resistance. The susceptibility to antifungal agents of yeasts present in the wastewater and natural waters of the city of Cali was evaluated. Samples were taken from two types of water: drinking water (Meléndez River, drinking water treatment plant "Puerto Mallarino" in the Cauca River) and wastewater (South Channel of the Cauca River, "Cañaveralejo-PTAR" wastewater treatment plant). Physico-chemical parameters, heavy metal concentration, and yeast levels were determined using standard procedures. Yeasts were identified using API 20 C AUX (BioMérieux) and sequence analysis of the ITS1-5.8S-ITS2 and D1/D2 regions of the large subunit of the ribosome. Susceptibility assays against fluconazole and amphotericin B using the minimum inhibitory concentration (MIC) test were determined using the microdilution method. The influence of physico-chemical parameters and heavy metals was established using principal component analysis (PCA). Yeast counts were higher at WWTP "PTAR" and lower at Melendez River, as expected. A total of 14 genera and 21 yeast species was identified, and the genus Candida was present at all locations. Susceptibility tests showed a 32.7% resistance profile to fluconazole in the order DWTP "Puerto Mallarino = WWTP "PTAR" > South Channel "Navarro". There were significant differences (p < 0.05) in the physico-chemical parameters/concentration of heavy metals and yeast levels between the aquatic systems under study. A positive association was observed between yeast levels and total dissolved solids, nitrate levels, and Cr at the "PTAR" WWTP; conductivity, Zn, and Cu in the South Channel; and the presence of Pb in the "Puerto Mallarino" DWTP. Rhodotorula mucilaginosa, Candida albicans, and Candida sp. 1 were influenced by Cr and Cd, and Diutina catelunata was influenced by Fe (p < 0.05). The water systems explored in this study showed different yeast levels and susceptibility profiles, and, therefore, possible genetic differences among populations of the same species, and different physico-chemical and heavy metals concentrations, which were probably modulating the antifungal-resistant yeasts. All these aquatic systems discharge their content into the Cauca River. We highlight the importance to further investigate if these resistant communities continue to other locations in the second largest river of Colombia and to determine the risk posed to humans and animals.

High diversity of the emerging pathogen Acinetobacter baumannii and other Acinetobacter spp. in raw manure, biogas plants digestates, and rural and urban wastewater treatment plants with system specific antimicrobial resistance profiles

Carbapenem-resistant Acinetobacter baumannii causing immense treatment problems in hospitals. There is still a knowledge gap on the abundance and stability of acquired resistances and the diversity of resistant Acinetobacter in the environment. The aim of the study was to investigate the diversity and antimicrobial resistances of Acinetobacter spp. released from livestock and human wastewater into the environment. Raw and digested manure of small scale on farm biogas plants as well as untreated and treated wastewater and sewage sludge of rural and urban wastewater treatment plants (WWTPs) were studied comparatively. A total of 132 Acinetobacter isolates were phylogenetically identified (16S rRNA gene and rpoB sequence analyses) and 14 different phylotypes were detected. Fiftytwo isolates represented A. baumannii which were cultured from raw and digested manure of different biogas plants, and most stages of the rural WWTP (no hospital wastewater receiving) and the two studied urban WWTPs receiving veterinarian and human hospital wastewater. Multi-locus sequence typing (Pasteur_MLST) identified 23 novel and 12 known STs of A. baumannii. Most novel STs (18/23) were cultured from livestock samples and the rural WWTP. A. baumannii isolates from livestock and the rural WWTP were susceptible to carbapenems, colistin, ciprofloxacin, ceftazidime, and piperacillin. In contrast, A. baumannii isolates from the two urban WWTPs showed clinical linkage with respect to MLST and were multi-drug resistant (MDR). The presence of viable A. baumannii in digested manure and sewage sludge confirmed the survival of the strict aerobic bacteria during anoxic conditions. The study indicated the spread of diverse Acinetobacter from anthropogenic sources into the environment with a strong linkage of clinial associated MDR A. baumannii strains to the inflow of hospital wastewater to WWTPs. A more frequent detection of Acinetobacter in sewage sludge than effluent waters indicated that particle-attachment of Acinetobacter must be considered by the risk assessment of these bacteria.

Antibiotic and metal resistance of Stenotrophomonas maltophilia isolates from Eboling permafrost of the Tibetan Plateau

Whole-genome sequencing of pathogenic bacteria Stenotrophomonas maltophilia from a less polluted environment of permafrost can help understand the intrinsic resistome of both antibiotics and metals. This study aimed to examine the maximum minimum inhibitory concentration (MIC) of both antibiotics and metals, as well as antibiotic resistance genes and metal resistance genes annotated from whole-genome sequences. The permafrost S. maltophilia was sensitive to ciprofloxacin, tetracycline, streptomycin, and bacitracin, and resistant to chloramphenicol, trimethoprim-sulfamethoxazole, erythromycin, Zn²⁺, Ni²⁺, Cu²⁺, and Cr⁶⁺, with a lower maximum MIC, compared with clinical S. maltophilia. The former strain belonged to the lower antibiotic resistance gene (ARG) and metal resistance gene (MRG) clusters compared with the latter ones. The permafrost strain contained no or only one kind of ARG or MRG on a single genomic island, which explained the aforementioned lower maximum MIC and less diversity of ARGs or MRGs. The result indicated that the co-occurrence of antibiotic and metal resistance was due to a certain innate ability of S. maltophilia. The continuous human use of antibiotics or metals induced selective pressure, resulting in higher MIC and more diverse ARGs and MRGs in human-impacted environments.

New insight into the microbiome, resistome, and mobilome on the dental waste water in the context of heavy metal environment

Object

Hospital sewage have been associated with incorporation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into microbes, which is considered as a key indicator for the spread of antimicrobial resistance (AMR). The compositions of dental waste water (DWW) contain heavy metals, the evolution of AMR and its effects on the water environment in the context of heavy metal environment have not been seriously investigated. Thus, our major aims were to elucidate the evolution of AMR in DWW.

Methods

DWW samples were collected from a major dental department. The presence of microbial communities, ARGs, and MGEs in untreated and treated (by filter membrane and ozone) samples were analyzed using metagenomics and bioinformatic methods.

Results

DWW-associated resistomes included 1,208 types of ARGs, belonging to 29 antibiotic types/subtypes. The most abundant types/subtypes were ARGs of multidrug resistance and of antibiotics that were frequently used in the clinical practice. Pseudomonas putida, Pseudomonas aeruginosa, Chryseobacterium indologenes, Sphingomonas laterariae were the main bacteria which hosted these ARGs. Mobilomes in DWW consisted of 93 MGE subtypes which belonged to 8 MGE types. Transposases were the most frequently detected MGEs which formed networks of communications. For example, ISCrsp1 and tnpA.5/4/11 were the main transposases located in the central hubs of a network. These significant associations between ARGs and MGEs revealed the strong potential of ARGs transmission towards development of antimicrobial-resistant (AMR) bacteria. On the other hand, treatment of DWW using membranes and ozone was only effective in removing minor species of bacteria and types of ARGs and MGEs.

Conclusion

DWW contained abundant ARGs, and MGEs, which contributed to the occurrence and spread of AMR bacteria. Consequently, DWW would seriously increase environmental health concerns which may be different but have been well-documented from hospital waste waters.

Metagenomic insights into the spatiotemporal responses of antibiotic resistance genes and microbial communities in aquaculture sediments

The dissemination of antibiotic resistance genes (ARGs) in aquaculture systems is a potential threat to environmental safety and human health. However, the spatiotemporal distribution pattern of ARGs and key factors associated with their dissemination in aquaculture sediments remain unclear. In this study, ARGs, mobile genetic elements, microbial community composition, heavy metal contents, and nutrient contents of samples collected from a whole culture cycle of fish in a representative aquaculture farm were characterized. The distribution patterns of nine subtypes of ARGs (tetW, tetM, tetA, ermC, ermB, sul1, sul2, floR, and qnrS) showed clear spatiotemporal differences. The absolute abundance of ARGs in aquaculture sediments was higher in winter and in rivers of the aquaculture farm. Proteobacteria was the dominant phylum in all sediment samples. The results of network and redundancy analyses confirmed that the Dechloromonas, Candidatus Accumulibacter, Smithella, Geobacter, and Anaeromyxobacter belonging to Proteobacteria were positively correlated with ARGs, suggesting that these microbial species are potential hosts of corresponding ARGs. Our study highlights that the microbial community is the determining factor for ARG dissemination. Strategies for inhibiting these potential hosts of ARGs should be developed based on controllable factors.

Spent waste from edible mushrooms offers innovative strategies for the remediation of persistent organic micropollutants: A review

Urgent and innovative strategies for removal of persistent organic micropollutants (OMPs) in soil, groundwater, and surface water are the need of the hour. OMPs detected in contaminated soils and effluents from wastewater treatment plants (WWTPs) are categorized as environmentally persistent pharmaceutical pollutants (EPPPs), and endocrine disrupting chemicals (EDCs), their admixture could cause serious ecological issues to the non-target species. As complete eradication of OMPs is not possible with the extant conventional WWTPs technology, the inordinate and reckless application of OMPs negatively impacts environmental regenerative and resilience capacity. Therefore, the cardinal focus of this review is the bioremediation of persistent OMPs through efficient application of an agro-waste, i.e. spent mushroom waste (SMW). This innovative, green, long-term strategy embedded in the circular economy, based on state of the art information is comprehensively assessed in this paper. SMW accrues ligninolytic enzymes such as laccase and peroxidase, with efficient mechanism to facilitate biodegradation of recalcitrant organic pollutants. It is vital in this context that future research should address immobilization of such enzymes to overcome quantitative and qualitative issues obstructing their widespread use in biodegradation. Therefore, dual benefit is gained from cultivating critical cash crops like mushrooms to meet the escalating demand for food resources and to aid in biodegradation. Hence, mushroom cultivation has positive environmental, social, and economic implications in developing countries like India.

Fate of antibiotic resistant genes in wastewater environments and treatment strategies - A review

Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) have emerged in aquatic environments through the discharge of large amounts of antibiotics into wastewater. Well-designed wastewater treatment plants (WWTPs) with effective treatment processes are essential to prevent the release of ARGs directly into the environment. Although some systematic sequential treatment methods are used to remove ARGs, considerable gaps in removal mechanisms will be discussed. Therefore, deep analysis and discussion of various treatment methods are required to understand the ARGs removal mechanisms. In this manuscript, the role of antibiotics and the resistance mechanism of ARB are discussed in depth. In addition, the fate of ARGs in an aquatic environment and detection methods are compared comprehensively and discussed. In particular, the advantages and disadvantages of various methods are summarized and reviewed critically. Finally, combined technologies, such as advanced oxidation process (AOP) with biochemical systems, membrane separation with electrochemical AOP, ultrafiltration (UF) membrane coupled with photocatalytic treatment, and UF membrane separation coupled with sonication, are introduced. Overall, low-energy anaerobic treatment reactors with any of the above combined treatments might reduce the discharge of large quantities of ARGs into the environment. Finally, this review provides valuable insights for better ARG removal technologies by introducing combined effective treatment strategies used in real WWTPs.

Metagenomics analysis of probable transmission of determinants of antibiotic resistance from wastewater to the environment - A case study

During mechanical-biological treatment, wastewater droplets reach the air with bioaerosols and pose a health threat to wastewater treatment plant (WWTP) employees and nearby residents. Microbiological pollutants and antimicrobial resistance determinants are discharged to water bodies with treated wastewater (TWW), which poses a potential global epidemiological risk. In the present study, the taxonomic composition of microorganisms was analyzed, and the resistome profile and mobility of genes were determined by metagenomic next-generation sequencing in samples of untreated wastewater (UWW), wastewater collected from an activated sludge (AS) bioreactor, TWW, river water collected upstream and downstream from the wastewater discharge point, and in upper respiratory tract swabs collected from WWTP employees. Wastewater and the emitted bioaerosols near WWTP's facilities presumably contributed to the transmission of microorganisms, in particular bacteria of the phylum Actinobacteria and the associated antibiotic resistance genes (ARGs) (including ermB, ant(2″)-I, tetM, penA and cfxA2) to the upper respiratory tract of WWTP employees. The discharged wastewater increased the taxonomic diversity of microorganisms and the concentrations of various ARGs (including bacA, emrE, sul1, sul2 and tetQ) in river water. This study fills in the knowledge gap on the health risks faced by WWTP employees. The study has shown that microbiological pollutants and antimicrobial resistance determinants are also in huge quantities discharged to rivers with TWW, posing a potential global epidemiological threat.

Metagenomic analysis of microbial community structure and distribution of resistance genes in Daihai Lake, China

The emergence of resistance genes is a global phenomenon that poses a significant threat to both animals and humans. Lakes are important reservoirs of genes that confer resistant to antibiotics and metals. In this study, we investigated the distribution and diversity of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the sediment of Daihai Lake using high-throughput sequencing and metagenomic analysis. The results indicated that all sampling sites had similar bacterial community structures, with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes being the most abundant. A total of 16 ARG types containing 111 ARG subtypes were deposited in the sediment. Among the resistance genes to bacitracin, multidrug, macrolide-lincosamide-streptogramin (MLS), tetracycline, beta-lactam, and sulfonamide were the dominant ARG types, accounting for 89.9-94.3% of the total ARGs. Additionally, 15 MRG types consisting of 146 MRG subtypes were identified. In all samples, MRGs of the same type presented resistance to Pb, Ni, Hg, W, Zn, Ag, Cr, Fe, As, Cu, and multimetals. Overall, the distribution and diversity of antibiotic and metal resistance genes showed no significant differences in the samples. Plasmids (91.03-91.82%) were the most dominant mobile genetic elements in the sediments of Daihai Lake. Network analysis indicated that the target ARGs and MRGs were significantly positively correlated with the microorganisms. Potential hosts for various ARGs and MRGs include Proteobacteria, Euryarchaeota, Actinobacteria, Chloroflexi, and Bacteroidetes.

Municipal Wastewaters Carry Important Carbapenemase Genes Independent of Hospital Input and Can Mirror Clinical Resistance Patterns

The spatiotemporal variation of several carbapenemase-encoding genes (CRGs) was investigated in the influent and effluent of municipal WWTPs, with or without hospital sewage input. Correlations among gene abundances, bacterial community composition, and wastewater quality parameters were tested to identify possible predictors of CRGs presence. Also, the possible role of wastewaters in mirroring clinical resistance is discussed. The taxonomic groups and gene abundances showed an even distribution among wastewater types, meaning that hospital sewage does not influence the microbial diversity and the CRG pool. The bacterial community was composed mainly of Proteobacteria, Firmicutes, Actinobacteria, Patescibacteria, and Bacteroidetes. Acinetobacter spp. was the most abundant group and had the majority of operational taxonomic units (OTUs) positively correlated with CRGs. This agrees with recent reports on clinical data. The influent samples were dominated by blaKPC, as opposed to effluent, where blaIMP was dominant. Also, blaIMP was the most frequent CRG family observed to correlate with bacterial taxa, especially with the Mycobacterium genus in effluent samples. Bacterial load, blaNDM, blaKPC, and blaOXA-48 abundances were positively correlated with BOD5, TSS, HEM, Cr, Cu, and Fe concentrations in wastewaters. When influent gene abundance values were converted into population equivalent (PE) data, the highest copies/1 PE were identified for blaKPC and blaOXA-48, agreeing with previous studies regarding clinical isolates. Both hospital and non-hospital-type samples followed a similar temporal trend of CRG incidence, but with differences among gene groups. Colder seasons favored the presence of blaNDM, blaKPC and blaOXA-48, whereas warmer temperatures show increased PE values for blaVIM and blaIMP. IMPORTANCE Wastewater-based epidemiology has recently been recognized as a valuable, cost-effective tool for antimicrobial resistance surveillance. It can help gain insights into the characteristics and distribution of antibiotic resistance elements at a local, national, and even global scale. In this study, we investigated the possible use of municipal wastewaters in the surveillance of clinically relevant carbapenemase-encoding genes (CRGs), seen as critical antibiotic resistance determinants. In this matter, our results highlight positive correlations among CRGs, microbial diversity, and wastewater physical and chemical parameters. Identified predictors can provide valuable data regarding the level of raw and treated wastewater contamination with these important antibiotic resistance genes. Also, wastewater-based gene abundances were used for the first time to observe possible spatiotemporal trends of CRGs incidence in the general population. Therefore, possible hot spots of carbapenem resistance could be easily identified at the community level, surpassing the limitations of health care-associated settings.

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Metagenomic and Metatranscriptomic Analyses Reveal that Biobed Systems can Enrich for Antibiotic Resistance and Genetic Mobility Genes

Antibiotic resistance gene pollution in the environment has been identified as a potential contributor to the global issue of antibiotic resistance prevalence, creating a need to identify and characterize environmental reservoirs for antibiotic resistance genes. Because many polluted environments have been shown to contain elevated levels of antibiotic resistance genes, agriculturally-based pesticide bioremediation systems called 'biobeds' could serve as environmental reservoirs for antibiotic resistance genes, although this has never been extensively explored. Metagenomic and metatranscriptomic analyses of an on-farm biobed system sampled before and after a season of pesticide use demonstrated that in situ pesticide applications applied to biobeds can enrich for multidrug, sulfonamide, aminoglycoside, and beta-lactam resistance genes. Additionally, this study demonstrated an enrichment for genes associated with gene mobilization, such as genes involved in horizontal gene transfer and plasmid mobility, as well as transposons and integrases.

Metagenomic analysis reveals the response of microbial community in river sediment to accidental antimony contamination

The mining of deposits containing metals like antimony (Sb) causes serious environmental issues that threaten human health and ecological systems. However, information on the effect of Sb on freshwater sediment microorganisms and the mechanism of microbial Sb resistance is still very limited. This was the first attempt to explore microbial communities in river sediments impacted by accidental Sb spill. Metagenomic analysis revealed the high relative abundance of Proteobacteria and Actinobacteria in all the studied river sediments, showing their advantage in resistance to Sb pollution. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced. Increase in heavy metal resistance genes (HMRGs), particularly Sb transport-related arsB gene, was observed at Sb spill-impacted sites. HMRGs were significantly correlated with ARGs and MGEs, and the abundant MGEs at Sb spill-impacted sites might contribute to the increase in HMRGs and ARGs via horizontal gene transfer. Deinococcus, Sphingopyxis and Paracoccus were identified as potential tolerant genera under Sb pressure and might be related to the transmission of HMRGs and ARGs. This study can add new insights towards the effect of accidental metal spill on sediment microbial community.

Contribution of plasmidome, metal resistome and integrases to the persistence of the antibiotic resistome in aquatic environments

Wastewater treatment plants (WWTPs) are among the main hotspots of antibiotic resistance genes (ARGs) in the environment. Previously, we demonstrated that, by increasing anthropogenic pollution, the antibiotic resistome persisted in the microbial community of rivers and lakes, independently by changes in community composition. In this study, we reanalysed the data to test for the relation of metal resistance genes (MRGs), plasmids, and integrons to the persistence of the antibiotic resistome. The experiment consisted in replicated co-cultures of riverine or lacustrine microbial communities and WWTP effluents in different proportions. Samples before (T0) and after a short period of incubation (TF) were collected and community metagenomic data were obtained by shotgun sequencing. The data were processed to annotate MRGs, plasmids, and integrases. The integrases stabilized in the aquatic environment following the degree of contamination with effluent water (in particular in one site), whereas MRGs and plasmids showed stochastic trajectories. These results confirm the potential correlation between integrons and anthropogenic pollution, and the reliability of intI1 as a pollution marker. Only in one site MRGs, plasmids, and ARGs were correlated, highlighting their partial contribution to the persistence of ARGs in surface waters.

Metagenomic Analysis of the Long-Term Synergistic Effects of Antibiotics on the Anaerobic Digestion of Cattle Manure

The conversion of cattle manure into biogas in anaerobic digestion (AD) processes has been gaining attention in recent years. However, antibiotic consumption continues to increase worldwide, which is why antimicrobial concentrations can be expected to rise in cattle manure and in digestate. This study examined the long-term synergistic effects of antimicrobials on the anaerobic digestion of cattle manure. The prevalence of antibiotic resistance genes (ARGs) and changes in microbial biodiversity under exposure to the tested drugs was investigated using a metagenomic approach. Methane production was analyzed in lab-scale anaerobic bioreactors. Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant bacteria in the samples. The domain Archaea was represented mainly by methanogenic genera Methanothrix and Methanosarcina and the order Methanomassiliicoccales. Exposure to antibiotics inhibited the growth and development of methanogenic microorganisms in the substrate. Antibiotics also influenced the abundance and prevalence of ARGs in samples. Seventeen types of ARGs were identified and classified. Genes encoding resistance to tetracyclines, macrolide–lincosamide–streptogramin antibiotics, and aminoglycosides, as well as multi-drug resistance genes, were most abundant. Antibiotics affected homoacetogenic bacteria and methanogens, and decreased the production of CH4. However, the antibiotic-induced decrease in CH4 production was minimized in the presence of highly drug-resistant microorganisms in AD bioreactors.

Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals

Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.

Higher abundance of core antimicrobial resistant genes in effluent from wastewater treatment plants

Wastewater treatment plants (WWTPs) receive sewage water from a variety of sources, including livestock farms, hospitals, industries, and households, that contain antimicrobial resistant bacteria (ARB) and antimicrobial resistant genes (ARGs). Current treatment technologies are unable to completely remove ARB and ARGs, which are eventually released into the aquatic environment. This study focused on the core resistome of urban WWTPs that are persistent through wastewater treatment processes. We adopted the Hiseq-based metagenomic sequencing approach to identify the core resistome, their genetic context, and pathogenic potential of core ARGs in the influent (IN) and effluent (EF) samples of 12 urban WWTPs in South Korea. In this study, the abundance of ARGs ranged from 0.32 to 3.5 copies of ARGs per copy of the 16S rRNA gene, where the IN samples were relatively higher than the EF samples, especially for the macrolide-lincosamide-streptogramin (MLS)- and tetracycline- resistant genes. On the other hand, there were 43 core ARGs sharing up to 90% of the total, among which the relative abundance of sul1, APH(3'')-lb, and RbpA was higher in EF than in IN (p < 0.05). Moreover, tetracycline and sulfonamide-related core ARGs in both EF and IN were significantly more abundant on plasmids than on chromosomes (p < 0.05). We also found that the majority of core ARGs were carried by opportunistic pathogens such as Acinetobacter baumannii, Enterobacter cloacae, and Pseudomonas aeruginosa in both IN and EF. In addition, phages were the only mobile elements whose abundance correlated with that of core ARGs in EF, suggesting that transduction may play a major role in disseminating ARGs in the receiving water environment of the urban WWTP. The persistent release of core ARGs with pathogenic potential into environmental water is of immediate concern. The mobility of ARGs and ARBs in the environment is a major public health concern. These results should be taken into consideration when developing policy to mitigate environmental dissemination of ARG by WWTPs.

Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

Effects on microbiomes and resistomes and the source-specific ecological risks of heavy metals in the sediments of an urban river

This study aims to better understand the effects of heavy metal enrichment on microbiomes and resistomes and the source-specific ecological risks of metals in the sediments of an urban river. Geo-accumulation index and enrichment factor suggested the river sediments were contaminated by Cd, Cu, Pb, and Zn in varying degrees. High-throughput sequencing-based metagenomics analysis identified 430 types of antibiotic resistance genes (ARGs), dominated by the multidrug, MLS, bacitracin, quinolone, and aminoglycoside ARGs, and 52 metal resistance genes (MRGs) mainly conferring resistance to zinc, copper, cadmium, lead, mercury and multiple metals. Spearman correlation analysis and Mantel test showed the heavy metal enrichment exerted significant effects on the microbial community, ARGs and MRGs. Source apportionment using positive matrix factorization revealed that natural source (42.8%) was the largest contributor of metals in the river sediments, followed by urban activities (35.4%) and a mixed source (21.7%). However, when incorporating the apportionment results into a modified risk model to evaluate the source-specific ecological risks, results showed human activities dominated the risks of metals. Comparatively, the urban activities majorly caused moderate- and considerable- ecological risks, while the mixed source with respect to agricultural and industrial activities contributed higher percentages on high- and extremely high- ecological risks.

Profiling of emerging contaminants and antibiotic resistance in sewage treatment plants: An Indian perspective

In India, sewage (partially-treated/ untreated) is randomly used for irrigation because of easy availability and presence of residual organics and nutrients. However, data on the occurrence of contaminants of emerging concerns (CECs) such as pharmaceuticals and personal care products (PPCPs) and antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in sewage is scarce in Indian perspective. Herein, for the first time, we present a quantitative contamination profiling of selected PPCPs and antibiotic resistance in untreated and biologically-treated sewage from three different sewage treatment plants, located in northern and central part of India. Profiling of PPCPs were done using LC-ESI-MS/MS whereas antibiotic resistance was analyzed using gradient PCR and qPCR techniques. PPCPs were detected both in untreated and treated samples (0.4 - 1340 μg/L). A reduction in ARB and ARG load (2-3 log) and an increase in ARG copy number with respect to beta lactams and tetracycline were observed in treated sewage. Triclosan, estrone and 17α-ethynylestradiol, ubiquitous in all samples, could be used as markers for performance monitoring of sewage treatment facilities. The results obtained in this study help evaluate health and ecological risks associated with the presence of CECs in treated sewage used for irrigation and frame future policies.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Metagenomic exploration of antibiotic resistome in treated wastewater effluents and their receiving water

Environmental dissemination of antimicrobial resistance is a global health problem. Antimicrobial-resistant bacteria and antibiotic-resistant genes (ARGs) are constantly released into the environment through effluents (EFs) from wastewater treatment plants (WWTPs). Thus, requiring a better understanding of the selection and fate of ARGs in wastewater treatment processes. Therefore, we investigated the impacts of urban WWTP EFs on receiving water in the context of their resistomes and mobilomes. We used a HiSeq-based short read metagenomic approach to address the dynamics and diversity of ARGs in WWTP EF as well as the upstream (UP) and downstream (DN) river waters, followed by an investigation of plasmid-mediated ARGs. The abundance of ARGs at each site varied from 7.2 × 10^-2 to 7.4 × 10^-1 ARG copies per 16S rRNA gene copy, and EF samples showed the highest abundance, followed by DN and UP water samples. ARG diversity ranged from 121 to 686 types per site, and EF had the most diverse ARGs. Commonly identified ARGs in the EF and DN samples were clinically important and were absent in UP samples. The abundance of ARGs, mobile genetic elements (MGEs), and plasmid contigs found only in EF and DN were positively correlated with each other, indicating the importance of mobilomes in the dissemination of ARGs in the environment. Moreover, the proportions of plasmid-mediated ARGs was highest in the EF samples, followed by the DN and UP samples. These findings suggest that WWTP EF may act as a driving factor shaping the resistomes and mobilomes of receiving waters. In particular, a higher abundance of plasmid-mediated ARGs in WWTP EF suggests higher transmissibility in the DN environment.

Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis

Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is of relatively less interest. In this study, metagenomic analysis was carried out to investigate whether the WWTP scale could be affected by the prevalence and persistence of ARGs and mobile genetic elements (MGEs). As a result, 152 ARG subtypes were identified in small-scale WWTP samples, while 234 ARG subtypes were identified in large-scale WWTP samples. Among the detectable ARGs, multidrug, MLS (macrolide–lincosamide–streptogramin), sulfonamide, and tetracycline resistance genes had the highest abundance, and large and small WWTPs had similar composition characteristics of ARGs. In MGE analysis, plasmids and integrons were 1.5–2.0-fold more abundant in large-scale WWTPs than in small-scale WWTPs. The profile of bacteria at the phylum level showed that Proteobacteria and Actinobacteria were the most dominant bacteria, representing approximately 70% across large- and small-scale WWTPs. Overall, the results of this study elucidate the different abundances and dissemination of ARGs between large- and small-scale WWTPs, which facilitates the development of next-generation engineered wastewater treatment systems.

Antibiotic Resistance in Recreational Waters: State of the Science

Ambient recreational waters can act as both recipients and natural reservoirs for antimicrobial resistant (AMR) bacteria and antimicrobial resistant genes (ARGs), where they may persist and replicate. Contact with AMR bacteria and ARGs potentially puts recreators at risk, which can thus decrease their ability to fight infections. A variety of point and nonpoint sources, including contaminated wastewater effluents, runoff from animal feeding operations, and sewer overflow events, can contribute to environmental loading of AMR bacteria and ARGs. The overall goal of this article is to provide the state of the science related to recreational exposure and AMR, which has been an area of increasing interest. Specific objectives of the review include (1) a description of potential sources of antibiotics, AMR bacteria, and ARGs in recreational waters, as documented in the available literature; (2) a discussion of what is known about human recreational exposures to AMR bacteria and ARGs, using findings from health studies and exposure assessments; and (3) identification of knowledge gaps and future research needs. To better understand the dynamics related to AMR and associated recreational water risks, future research should focus on source contribution, fate and transport-across treatment and in the environment; human health risk assessment; and standardized methods.

Acinetobacter sp. as the key player in diesel oil degrading community exposed to PAHs and heavy metals

The aim of this study was to verify the hypothesis that a hydrocarbon degrading community isolated from a site heavily polluted with polycyclic aromatic hydrocarbons (PAHs) and heavy metals should exhibit a high activity and biodegradation efficiency, despite decreased biodiversity resulting from the presence of such contaminants. Microbial community isolated from soil collected at an abandoned creosote railway wood-sleepers impregnation plant using diesel oil was used during the studies. Four parallel systems spiked with diesel oil, diesel oil + PAHs, diesel oil + heavy metals and diesel oil + PAHs + heavy metals were analysed in terms of relative abundance and biodiversity of the microbial community (Illumina), biodegradation efficiency (GCMS) and cellular metabolic activity (flow cytometry). Principal Component Analysis and biodiversity parameters indicated that the mixture of PAHs and heavy metals was the dominant factor which resulted in the enrichment of the Gammaproteobacteria class. This was associated with higher degradation of additional PAHs in the presence of heavy metals and an increase of metabolically active sub-populations during flow cytometry analysis. The increased abundance of the Acinetobacter genus in systems with both PAHs and heavy metals implies that it may play a crucial role in soil populations exposed to mixed contaminations.

Evidence of mutations conferring resistance to clarithromycin in wastewater and activated sludge

The occurrence of clarithromycin in wastewater samples and of the activated sludge bacteria possibly resistant to this pharmaceutical was the object of the study. Samples of wastewater or activated sludge were taken from a municipal wastewater treatment plant in summer and winter and characterised regarding their clarithromycin concentrations and the presence of nucleic acid fragments (Cla-sequences) known to be responsible for clarithromycin resistance in Helicobacter pylori. The concentrations of clarithromycin in raw wastewater were about 1086-2271 ng/L. Around 50-60% less of the pharmaceutical was found in treated wastewater. The concentrations were much higher in winter samples, as compared to summer samples. The clarithromycin resistance markers in H. pylori were detected by fluorescence in situ hybridisation in activated sludge bacterial cells. Cla-sequences were found in all the detected Proteobacteria, independently of the sampling season. Among nitrifying or phosphate or glycogen accumulating bacteria only Nitrosomonas spp. revealed presence of the clarithromycin sequences.

The correlation between antibiotic resistance gene abundance and microbial community resistance in pig farm wastewater and surrounding rivers

Antimicrobial resistance gene (ARG) abundance and microbial resistance (MR) are often used as important indicators of pollution risk; however, the relationship between ARGs abundance and MR in pig farm wastewater remains unknown. In this study, the raw pig farm wastewater, effluent water, upstream river water, domestic wastewater and downstream river water samples were collected. The concentration of 20 subtypes of ARGs and 2 integrons, minimal inhibit concentration (MIC), and bacterial communities were investigated. In this study, 20 subtypes of ARGs and integrons were detected in all sampling sites. The highest abundance of 17 of the 20 subtypes of ARGs was detected in raw pig farm wastewater, and ermA had the maximum average abundance of 10⁸ copies/mL, with up to 2.41 ± 0.12 × 10⁸ copies/mL. There was no significant correlation between MR to three antibiotics (ciprofloxacin, streptomycin and tetracycline hydrochloride) and the abundance of their corresponding ARGs (P > 0.05), and a large difference was detected between the types of ARGs co-occur bacteria and resistance co-occur bacteria in the 5 sampling sites. And the pig farm wastewater treatment (WWT) could effectively reduce the ARGs and MR to the 3 antibiotics. The results presented here show that there may be no obvious correlation between ARGs and MCR in pig farm wastewater and surrounding rivers, which may be due to various environmental factors, highlighting the urgent need for a comprehensive evaluation of relationship between ARGs abundance and MR.

Distribution and co-occurrence of antibiotic and metal resistance genes in biofilms of an anthropogenically impacted stream

Urban stream biofilms are potential hotspots for resistomes and antibiotic resistance genes (ARGs). Biofilm communities that harbor resistance genes may be influenced by contaminant input (e.g., metals and antibiotics) from urban drainage (i.e., Wastewater Treatment Plant effluent and stormwater runoff); understanding the ecology of these communities and their resistome is needed. Given the potential importance of the co-occurrence of ARGs and metal resistance genes (MRGs), we investigated the spatial and temporal distribution of three ARGs (tetracycline [tetW] and sulfonamides [sulI and sulII]), four MRGs (lead [pbrT], copper [copA], and cadmium/cobalt/zinc [czcA and czcC]) via quantitative PCR and biofilm bacterial community composition via MiSeq 16S sequencing at four time points along an urbanization gradient (i.e., developed, agriculture, and forested sites) in a stream's watershed. Our results revealed that ARG and MRG abundances were significantly affected by land use-time interaction, with greater resistance abundances occurring in more urban locations during particular times of the year. It was also observed that changes in ARG and MRG profiles were influenced by differences in community composition among land use types, and that these differences were in response to changes in stream physicochemical parameters (pH, redox, temperature, nutrient availability, and metal concentration) that were driven by sub-watershed land use. Moreover, the dynamics between ARGs and MRGs within these communities correlated strongly and positively with one another. Taken altogether, our results demonstrate that changes in environmental properties due to human activity may drive the ARG-MRG profiles of biofilm communities by modulating community structure over time and space.

Rhodoferax lacus sp. nov., isolated from a large freshwater lake

A Gram-staining-negative, aerobic, motile with a single polar flagellum and rod-shaped bacterium as a bacterial host of podovirus P26218, designated IMCC26218^T, was isolated from Lake Soyang, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC26218^T belonged to the genus Rhodoferax of the family Comamonadaceae and shared 97.7-99.0 % sequence similarities with Rhodoferax species. The draft whole genome sequence of strain IMCC26218^T was ca. 4.9 Mbp in size with the DNA G+C content of 62.3 mol%. Average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between strain IMCC26218^T and other Rhodoferax were 74.0-77.3 % and 19.5-21.0 %, respectively, showing that the strain represents a new Rhodoferax species. The strain contained summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c) and C_16 : 0 as the major fatty acids and phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminolipids and two unidentified lipids as major polar lipids. The predominant isoprenoid quinone of the strain was ubiquinone-8 (Q-8). On the basis of the phylogenetic and phenotypic characteristics, strain IMCC26218^T is considered to represent a novel species of the genus Rhodoferax, for which the name Rhodoferax lacus sp. nov. is proposed. The type strain is IMCC26218^T (=KACC 18983^T=NBRC 112709^T).

Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent

Background

Comparative knowledge of microbiomes and resistomes across environmental interfaces between animal production systems and urban settings is lacking. In this study, we executed a comparative analysis of the microbiota and resistomes of metagenomes from cattle feces, catch basin water, manured agricultural soil and urban sewage.

Results

Metagenomic DNA from composite fecal samples (FC; n = 12) collected from penned cattle at four feedlots in Alberta, Canada, along with water from adjacent catchment basins (CB; n = 13), soil (n = 4) from fields in the vicinity of one of the feedlots and urban sewage influent (SI; n = 6) from two municipalities were subjected to Illumina HiSeq2000 sequencing. Firmicutes exhibited the highest prevalence (40%) in FC, whereas Proteobacteria were most abundant in CB (64%), soil (60%) and SI (83%). Among sample types, SI had the highest diversity of antimicrobial resistance (AMR), and metal and biocide resistance (MBR) classes (13 & 15) followed by FC (10 & 8), CB (8 & 4), and soil (6 & 1). The highest antimicrobial resistant (AMR) gene (ARG) abundance was harboured by FC, whereas soil samples had a very small, but unique resistome which did not overlap with FC & CB resistomes. In the beef production system, tetracycline resistance predominated followed by macrolide resistance. The SI resistome harboured β-lactam, macrolide, tetracycline, aminoglycoside, fluoroquinolone and fosfomycin resistance determinants. Metal and biocide resistance accounted for 26% of the SI resistome with a predominance of mercury resistance.

Conclusions

This study demonstrates an increasing divergence in the nature of the microbiome and resistome as the distance from the feedlot increases. Consistent with antimicrobial use, tetracycline and macrolide resistance genes were predominant in the beef production system. One of the feedlots contributed both conventional (raised with antibiotics) and natural (raised without antibiotics) pens samples. Although natural pen samples exhibited a microbiota composition that was similar to samples from conventional pens, their resistome was less complex. Similarly, the SI resistome was indicative of drug classes used in humans and the greater abundance of mercury resistance may be associated with contamination of municipal water with household and industrial products.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1548-x) contains supplementary material, which is available to authorized users.

Graphene oxide as a tool for antibiotic-resistant gene removal: a review

Environmental pollutants, including antibiotics (ATBs), have become an increasingly common health hazard in the last several decades. Overdose and abuse of ATBs led to the emergence of antibiotic-resistant genes (ARGs), which represent a serious health threat. Moreover, water bodies and reservoirs are places where a wide range of bacterial species with ARGs originate, owing to the strong selective pressure from presence of ATB residues. In this regard, graphene oxide (GO) has been utilised in several fields including remediation of the environment. In this review, we present a brief overview of resistant genes of frequently used ATBs, their occurrence in the environment and their behaviour. Further, we discussed the factors influencing the binding of nucleic acids and the response of ARGs to GO, including the presence of salts in the water environment or water pH, because of intrinsic properties of GO of not only binding to nucleic acids but also catalysing their decomposition. This would be helpful in designing new types of water treatment facilities.

Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

A global survey was performed with 122 aquatic metagenomic DNA datasets (92 lake water and 30 seawater) obtained from the Sequence Read Archive (SRA). Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were derived from the dataset sequences via bioinformatic analysis. The relative abundances of ARGs and MRGs in lake samples were in the ranges ND (not detected)-1.34 × 10⁰ and 1.22 × 10^-3-1.98 × 10^-1 copies per 16S rRNA, which were higher than those in seawater samples. Among ARGs, multidrug resistance genes and bacitracin resistance genes had high relative abundances in both lake and sea water samples. Multi-metal resistance genes, mercury resistance genes and copper resistance genes had the greatest relative abundance for MRGs. No significant difference was found between epilimnion and hypolimnion in abundance or the Shannon diversity index for ARGs and MRGs. Principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA) test showed that stratification and geography had significant influence on the composition of ARGs and MRGs in lakes (p < 0.05, PERMANOVA). Coastal seawater samples had significantly greater relative abundance and a higher Shannon index for both ARGs and MRGs than deep ocean and Antarctic seawater samples (p < 0.05, Kruskal-Wallis one-way ANOVA), suggesting that human activity may exert more selective pressure on ARGs and MRGs in coastal areas than those in deep ocean and Antarctic seawater.

Specificity in the Susceptibilities of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus Clinical Isolates to Six Metal Antimicrobials

In response to the occurrence of antibiotic resistance, there has been rapid developments in the field of metal-based antimicrobials. Although it is largely assumed that metals provide broad-spectrum microbial efficacy, studies have shown that this is not always the case. Therefore, in this study, we compared the susceptibilities of 93 clinical isolates belonging to the species Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus against six metals, namely aluminum, copper, gallium, nickel, silver and zinc. To provide qualitative comparative information, the resulting zones of growth inhibition were compared to the minimal inhibitory concentrations of three indicator strains E. coli ATCC 25922, P. aeruginosa ATCC 27853 and S. aureus ATCC 25923. Here, we demonstrate that the metal efficacies were species- and isolate-specific. Only several isolates were either resistant or sensitive to all of the six metals, with great variability found between isolates. However, the greatest degree of similarity was found with the E. coli isolates. In contrast, the susceptibilities of the remaining two collections, S. aureus and P. aeruginosa, were more highly dispersed. Using this information, we have shown that metals are not equal in their efficacies. Hence, their use should be tailored against a particular microorganism and care should be taken to ensure the use of the correct concentration.

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

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

Metagenomic and Resistome Analysis of a Full-Scale Municipal Wastewater Treatment Plant in Singapore Containing Membrane Bioreactors

Reclaimed water provides a water supply alternative to address problems of scarcity in urbanized cities with high living densities and limited natural water resources. In this study, wastewater metagenomes from 6 stages of a wastewater treatment plant (WWTP) integrating conventional and membrane bioreactor (MBR) treatment were evaluated for diversity of antibiotic resistance genes (ARGs) and bacteria, and relative abundance of class 1 integron integrases (intl1). ARGs confering resistance to 12 classes of antibiotics (ARG types) persisted through the treatment stages, which included genes that confer resistance to aminoglycoside [aadA, aph(6)-I, aph(3')-I, aac(6')-I, aac(6')-II, ant(2″)-I], beta-lactams [class A, class C, class D beta-lactamases (bla OXA)], chloramphenicol (acetyltransferase, exporters, floR, cmIA), fosmidomycin (rosAB), macrolide-lincosamide-streptogramin (macAB, ereA, ermFB), multidrug resistance (subunits of transporters), polymyxin (arnA), quinolone (qnrS), rifamycin (arr), sulfonamide (sul1, sul2), and tetracycline (tetM, tetG, tetE, tet36, tet39, tetR, tet43, tetQ, tetX). Although the ARG subtypes in sludge and MBR effluents reduced in diversity relative to the influent, clinically relevant beta lactamases (i.e., bla KPC, bla OXA) were detected, casting light on other potential point sources of ARG dissemination within the wastewater treatment process. To gain a deeper insight into the types of bacteria that may survive the MBR removal process, genome bins were recovered from metagenomic data of MBR effluents. A total of 101 close to complete draft genomes were assembled and annotated to reveal a variety of bacteria bearing metal resistance genes and ARGs in the MBR effluent. Three bins in particular were affiliated to Mycobacterium smegmatis, Acinetobacter Iwoffii, and Flavobacterium psychrophila, and carried aquired ARGs aac(2')-Ib, bla OXA-278, and tet36 respectively. In terms of indicator organisms, cumulative log removal values (LRV) of Escherichia coli, Enterococci, and P. aeruginosa from influent to conventional treated effluent was lower (0-2.4), compared to MBR effluent (5.3-7.4). We conclude that MBR is an effective treatment method for reducing fecal indicators and ARGs; however, incomplete removal of P. aeruginosa in MBR treated effluents (<8 MPN/100 mL) and the presence of ARGs and intl1 underscores the need to establish if further treatment should be applied prior to reuse.

Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes

Plastics have been accumulated offshore and in the deep oceans at an unprecedented scale. Microbial communities have colonized the plastisphere, which has become a reservoir for both antibiotic and metal resistance genes (ARGs and MRGs). This is the first analysis of the diversity, abundance, and co-occurrence of ARGs and MRGs, and their relationships within the microbial community, using metagenomic data of plastic particles observed in the North Pacific Gyre obtained from the National Centre for Biotechnology Information Sequence Read Archive database. The abundance of ARGs and MRGs in microbial communities on the plastics were in the ranges 7.07 × 10^-4-1.21 × 10^-2 and 5.51 × 10^-3-4.82 × 10^-2 copies per 16S rRNA, respectively. Both the Shannon-Wiener indices and richness of ARGs and MRGs in plastics microbiota were significantly greater than those of ARGs and MRGs in seawater microbiota in the North Pacific Gyre via one-way analysis of variance. Multidrug resistance genes and multi-metal resistance genes were the main classes of genes detected in plastic microbiota. There were no significant differences in the abundance or diversity of ARGs and MRGs between macroplastics biota and microplastics biota, indicating that particle size had no effect on resistance genes. Procrustes analysis suggested that microbial community composition was the determining factor of the ARG profile but not for MRG. Some ARGs and MRGs had a higher incidence of non-random co-occurrence, suggesting that the co-effects of selection for antibiotic or metal resistance are important factors influencing the resistome of the microbiota on the plastic particles.

Monitoring Antimicrobial Resistance Dissemination in Aquatic Systems

This special issue on Antimicrobial Resistance in Environmental Waters features 11 articles on monitoring and surveillance of antimicrobial resistance (AMR) in natural aquatic systems (reservoirs, rivers), and effluent discharge from water treatment plants to assess the effectiveness of AMR removal and resulting loads in treated waters. The occurrence and distribution of antimicrobials, antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) was determined by utilizing a variety of techniques including liquid chromatography—mass spectrometry in tandem (LC-MS/MS), traditional culturing, antibiotic susceptibility testing (AST), molecular and OMIC approaches. Some of the key elements of AMR studies presented in this special issue highlight the underlying drivers of AMR contamination in the environment and evaluation of the hazard imposed on aquatic organisms in receiving environments through ecological risk assessments. As described in this issue, screening antimicrobial peptide (AMP) libraries for biofilm disruption and antimicrobial candidates are promising avenues for the development of new treatment options to eradicate resistance. This editorial puts into perspective the current AMR problem in the environment and potential new methods which could be applied to surveillance and monitoring efforts.