Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China

Multivariate statistical analysis of surface water quality in the capibaribe river (Pernambuco state, Northeast Brazil): Contributions to water management

Assessing the quality of surface waters is essential for identifying changes in freshwater ecosystems and supporting the planning/proposing of measures to mitigate polluting sources. However, many studies involving the identification of pathogenic bacteria and/or their resistance profile to antimicrobial agents need a more holistic approach to conditioning or modulating factors. Thus, we apply different multivariate statistical techniques to the data set from the Capibaribe River's surface water, one of the most important in the Northeast of Brazil. Our data, taken together, suggest that the waters of the Capibaribe River have been suffering impacts associated with different human activities. Due to its flow crossing a large urban area, different sources are contributing to the contamination/pollution of its aquatic ecosystem, whose multivariate analysis allowed us to identify site-dependent characteristics that reflect the degree and type of human influence. The study of physical-chemical and chemical parameters reveals the influence of the high load of effluents (industrial and domestic) on the chemical and microbiological quality of the waters sampled at the SS4 site. On the other hand, the antimicrobial resistance profile of the isolates evaluated, especially at SS1, SS2, and SS3 sites, provides a comprehensive sample of the "resistome" present in the fecal content of thousands of people living in the region surrounding the Capibaribe River. The presence of enterobacteria in water indicates contamination of fecal origin. It represents a public health problem since the waters of the Capibaribe River can be a source of dissemination and persistence of bacteria resistant to humans and the environment. In conclusion, our study provides a more comprehensive understanding of the relationships between surface water, basic sanitation, antibiotic exposure, bacterial gene transfer, and human colonization, whether in the context of the region studied or other locations.

Metagenomic insights into plasmid-mediated antimicrobial resistance in poultry slaughterhouse wastewater: antibiotics occurrence and genetic markers

Slaughterhouse wastewater represents important convergence and concentration points for antimicrobial residues, bacteria, and antibiotic resistance genes (ARG), which can promote antimicrobial resistance propagation in different environmental compartments. This study reports the assessment of the metaplasmidome-associated resistome in poultry slaughterhouse wastewater treated by biological processes, employing metagenomic sequencing. Antimicrobial residues from a wastewater treatment plant (WWTP) that treats poultry slaughterhouse influents and effluents were investigated through high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS). Residues from the macrolide, sulfonamide, and fluoroquinolone classes were detected, the latter two persisting after the wastewater treatment. The genetic markers 16S rRNA rrs (bacterial community) and uidA (Escherichia coli) were investigated by RT-qPCR and the sul1 and int1 genes by qPCR. After treatment, the 16S rRNA rrs, uidA, sul1, and int1 markers exhibited reductions of 0.67, 1.07, 1.28, and 0.79 genes copies, respectively, with no statistical significance (p > 0.05). The plasmidome-focused metagenomics sequences (MiSeq platform (Illumina®)) revealed more than 100 ARG in the WWTP influent, which can potentially confer resistance to 14 pharmacological classes relevant in the human and veterinary clinical contexts, in which the qnr gene (resistance to fluoroquinolones) was the most prevalent. Only 7.8% of ARG were reduced after wastewater treatment, and the remaining 92.2% were associated with an increase in the prevalence of ARG linked to multidrug efflux pumps, substrate-specific for certain classes of antibiotics, or broad resistance to multiple medications. These data demonstrate that wastewater from poultry slaughterhouses plays a crucial role as an ARG reservoir and in the spread of AMR into the environment.

Unveiling antibiotic contamination in surface water: A study of the Huaihe River Basin's Huaibei Plain, a significant Chinese herbal medicine planting region

The abuse of antibiotics has caused the accumulation of antibiotic residues in environmental media, threatening the ecosystem and human health. Many studies on the distribution of aqueous antibiotics have been reported. However, the pollution status of antibiotics in the environment in Chinese herbal medicine planting areas is rarely comprehensively clarified, resulting in the lack of updated pollution data and conducive suggestions for ecological cultivation and sustainable development of Chinese herbal medicine. Thus, we comprehensively investigated the distribution, profiles, sources, and risks of the antibiotics in the surface water of an important tributary of the Huaihe River Basin, located in Bozhou City, a significant Chinese herbal medicine planting region. Solid-phase extraction coupled with an ultra-performance liquid chromatography-tandem mass spectrometer (SPE-UPLC-MS) was utilized to detect the antibiotics in the water. 27 kinds of antibiotics were identified with total concentrations ranging from 75.01 to 1737.99 ng·L-1, with doxycycline (DC) and doxycycline hydrochloride (DCH) possessed the highest concentration. And DC, DCH, oxilinic acid (OA), sulfamethoxazole (SMZ), clarithromycin (CLA), and roxithromycinum (ROX) were the main antibiotics detected in this basin. Correlation analysis and principal component analysis (PCA) indicated that animal husbandry was the primary source of antibiotics. Furthermore, the ecological risk assessment revealed that certain antibiotics could seriously threaten the survival of aquatic organisms, implying that local Chinese herbal medicines might be at similar growth risk. The drinking risk assessment showed that antibiotics in the water posed low risks for human, and children faced a greater drinking risk than adults. The study can help to facilitate the management of aqueous antibiotic pollution for the ecological cultivation and safe production of Chinese herbal medicine.

Performance and mechanism of SMX removal by an electrolysis-integrated ecological floating bed at low temperatures: A new perspective of plant activity, iron plaque, and microbial functions

Improvements in plant activity and functional microbial communities are important to ensure the stability and efficiency of pollutant removal measures in cold regions. Although electrochemistry is known to accelerate pollutant degradation, cold stress acclimation of plants and the stability and activity of plant-microbial synergism remain poorly understood. The sulfamethoxazole (SMX) removal, iron plaque morphology, plant activity, microbial community, and function responses were investigated in an electrolysis-integrated ecological floating bed (EFB) at 6 ± 2 ℃. Electrochemistry significantly improved SMX removal and plant activity. Dense and uniform iron plaque was found on root surfaces in L-E-Fe which improved the plant adaptability at low temperatures and provided more adsorption sites for bacteria. The microbial community structure was optimized and the key functional bacteria for SMX degradation (e.g., Actinobacteriota, Pseudomonas) were enriched. Electrochemistry improves the relative abundance of enzymes related to energy metabolism, thereby increasing energy responses to SMX and low temperatures. Notably, electrochemistry improved the expression of target genes (sadB and sadC, especially sadC) involved in SMX degradation. Electrochemistry enhances hydrogen bonding and electrostatic interactions between SMX and sadC, thereby enhancing SMX degradation and transformation. This study provides a deeper understanding of the electrochemical stability of antibiotic degradation at low temperatures.

Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective

Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.

A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens

Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.

Differences in pathogenic community assembly processes and their interactions with bacterial communities in river and lake ecosystems

Pathogenic bacterial infections caused by water quality degradation are one of the most widespread environmental problems. Clarifying the structure of pathogens and their assembly mechanisms in lake ecosystems is vital to prevent the infestation of waterborne pathogens and maintain human health. However, the composition and assembly mechanisms of pathogenic bacterial communities in river and lake ecosystems are still poorly understood. In this study, we collected 17 water and 17 sediment samples from Lake Chaohu and its 11 inflow rivers. Sequencing of 16S rRNA genes was used to study bacterial pathogen communities. The results of the study showed that there was a significant difference (P < 0.05) in the composition of the pathogen community between riverine and lake habitats. Acinetobacter (36.49%) was the dominant bacterium in the river, whereas Flavobacterium (21.6%) was the most abundant bacterium in the lake. Deterministic processes (i.e., environmental filtering and species interaction) drove the assembly of pathogenic bacterial communities in the lake habitat, while stochastic processes shaped river pathogenic bacterial communities. Spearman correlation analysis showed that the α-diversity of bacterial communities was linearly and negatively linked to the relative abundance of pathogens. Having a higher bacterial community diversity had a suppressive effect on pathogen abundance. In addition, co-occurrence network analysis showed that bacterial communities were tightly linked to pathogenic bacteria. Pseudomonas aeruginosa and Salmonella enterica were identified as keystone species in an inflow water sampling network (W_FR), reducing the complexity of the network. These results provide a reference for assessments of water quality safety and pathogenic bacteria posing risks to human health in large freshwater lakes.

Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem

IMPORTANCE

Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.

Directed evolution of TetR for constructing sensitive and broad-spectrum tetracycline antibiotics whole-cell biosensor

Antibiotic abuse is the main reason for the drug resistance of pathogenic bacteria, posing a potential health risk. Antibiotic surveillance is critical for preventing antibiotic contamination. This study aimed to develop a sensitive and broad-spectrum whole-cell biosensor for tetracycline antibiotics (TCs) detection. Wild-type TCs-responsive biosensor was constructed by introducing a tetracycline operon into a sfGFP reporter plasmid. Using error-prone PCR, mutation libraries containing approximately 107 variants of the tetracycline repressor (TetR) gene were generated. The tigecycline-senstive mutants were isolated using high-throughput flow cytometric sorting. After 2 rounds of directed evolution, a mutant epS2-22 of TerR was isolated and assembled as a TCs biosensor. The epS2-22 biosensor was more sensitive and broad-spectrum than the wild-type biosensors. The detection limits of the epS2-22 biosensor for seven TCs were 4- to 62-fold lower than the wild-type biosensor (no response to tigecycline). Meanwhile, the epS2-22 biosensor had a shorter detection time and a stronger signal output than the wild type. In addition, the evolved epS2-22 biosensor showed excellent performance in detecting low traces of TCs in environmental water. These results suggest that directed evolution is a powerful tool for developing high-performance whole-cell biosensors, and the evolved epS2-22 biosensors have the potential for wider applications in real-world TCs detection.

An indirect competitive assay-based method for the sensitive determination of tetracycline residue using a real-time fluorescence-based quantitative polymerase chain reaction

Tetracycline (TC) is an effective antibiotic used to treat humans and livestock, but its inappropriate use imposes toxic effects, including pollution, on environmental ecology and food. Currently, sensitive, accurate, and cost-effective methods that can detect lower concentrations of TC residues in environmental and food samples are needed. In this study, a novel indirect competitive assay-based aptamer method was developed for detecting TC residues through signal amplification by real-time fluorescence-based quantitative polymerase chain reaction. The response surface methodology was introduced to optimize the optimal concentrations (influencing factors) of the three types of single-stranded DNA in the competitive assay process. The optimal conditions for the three types of ssDNA were 112 nM for the specific aptamer of TC (Apt40), 115 nM for the signal DNA, and 83 nM for the DNA catcher. As expected, under optimal conditions, the Ct value was linearly related to the logarithm of TC concentration. The calibration curve equation was Ct = -0.34516 log[TC] + 9.9345 (R2 = 0.998) in the range of 10-3-103 ng mL-1, and the limit of detection was 7.02 × 10-5 ng mL-1. The new method was effectively applied to detect TC residues in wastewater, honey, and milk samples. It achieved an average recovery rate of 101.19% with a small variation of 5.16%. The validation was carried out using an enzyme-linked immunosorbent assay. This approach demonstrates high sensitivity and selectivity, making it well suited for detecting leftover antibiotics in food when using suitable aptamers.

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep sequencing

BACKGROUND

Colorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non-targeted deep-sequencing strategies enable nowadays full microbiome characterization up to species level.

AIM

We aimed to analyze both bacterial and viral communities in CRC using these strategies.

MATERIALS & METHODS

We analyzed bacterial and viral communities using both DNA and RNA deep-sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples.

RESULTS

No viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002).

DISCUSSION

Sequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC.

CONCLUSION

Joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.

Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater

BACKGROUND

Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants.

RESULTS

Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MICAs (2 to 32 mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization.

CONCLUSIONS

Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.

The occurrence and abundance of antibiotic resistance genes in rivers of tropical islands: a case of Hainan Island, China

In this study, the occurrence and distribution of 49 antibiotic resistance genes (ARGs) and two integrase genes (intl1, intl2) in three major rivers of Hainan Island, China, were investigated in July 2021, and to explore the spatial distribution of the target genes in the three rivers with the potential influencing factors such as regional characteristics and environmental factors. The results showed that a total of 46 ARGs and two integrase genes were detected in water and sediment, and the absolute abundance of ARGs ranged from 1.16 × 103 to 2.97 × 107 copies/L and 3.34 × 103-1.55 × 107 copies/g. ARGs of macrolides, aminoglycosides, and sulfonamides were this study's main types of ARGs. The aadA2, tetE, ermF, tetX, aac(6')-Ib, tetW, and qnrS genes are predominant ARGs in the water and sediment of the three rivers. The relative abundance of ARGs shows higher abundance in the midstream and downstream and lower abundance in the upstream and estuarine. After conducting a correlation analysis, it was found that there was a significant positive correlation between the ARGs detected in the water of the three main rivers. However, in sediment, tetC was negatively correlated with tetQ, macB was negatively correlated with ermF and ereA (p < 0.05), while the remaining ARGs showed positive correlations. Specifically, there was no significant positive correlation between tetQ and tetC, macB and ereA, and ermF in the sediments. Among the nine environmental factors studied, pH was found to be the main factor associated with the occurrence of ARGs in the aquatic environment, but it was also significantly associated with only nine ARGs. Among the detected heavy metals, only Cd and Zn showed significant correlations with the two ARGs in the water bodies of the three main rivers. It indicated that the pollution of ARGs in the three major rivers was in the initial stage, the detection abundance was low, the influence of environmental factors was small, and the interaction between ARGs seemed to be the main driving force. This study provides a scientific basis for further understanding the occurrence of ARGs and their influencing factors in a tropical island environment, and lays a foundation for subsequent management.

Resource degradation of pharmacy sludge in sub-supercritical system with high degradation rate of 99% and formic acid yield of 32.44

In response to the social goal of 'carbon peak and carbon neutral' in the 14th Five-Year Plan of China, this article used Enrofloxacin (ENR), a common antibiotic, as a model compound to study the method of efficiently degrading pharmaceutical sludge and simultaneously producing Formic Acid (FA), hydrogen storage energy, in a sub-supercritical system. The Ni/SnO2 bimetallic catalyst, which was prepared by the equal volume impregnation method, was used for the liquid phase catalysis. As shown by the results, when the reaction temperature was 330°C, and the addition amount of H2O2 was 0.38 mL, the degradation rate of antibiotics could reach 99% after the reaction proceeded for 6 h. In terms of the resource utilization, the yield of FA could reach up to 32.44%. The resource utilization efficiency with Ni/SnO2 catalyst in sub-/supercritical reaction was about 2.5 times higher than that without catalyst. The kinetic reaction model was established to explore the reaction rate of the antibiotic degradation process. In addition, the Ea and the frequency factor of the reaction were 6455 J/mol and 5.78, respectively. As shown by characterization, the prepared Ni/SnO2 bimetallic catalyst had good activity and has already passed repeated stability experiments. In short, this method has broad application prospects in antibiotic catalysis and resource degradation.

Antimicrobial resistome during the transition from an integrated to a monoculture aquaculture farm in southern China

Integrated and monoculture freshwater aquaculture systems are often regarded as important reservoirs for antimicrobial resistance genes (ARGs) and antimicrobial resistance bacteria (ARBs), yet only a few studies have assessed differences in the antimicrobial resistome and antibiotic residues between aquaculture modes. In this study, a metagenomic approach was used to comprehensively explore the dynamic patterns and potential transmission mechanisms of ARGs in ducks, human workers, fish, water and sediments during the transition from an integrated to a monoculture freshwater aquaculture mode and to investigate the associations of ARGs with potential hosts in microbial communities using network analysis and a binning approach. The results showed that the abundance and diversity of ARGs were higher under integrated fish-duck farming than in single fish ponds. During the transition from an integrated to a monoculture aquaculture farm, ARGs in workers and sediments were not easily removed. However, ARGs in the aquatic environment underwent regular changes. In addition, duck manure was probably the most dominant source of ARGs in the duck farm environment. Network analysis indicated that Escherichia spp. were the most dominant hosts of ARGs. Variation partitioning analysis (VPA) showed that in water samples, the bacterial community played an important role in the ARG profile. In addition, we identified a potential risk of the presence of highly virulent and antimicrobial-resistant Klebsiella pneumoniae in workers. These results help assess the risk of ARG transmission in integrated and monoculture aquaculture farms and suggest that we should strengthen the monitoring of long-term resistance in integrated aquaculture environments.

Reservoirs of antimicrobial resistance in the context of One Health

The emergence and spread of antimicrobial resistance (AMR) and resistant bacteria, are a global public health challenge. Through horizontal gene transfer, potential pathogens can acquire antimicrobial resistance genes (ARGs) that can subsequently be spread between human, animal, and environmental reservoirs. To understand the dissemination of ARGs and linked microbial taxa, it is necessary to map the resistome within different microbial reservoirs. By integrating knowledge on ARGs in the different reservoirs, the One Health approach is crucial to our understanding of the complex mechanisms and epidemiology of AMR. Here, we highlight the latest insights into the emergence and spread of AMR from the One Health perspective, providing a baseline of understanding for future scientific investigations into this constantly growing global health threat.

Removal performance, biotransformation pathways and products of sulfamethoxazole in vertical subsurface flow constructed wetlands with different substrates

For decades, sulfamethoxazole (SMX) has been frequently detected in the aquatic environments due to its high usage and refractory to degradation. Constructed wetland (CW) is regarded as an efficient advanced wastewater technology to eliminate organic pollutants including SMX. In CW system, substrate adsorption and further biodegradation are extremely important in SMX removal; however, the removal performance of SMX by CWs with different substrates varies greatly, and the biotransformation pathways, products, and mechanisms of SMX remain unclear. To address this, we constructed a CW with conventional substrate (CS, gravel) as control (C-CW) and three CWs with emerging substrates (ES, biochar, zeolite and pyrite for B-CW, Z-CW and P-CW, respectively), and explored the performance and mechanisms of SMX removal in CWs. Results illustrated that the removal performance of SMX in CWs with ES reached 94.89-99.35%, and significantly higher than that with CS of 89.50% (p < 0.05). Biodegradation contributed >90% SMX removal in all CWs. The microbial compositions and functions differed among CWs at the middle layer (mixed layer), which shaped diverse resistance pattern and metabolism pathways of microbiomes under SMX stress: P-CW and B-CW cope with SMX stress by enhancing material and energy metabolism, whereas Z-CW does that by enhancing metabolism and exocytosis of xenobiotics. Additionally, nine transformation pathways with 15 transformation products were detected in this study. A reversible process of desamino-SMX being reconverted to SMX might exist in P-CW, which caused a lower SMX removal efficiency in P-CW. This study provided a comprehensive insight into the processes and mechanisms of SMX removal in CWs with different substrates, which would be a useful guidance for substrate selection in CWs in terms of enhanced micropollutants removal.

Review: Current understanding on biological filtration for the removal of microcystins

Harmful algal blooms (HABs) have become a global problem not only in aquatic habitats but also in public health and safety due to the production of cyanotoxins as their secondary metabolites. Among the various identified cyanotoxin groups, microcystins (MCs) are one of the most prevalent cyanotoxin detected during HABs. Different strategies including advanced physical and chemical treatment processes have been developed to mitigate the threat of cyanotoxins in water utilities, but these have revealed certain limitations in terms of high operational costs, low removal efficacy, and harmful by-products formation. Recently, biological filtration systems (BFS) have gained attention for safe drinking water production as they can treat various natural organic matter (NOM) and emerging contaminants through a highly efficient and environmentally sustainable process. However, limited attention has been given to understand the current research progress, research challenges, and knowledge gaps for the successful implementation of BFS for MC removal. Therefore, in this review, currently identified MC biodegradation pathways and MC-degrading microorganisms with their degradation rates are summarized, which may be pivotal for studying bioaugmented BFS to enhance the MC removal during HABs. Moreover, both laboratory and field studies on BFS for MC removal are reviewed, followed by a discussion of current challenges and future research needs for the practical application of BFS.

Growth and prevalence of antibiotic-resistant bacteria in microplastic biofilm from wastewater treatment plant effluents

It is accepted that Microplastic (MP) biofilms accumulates antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in water. ARB/ARGs and MPs are emerging pollutants of concern due to various associated health risks. The objective of this study was to 1) investigate the ARB community in a pilot-scale wastewater treatment plant (WWTP) effluent, 2) to study and visualize the ARB/ARGs in MP biofilm grown in WWTP effluent and tap water, and 3) to analyze microplastic adherent ARB/ARGs in the biofilm and planktonic ARB/ARGs in the filtrate under controlled conditions. Results indicated the dominance of Pseudomonas, Aeromonas, and Bacillus among isolated ARB in WWTP effluent. Representative resistance strains were incubated in 300 mL water containing commercial polystyrene beads of 300550 μm diameter (MP) in a series of batch experiments. Microbiological, molecular, and microscopic analyses were performed by enumeration, 16srRNA, real-time polymerase chain reaction (qPCR), and Field Emission-Scanning Electron Microscopy (FEG-SEM) techniques. The analyzed viable ARB indicated an increasing trend in MP biofilms between days 3 and 5. It further decreased on days 7 and 9. The prevalence of ARB in the filtrate and MP biofilm varied as a function of time and TOC level, while no significant impacts were observed for minor temperature variation, low antibiotic pressure, and increased MP mass with few exceptions. Relative abundance of ARGs (vanA, sul1) and integron integrase gene (intl1) in MP biofilm were significantly different across different TOC levels, time, and antibiotic pressure. ARGs and intl1 were detected in the MP biofilm in tap water and WWTP effluent on day 30.

Removal of tetracycline from wastewater using g-C3N4 based photocatalysts: A review

Tetracycline is currently one of the most consumed antibiotics for human therapy, veterinary purpose, and agricultural activities. Tetracycline worldwide consumption is expected to rise by about more than 30% by 2030. The persistence of tetracycline has necessitated implementing and adopting strategies to protect aquatic systems and the environment from noxious pollutants. Here, graphitic carbon nitride-based photocatalytic technology is considered because of higher visible light photocatalytic activity, low cost, and non-toxicity. Thus, this review highlights the recent progress in the photocatalytic degradation of tetracycline using g-C₃N₄-based photocatalysts. Additionally, properties, worldwide consumption, occurrence, and environmental impacts of tetracycline are comprehensively addressed. Studies proved the occurrence of tetracycline in all water matrices across the world with a maximum concentration of 54 μg/L. Among different g-C₃N₄-based materials, heterojunctions exhibited the maximum photocatalytic degradation of 100% with the reusability of 5 cycles. The photocatalytic membranes are found to be feasible due to easiness in recovery and better reusability. Limitations of g-C₃N₄-based wastewater treatment technology and efficient solutions are also emphasized in detail.

The variations of antibiotics and antibiotic resistance genes in two subtropical large river basins of south China: Anthropogenic impacts and environmental risks

Emission of antibiotics into riverine environments affects aquatic ecosystem functions and leads to the development of antibiotic resistance. Here, the profiles of forty-four antibiotics and eighteen antibiotic resistance genes (ARGs) were analyzed in two large rivers of the Pearl River System. In addition, the risks of ecotoxicity and resistance selection posed by the antibiotics were estimated. As compared to the reservoirs, the river sections close to the urban and livestock areas contained more antibiotics and ARGs. Seasonal variations of antibiotics (higher in the dry season) and relative ARGs (normalized by 16S rRNA gene, higher in the wet season) were found in the water, but not in the sediment. Sulfonamide resistance genes were the most prevalent ARGs in both river water and sediment. Antibiotic concentration was correlated with ARG abundance in the water, indicating that antibiotics play a critical role in ARG spread. In addition, oxytetracycline was the most abundant antibiotic with concentrations up to 2030 ng/L in the water and 2100 ng/g in the sediment respectively, and posed the highest risks for resistance selection. Oxytetracycline, tetracycline and sulfamethoxazole were expected to be more ecotoxicologically harmful to aquatic organisms, while ofloxacin, enrofloxacin, norfloxacin, chlortetracycline, oxytetracycline and tetracycline posed ecotoxicological risks in the sediment. The Nanliujiang river with intensive livestock activities was contaminated by antibiotics and ARGs and faced high ecotoxicological and resistance selection risks. Collectively, these findings reflect the impacts of anthropogenic activities on the spread of antibiotic resistance in large river basins.

Metagenomics-based antibiotic resistance genes diversity and prevalence risk revealed by pathogenic bacterial host in Taihu Lake, China

In recent decades, antibiotics and antibiotic resistance genes (ARGs) have been regarded as emerging pollutants. In Taihu Lake, as a typical representative of freshwater system in China, the ARGs occurrence and abundance was of great importance for ecological risk control and public health protection. In this research, high-throughput sequencing and metagenomics technique were used to investigate the seasonal ARGs profile in overlying water and sediment at typical area of Taihu Lake. Besides, taxonomy pattern of ARGs host bacteria and potential pathogens were identified. The results showed that 33 ARG subtypes and 11 ARG types were detected in research area, among which bacitracin, multidrug and sulfonamides resistance gene were with the highest abundance. The relative abundance of ARGs in overlying water and sediment ranged from 1.68 to 661.05 ppm and from 1.93 to 49.47 ppm, respectively. ARG host (18 bacteria genus) were identified and annotated, among which Clostridium botulinum, Pseudomonas aeruginosa and Klebsiella pneumonia were pathogenic bacteria. The pathogens were mostly detected at Xukou Bay in spring and fall, which might be caused by the inlet water from aquaculture area of Yangcheng Lake. Pseudomonas was the most abundant ARGs host (ant2ib, baca, bl2d_oxa2,mexb, mexf, mexw and oprn), which may facilitate the propagation of ARGs in freshwater system.

Molecular characterization of resistance determinants and mobile genetic elements of ESBL producing multidrug-resistant bacteria from freshwater lakes in Kashmir, India

BACKGROUND

Antibiotic resistance conceded as a global concern is a phenomenon that emerged from the bacterial response to the extensive utilization of antimicrobials. The expansion of resistance determinants through horizontal transfer is linked with mobile genetic elements (MGEs) like transposons, insertion sequences, and integrons. Heavy metals also create consequential health hazards. Metal resistance gene in alliance with antibiotic resistance genes (ARGs) and MGEs is assisting bacteria to attain exalted quantity of resistance.

METHODOLOGY

The present work was carried out to study ARGs blaCTX-M, AmpC, qnrS, MGEs like ISecp1, TN3, TN21, and Int I by performing PCR and sequencing from Wular and Dal lakes of Kashmir; India. The genetic environment analysis of blaCTX-M-15 was carried out using PCR amplification, and sequencing approach followed by in-silico docking and mutational studies. Co-occurrence of ARGs and HMRGs was determined. Plasmid typing was done using PCR-based replicon typing (PBRT) and conjugation assay was also performed.

RESULTS

Out of 201 isolates attained from 16 locations, 33 were ESBLs producers. 30 ESBL displaying isolates were perceived positive for CTX-M gene, followed by AmpC (17), qnrS (13), ISecp1 (15), TN3 (11), TN21 (11), Int I (18), and SulI (14). The genetic environment of blaCTX-M-15 was observed as (ISEcp1-blaCTX-M-15-orf477), classical promoter-10 TACAAT and -35 TTGAA was found at the 3' region. The 3D structure of CTX-M-15 and ISEcp1 was generated and CTX-M-15-ISEcp1 (R299L) docking and mutation showed a reduction in hydrogen bonds. Co-occurrence of antibiotics and HMRGs (mer, sil, and ars) was found in 18, 14, and 8 isolates. PBRT analysis showed the presence of Inc. groups- B/O, F, I1, HI1, FIA, HI2, N, FIB, L/M. Molecular analysis of transconjugants showed the successful transfer of ARGs, MGEs, and HMRGs in the E. coli J53 AZ^R strain.

CONCLUSION

This study highlights the occurrence of ESBL producing bacteria in the aquatic environment of Kashmir India that can serve as a reservoir of ARGs. It also discussed the molecular mechanisms of MGEs which can help in containing the spread of antibiotic resistance.

Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China

Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in selected original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Twenty types of ARG were detected in the water samples. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16S rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion. The composition of ARGs in three different rivers was similar, indicating that climate plays an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological and geographical distribution characteristics should be further explored.

Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.

Anaerobes and methanogens dominate the microbial communities in water harvesting ponds used by Kenyan rural smallholder farmers

Many rural smallholder farmers in Kenya use water-harvesting ponds, to collect rainwater, as sustainable sources of water for domestic and agricultural purposes. There is currently limited information regarding the microbial ecology in these ponds. Here, we used High Throughput Sequencing (HTS) to characterize the microorganisms present (including potential pathogens and indicator species) alongside ion chromatography to measure water chemistry (anion and cation concentration). Fluoride and magnesium concentration were the strongest predictor variables of the microbial community. Obligately or facultatively anaerobic bacterial genera (e.g. Spirochaeta and Opitutus) were abundant within the bacterial community, whilst Woesearchaeota and methanogens dominated the archaeal community. This suggests the water in the ponds is hypoxic or anoxic, and if used for irrigation, may potentially impact crop yield and viability. In addition, the opportunistic pathogen non-tuberculous mycobacteria (NTM), Mycobacterium fortuitum was found, comprising >1% of the bacterial community, suggesting a potential human health risk. Here we suggest low-cost changes to pond management, to improve or ameliorate pond anoxia and remove pathogens to benefit the livelihoods and welfare of these farms. This study also shows the applicability of HTS to broadly screen the microbial communities, assess water quality, and identify potentially pathogenic groups.

A comprehensive review on biodegradation of tetracyclines: Current research progress and prospect

The release of tetracyclines (TCs) in the environment is of significant concern because the residual antibiotics may promote resistance in pathogenic microorganisms, and the transfer of antibiotic resistance genes poses a potential threat to ecosystems. Microbial biodegradation plays an important role in removing TCs in both natural and artificial systems. After long-term acclimation, microorganisms that can tolerate and degrade TCs are retained to achieve efficient removal of TCs under the optimum conditions (e.g. optimal operational parameters and moderate concentrations of TCs). To date, cultivation-based techniques have been used to isolate bacteria or fungi with potential degradation ability. Moreover, the biodegradation mechanism of TCs can be unveiled with the development of chemical analysis (e.g. UPLC-Q-TOF mass spectrometer) and molecular biology techniques (e.g. 16S rRNA gene sequencing, multi-omics sequencing, and whole genome sequencing). In this review, we made an overview of the biodegradation of TCs in different systems, refined functional microbial communities and pure isolates relevant to TCs biodegradation, and summarized the biodegradation products, pathways, and degradation genes of TCs. In addition, ecological risks of TCs biodegradation were considered from the perspectives of metabolic products toxicity and resistance genes. Overall, this article aimed to outline the research progress of TCs biodegradation and propose future research prospects.

Microbial Community Structure and Bacterial Lineages Associated with Sulfonamides Resistance in Anthropogenic Impacted Larut River

Anthropogenic activities often contribute to antibiotic resistance in aquatic environments. Larut River Malaysia is polluted with both organic and inorganic pollutants from domestic and industrial wastewater that are probably treated inadequately. The river is characterized by high biochemical oxygen demand, chemical oxygen demand, total suspended solids, ammonia, and heavy metals. In our previous study, sulfonamides (SAs) and sulfonamide resistance genes (sul) were detected in the Larut River. Hence, in this study, we further examined the microbial community structure, diversity of sulfonamide-resistant bacteria (SARB), and their resistance genes. The study also aimed at identifying cultivable bacteria potential carriers of sul genes in the aquatic environment. Proteobacteria (22.4–66.0%), Firmicutes (0.8–41.6%), Bacteroidetes (2.0–29.4%), and Actinobacteria (5.5–27.9%) were the most dominant phyla in both the effluents and river waters. SARB isolated consisted only 4.7% of the total genera identified, with SAR Klebsiella as the most dominant (38.0–61.3%) followed by SAR Escherichia (0–22.2%) and Acinetobacter (3.2–16.0%). The majority of the SAR Klebsiella isolated from the effluents and middle downstream were positive for sul genes. Sul genes-negative SAR Escherichia and Acinetobacter were low (<20%). Canonical-correlation analysis (CCA) showed that SAs residues and inorganic nutrients exerted significant impacts on microbial community and total sul genes. Network analysis identified 11 SARB as potential sul genes bacterial carriers. These findings indicated that anthropogenic activities exerted impacts on the microbial community structure and SAs resistance in the Larut River.

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.

Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing

The contamination of antibiotic resistance genes (ARGs) may directly threaten human health. This study used a metagenomic approach to investigate the ARG profile in a drinking water treatment system (DWTS) in south China. In total, 317 ARG subtypes were detected; specifically, genes encoding bacitracin, multidrug, and sulfonamide were widely detected in the DWTS. Putative ARG hosts included Acidovorax (6.0%), Polynucleobacter (4.3%), Pseudomonas (3.4%), Escherichia (1.7%), and Klebsiella (1.5%) as the enriched biomarkers in the DWTS, which mainly carried bacitracin, beta-lactam, and aminoglycoside ARGs. From a further analysis of ARG-carrying contigs (ACCs), Stenotrophomonas maltophilia and Pseudomonas aeruginosa were the most common pathogens among the 49 ACC pathogens in the DWTS. The metagenomic binning results demonstrated that 33 high-quality metagenome-assembled genomes (MAGs) were discovered in the DWTS; particularly, the MAG identified as S. maltophilia-like (bin.195) harbored the greatest number of ARG subtypes (n = 8), namely, multidrug (n = 6; smeD, semE, multidrug_transporter, mexE, semB, and smeC), beta-lactam (n = 1; metallo-beta-lactamase), and aminoglycoside [n = 1; aph(3’)-IIb]. The strong positive correlation between MGEs and ARG subtypes revealed a high ARG dissemination risk in the DWTS. Based on the pure-culture method, 93 isolates that belong to 30 genera were recovered from the DWTS. Specifically, multidrug-resistant pathogens and opportunistic pathogens such as P. aeruginosa, Bacillus cereus, and S. maltophilia were detected in the DWTS. These insights into the DWTS’s antibiotic resistome indicated the need for more comprehensive ARG monitoring and management in the DWTS. Furthermore, more effective disinfection methods need to be developed to remove ARGs in DWTSs, and these findings could assist governing bodies in the surveillance of antibiotic resistance in DWTSs.

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.

Silver and Gold Nanoparticles for Antimicrobial Purposes against Multi-Drug Resistance Bacteria

Several pieces of research have been done on transition metal nanoparticles and their nanocomplexes as research on their physical and chemical properties and their relationship to biological features are of great importance. Among all their biological properties, the antibacterial and antimicrobial are especially important due to their high use for human needs. In this article, we will discuss the different synthesis and modification methods of silver (Ag) and gold (Au) nanoparticles and their physicochemical properties. We will also review some state-of-art studies and find the best relationship between the nanoparticles' physicochemical properties and potential antimicrobial activity. The possible antimicrobial mechanism of these types of nanoparticles will be discussed in-depth as well.

Metagenomic profiles and health risks of pathogens and antibiotic resistance genes in various industrial wastewaters and the associated receiving surface water

The aquatic environment may represent an essential route for transmission of antibiotic resistance to opportunistic human pathogens. Since industrial wastewater is discharged into the river after treatment, understanding the distribution of antibiotic resistance genes (ARGs) in river systems and the possibility of pathogens acquiring antibiotic resistance are challenges with far-reaching significance. This work mainly studied distribution profiles of pathogens and ARGs, and compared their health risk in various industrial wastewater with that of river water. Results showed that 166 pathogens were concurrently shared by the six water samples, with Salmonella enterica and Pseudomonas aeruginosa being the most abundant, followed by Fusarium graminearum and Magnaporthe oryzae. The similar composition of the pathogens suggests that pathogens in river water may mainly come from sewage discharge of slaughterhouses and that changes in water quality contribute significantly to the prevalence of these pathogens. Of the 57 ARG types detected, bacitracin was the most abundant, followed by sulfonamide, chloramphenicol, tetracycline, and aminoglycoside. Strikingly, the wastewater from a pharmaceutical factory producing Chinese medicine was also rich in bacA, sul1, mexW, mexB, mexF and oprn. It can be seen from the co-occurrence patterns that pathogens and the main ARGs have strong co-occurrence. Higher abundance of offensive virulence factors in industrial wastewater and their strong correlation with pathogens containing ARGs suggest higher microbiological risk. These findings highlight the need to assess ARG acquisition by pathogens in the surface water of human-impacted environments where pathogens and ARGs may co-thrive.

Ecological insights into the elevational biogeography of antibiotic resistance genes in a pristine river: Metagenomic analysis along the Yarlung Tsangpo River on the Tibetan Plateau

Presently, the prevalence of antibiotic resistance genes (ARGs) is regarded as an emerging environmental issue, and many studies have illuminated biogeographical patterns of the antibiotic resistome. However, few studies have investigated elevational biogeography and associated assembly mechanisms of ARGs in natural river systems. Accordingly, in the present study, we used metagenomics approaches to analyze the biogeographical pattern of ARGs along the pristine Yarlung Tsangpo River on the Tibetan Plateau. Our study retrieved the baseline profiles of ARGs in the pristine river and showed that the ARGs were dominated by bacA, which was resistant to bacitracin and represented more than 91% of total ARGs. The diversity and abundance of ARGs in the pristine river were lower than those in the human-impacted area, suggesting that the antibiotic resistome evolved and was promoted in a human-impacted environment. Furthermore, an elevational distance-decay relationship of ARGs was observed along the pristine Yarlung Tsangpo River, which provided strong evidence of ARG dissimilarity under the elevational variation. Elevational gradients could lead to changes in environmental variables and spatial factors, and consequently alter ARG composition. Elevational gradients could influence the assembly processes of ARGs. The deterministic and stochastic assembly processes both played critical roles and equally participated in shaping ARG composition at the watershed scale along the Yarlung Tsangpo River, and with increasing elevational variation along the river, the ecological processes of ARG assembly shifted from deterministic to stochastic. Moreover, abundant and rare ARGs were tentatively separated to investigate the difference and similarity in their distributions. Although abundant and rare ARGs presented similar distance-decay relationships, rare ARGs were more diverse and vulnerable to the dispersal process and mutation. Overall, our study provides valuable ecological insights to profile the large-scale elevational patterns of ARGs in a pristine river system, thereby providing important information for public health and environmental management.

Distribution of antibiotic resistance genes in the environment

The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990-2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept.

Carbon-doped WO3 electrochemical aptasensor based on Box-Behnken strategy for highly-sensitive detection of tetracycline

Aptamer has been proved to be an important probe for antibiotic detection. Here, the electrical signal was doubly amplified by the synergistic effect of C-WO₃ and AuNPs. The probe structure has a specific recognition effect on tetracycline, which improves the selectivity and anti-interference of the sensor. With the assistance of BBD strategy, the experimental errors of the C-WO₃@AuNPs aptasensor were reduced and the best conditions for its preparation were obtained. This was conducive to obtain the best electrical signal transmission capacity of the electrode, greatly improved the sensor sensitivity. Under this mechanism, the antibiotic sensor achieved a low detection range (0.1 nM-100 nM) and a low detection limit (4.8 × 10^-2 nM). The sensor showed excellent selectivity even in the presence of coexisting pollutants. This work explored the mechanism of charge change and demonstrated the role of probes in antibiotic sensing, providing important prospects of future applications in electrochemical sensors.

Exploring the allochthonous pollution influence on bacterial community and co-occurrence dynamics of River Ganga water through 16S rRNA-tagged amplicon metagenome

River Ganga is one of the largest and most sacred rivers of India. This river is largely affected by anthropogenic activities causing significant increase in water pollution. The impact of drains discharging polluted water on the bacterial community dynamics in the river remains unexplored. To elucidate this, the targeted 16S rRNA V3-V4 variable region amplicon sequencing and bioinformatic analysis were performed using water from upstream, drain, and downstream of river Ganga. Analysis revealed significant difference in relative abundances of bacterial communities. The increase in bacterial abundance and alpha diversity was detected in the downstream compared to the upstream. Environmental factors were found significantly different between upstream and downstream water. At the phyla level, highly abundant taxa such as Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Verrucomicrobia were observed. Bacterial genera like Prevotella, Bacteroides, Blautia, and Faecalibacterium (fecal indicator) had higher abundance in the downstream site. Network co-occurrence revealed that bacterial communities have a modular profile with reduced interaction in drain and downstream water. The network of co-occurring bacterial communities consists of 283 nodes with edge connectivity of 6900, 7074, and 5294 in upstream, drain, and downstream samples, respectively. Upstream communities exhibited the highest positive interaction followed by the drain and the downstream sites. Additionally, highly abundant pathogenic species such as Acinetobacter baumannii and Prevotella copri were also detected in all samples. This study suggests the drain to be allochthonous pollution vector that significantly contributes to bacterial community enrichment. From the results of this study, it is apparent that the lotic water may be used as the ecological reference to understand and monitor the variations in the bacterial communities and their co-occurrence dynamics in the fresh water ecosystems.

Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission

The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain "live" (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines' implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.

Occurrence, fate, and risk assessment of typical tetracycline antibiotics in the aquatic environment: A review

Tetracyclines (TCs), used as human and veterinary medicines, are the most widely used antibiotics. More than 75% of TCs are excreted in an active form and released into the environment through human and animal urine and feces, causing adverse effects on the ecological system and human health. Few articles review the environmental occurrence and behaviors of TCs, as well as their risks and toxicities. Here, we comprehensively summarized the recent advances on the following important issues: (1) Environmental occurrence of TCs. TCs are used globally and their occurrence in the aquatic environment has been documented, including surface water, groundwater, drinking water, wastewater, sediment, and sludge. (2) Environmental behaviors of TCs, particularly the fate of TCs in wastewater treatment plants (WWTPs). Most WWTPs cannot effectively remove TCs from wastewater, so alternative methods for efficient removal of TCs need to be developed. The latest degradation methods of TCs are summarized, including adsorption, photocatalytic, photochemical and electrochemical, and biological degradations. (3) Toxicities and possible risks of TCs. The toxicological data of TCs indicate that several TCs are more toxic to algae than fish and daphnia. Risk assessments based on individual compound exposure indicate that the risks arising from the current concentrations of TCs in the aquatic environment cannot be ignored.

Characteristics and interactions of bioaerosol microorganisms from wastewater treatment plants

Bacteria and fungi are abundant and ubiquitous in bioaerosols from wastewater treatment plants (WWTPs). However, the specificity and interactions of bioaerosol microorganism, particularly of potential pathogens, from WWTPs are still poorly understood. In this study, we investigated 9 full-scale WWTPs in different areas of China for 3 years, and found microbial variations in bioaerosols to be associated with regions, seasons, and processes. Relative humidity, total suspended particulates, wind speed, temperature, total organic carbon, NH₄⁺, Cl^- and Ca²⁺ were the major factors influencing this variation, and meteorological factors were more strongly associated with the variation than chemical composition. In total, 95 and 22 potential bacterial and fungal pathogens were detected in bioaerosols, respectively. The linear discriminant analysis effect size method suggested that Serratia, Yersinia, Klebsiella, and Bacillus were discriminative genera in bioaerosols on the whole, and were also hub niches in the interactions within potential bacterial pathogens, based on network analysis. Strong co-occurrences such as Serratia-Bacillus and Staphylococcus-Candida, and co-exclusions such as Rhodotorula-Cladosporium and Pseudomonas-Candida, were found within and between potential bacterial and fungal pathogens in bioaerosols from WWTPs. This study furthers understanding of the biology and ecology of bioaerosols from WWTPs, and offers a theoretical basis for determining bioaerosol control.

Bacterial diversity and functional profile of microbial populations on surfaces in public hospital environments in South Africa: A high throughput metagenomic analysis

With the introduction of the One Health approach to global health advocated by the World Health Organization, the role of the environment as a reservoir and transmission route for diverse microorganisms is increasingly being recognised globally. This study investigated the diversity and functional profiles of bacterial communities using high-throughput metagenomics of the 16S rRNA gene in samples collected from environmental surfaces in different levels of healthcare in South Africa. A total of 150 samples were collected in three public hospitals [District (A), Regional (C) and Central (B)] from intensive care and paediatric wards. Military hospitals were excluded. Swabs were taken from mattresses, drip stands, ward telephones, patient files and sinks. A total of 7,996,346 reads were found, of which 7,319,569 were quality-filtered reads. Unique (and shared) microbial community structures were identified within the different hospital levels, locations and sample source. A total of 11 phyla, 29 classes, 50 orders, 105 families, 190 genera and 288 known species were identified. The primary phyla identified were Proteobacteria, Firmicutes and Actinobacteria. The dominant class identified was Gamma-proteobacteria, followed by Bacilli and Actinobacteria. Acinetobacter (16.08%), Citrobacter (13.64%), Staphylococcus (9.65%) and Corynebacterium (6.15%) were predominant genera. Although the functional profile analysis identified citrate cycle (TCA), signal transduction mechanisms, bisphenol degradation, tyrosine metabolism and transcription-factors as the dominant pathways, human disease functional classes, including involvement in antibiotic resistance, were significantly identified. The drip stands, patient files and ward telephones in all the wards of Hospitals A and C contained a higher number of human diseases functional classes. These findings highlight the potential of different hospital environments to serve as reservoirs and possible sources of bacterial pathogens; thus, the need for better monitoring and hygienic practices within the hospital environment.

Metagenomic insights into the profile of antibiotic resistomes in a large drinking water reservoir

Reservoirs play a vital role in the control and management of surface water resources. However, the long water residence time in the reservoir potentially increases the storage and accumulation of antibiotic resistant genes (ARGs). The full profiles and potential health risks of antibiotic resistomes in reservoirs are largely unknown. In this study, we investigated the antibiotic resistomes of water and sediment during different seasons in the Danjiangkou Reservoir, which is one of the largest reservoirs in China, using a metagenomic sequencing approach. A total of 436 ARG subtypes belonging to 20 ARG types were detected from 24 water and 18 sediment samples, with an average abundance of 0.138 copies/cell. The overall ARG abundance in the sediment was higher than that in the water, and bacitracin and vancomycin resistance genes were the predominant ARG types in the water and sediment, respectively. The overall ARG abundance in the dry season was higher than that in the wet season, and a significant difference in ARG subtype compositions was observed in water, but not in the sediment, between the different seasons. The potential horizontal gene transfer frequency in the water was higher than that in the sediment, and the ARGs in water mainly came from the sediment upstream of the reservoir. The metagenomic assembly identified 14 contigs as ARG-carrying pathogens including Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa, and 3 of 14 carried virulence factors. Overall, the potential public health risks posed by resistomes in the water of the Danjiangkou Reservoir were higher in the dry season than in the wet season. Based on these results, strategies including sediment control and pathogen monitoring are suggested for water safety management in drinking water reservoirs.

Co-selection and stability of bacterial antibiotic resistance by arsenic pollution accidents in source water

Frequent heavy-metal pollution accidents severely deteriorated the source water quality of drinking water treatment plants (DWTP). Limited data have explicitly addressed the impact of these incidents on bacterial antibiotic resistance (BAR). In present study, we investigated the shift of antibiotic resistome caused by heavy metal pollution incidents via simulating an arsenic shock loading [As (III)], along with the associated risks imposed on drinking water systems. The results indicated that a quick co-selection of antibiotic resistant bacteria (ARB) was achieved after exposure to 0.2-1 mg/L As (III) for only 6 h, meanwhile, there was an increase of relative abundance of antibiotic resistance genes (ARGs) and mobile genetic elements. Most of the co-selected BAR could be maintained for at least 4 days in the absence of As (III) and antibiotics, implying that the pollution in source water possibly contributed to the preservation and proliferation of antibiotic resistance determinants in the subsequent DWTP. Bacterial community structure analysis showed a strong correlation between bacterial community shift and BAR promotion, and enrichment of opportunistic bacteria (e.g. Escherichia-Shigella, Empedobacter sp. and Elizabethkingia sp.). The results indicated a potential epidemiological threat to the public due to accident-level arsenic contamination in the source water. This study gave insight into understanding the source water pollution accidents from the perspective of bio-hazard and biological risks, and highlighted a neglected important source of BAR in drinking water systems.

The impacts of different high-throughput profiling approaches on the understanding of bacterial antibiotic resistance genes in a freshwater reservoir

Bacterial antibiotic resistance genes (ARGs), a kind of emerging environmental pollutants, greatly threat human health through pathogenic bacteria. High-throughput quantitative PCR (HT-qPCR) and metagenomic approaches are two popular tools applied in aquatic environmental ARGs monitoring. However, current poor knowledge of different ARG profiling approaches' impacts on the understanding of the ARGs in aquatic environments greatly limit the further field application of these two approaches. For filling such knowledge gap, this study simultaneously employed these two approaches to examine and compare the ARGs in a freshwater reservoir across space and time. We found metagenomic approach detected more ARG subtypes and much higher bacitracin resistance genes' abundances than HT-qPCR. In general, HT-qPCR and metagenomics analyses both revealed similar ARG dynamic patterns and co-occurrence patterns between ARGs and bacterial taxa as well as the relationships between ARGs and environmental factors. Our results indicated the impacts of different ARG profiling approaches on the understanding of bacterial ARGs might be minor or negligible. HT-qPCR approach has the superiorities of time-saving, absolute quantification, low requirement for bioinformatics skills but also has some drawbacks including higher PCR amplification & primer bias, higher primer dependency and relative lower ARG subtype quantification capability compared to metagenomic approach. We suggest HT-qPCR approach can be employed for routine aquatic environmental monitoring, and metagenomic approach could be applied in comprehensive surveys for getting more ARG subtype information. Our data can be a useful reference for choosing right ARG profiling approaches for bacterial ARGs monitoring and risk assessment in aquatic environments.

Sediment records of polybrominated diphenyl ethers (PBDEs) in Huaihe River, China: Implications for historical production and household usage of PBDE-containing products

In recent decades, rapid development of industrialization and urbanization caused adverse impact on the aqueous ecology and environment of the Huaihe River basin, China. In this work, three ²¹⁰Pb-dated sediment cores extracted from the middle reach of Huaihe River in Anhui Province, China were analyzed to elucidate the temporal trends and sources of polybrominated diphenyl ethers (PBDEs). Source diagnostics indicated that commercial Deca-BDE, Penta-BDE and Octa-BDE products and debromination of higher brominated BDE compounds were likely the PBDE sources in the Huaihe River. The prevalence of BDE-47 in the sediment cores was attributed to the extensive use of commercial Bromkal 70-5DE and Bromkal DE-71 in the region. BDE-28 was another congener that was prevalent in all sediment samples, suggesting that reductive debromination occurred in the sediments. Dramatic increase of PBDE concentrations in both three cores since the post-1980s could be attributed to the rapid expansion of production of electronic and telecommunication equipment and household usage in China. PBDE temporal trends in core S1 located at rural area mainly reflected the regional and national inputs deriving from long distance atmospheric transport, and the positive correlations between PBDE concentration in core S1 and gross domestic product (GDP) and household appliances production volumes (HPVs) were observed. PBDE inputs at site S3 mainly include the transport of contaminated water and re-suspended fine sediment particles from the upstream site S2, which was located in the industrial area and adjacent to e-waste recycling area. The government efforts to protect the environment and improve the e-waste management resulted in the progressive decrease trends in PBDE concentrations in cores S2 and S3.