Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

COF nanotubes/2D nanosheets heterojunction for superior photocatalytic bactericidal activity even at low concentration and weak light

Microbial fouling is a huge nuisance to equipment operation and human health. Two-dimensional (2D) photocatalytic materials such as g-C3N4, WSe2, and Ti3C2Tx, show immense potential for solar-driven eradication of microbial fouling. However, limited photon absorption and rapid photogenerated electron-hole recombination curtail their photocatalytic efficiency and availability, resulting in the necessity to operate at high concentration and strong light. Herein, three kinds of covalent organic frameworks (COF) nanotubes/2D nanosheets heterojunctions (COF-x) were flexibly constructed by in-situ growing COF nanotubes on g-C3N4, WSe2, and Ti3C2Tx nanosheet substrates via one-pot method. The internal electric field at the COF-x coupling interface enhanced the separation and migration of photogenerated charge pairs, contributing to the antimicrobial reactive oxygen species (ROS) produced by COF-x, which was 2.8-270 times more efficient than those of nanosheets. The bactericidal effect enhanced from 34.13 %∼41.68 % of pure nanosheets to over 99.86 % of COF-x at an ultra-low concentration of 2 µg/mL and a weak visible light of 15 mW/cm2. At a low concentration of 20 µg/mL, the bactericidal rate of COF-x achieved nearly 100 % within 6 h. COF-x also showed exceptional environmental stability and antimicrobial properties under heat, light, acid, alkali, and aqueous conditions, offering a new perspective in photocatalytic antimicrobial/antifouling.

Deciphering the profiles and hosts of antibiotic resistance genes and evaluating the risk assessment of general and non-general hospital wastewater by metagenomic sequencing

Hospital wastewater (HWW) is a substantial environmental reservoir of antibiotic resistance genes (ARGs) and poses risks to public health and aquatic ecosystems. However, research on the diversity, transmission mechanisms, pathogenic hosts, and risks of ARGs in different HWW types is limited. This study involved the collection of HWW samples from 15 hospitals in Hefei, China, which were subsequently categorized as general hospitals (GHs) and non-general hospitals (NGHs). A 280.28-Gbp sequencing dataset was generated using a metagenomic sequencing strategy and analyzed using metagenomic assembly and binning approaches to highlight these issues in GHs and NGHs. Results showed significant differences between GHs and NGHs in ARG distribution, microbial community composition, and hosts of ARGs. Potential pathogens such as Rhodocyclaceae bacterium ICHIAU1 and Acidovorax caeni were more abundant in GHs. Furthermore, plasmid-mediated ARGs (45.21%) were more prevalent than chromosome-mediated ARGs (25.74%) in HWW, with a significantly higher proportion of plasmid-mediated ARGs in GHs compared to NGHs. The co-occurrence of ARGs and mobile genetic elements was more frequent in GHs. Additionally, the antibiotic resistome risk index was higher in GHs (38.73 ± 12.84) than NGHs (22.53 ± 11.80), indicating a greater risk of ARG transmission in GHs. This pioneering study provides valuable insights into the transmission mechanisms and hosts of ARGs in hospital settings, emphasizing the increased risk of ARG transmission in GHs.

Overlooked risk of dissemination and mobility of antibiotic resistance genes in freshwater aquaculture of the Micropterus salmoides in Zhejiang, China

Residual antibiotics in aquaculture ecosystems can exert selective pressures on bacterial communities, driving bacteria to acquire antibiotic resistance genes (ARGs) through gene mutations or horizontal gene transfer (HGT). This study investigated the antibiotic resistance risk in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province. The results revealed that oxytetracycline, ciprofloxacin and florfenicol were up to 300 ng/L, and the proportion of multidrug-resistant genes varied from 32.20 % to 50.70 % in the surveyed aquaculture water. Additionally, approximately 9.80 % of all annotated ARGs were identified as possessing plasmid-mediated horizontal transfer risks. The ARGs host prediction revealed that Actinobacteria carried the highest abundance of ARGs, up to 159.38 (coverage, ×/Gb). Furthermore, the abundance of Paer_emrE, ksgA, ompR and golS were positively correlated with Chlorophyll a concentration (p < 0.05), suggesting that algal blooms might facilitate the evolution and transfer of ARGs. Correlations between ARG abundances and total phosphorus, total nitrogen, pH, electrical conductivity indicated that modulating water quality parameters may serve as a viable strategy to mitigate the eco-environmental risk of ARGs in aquaculture water. This study identified antibiotic resistance characteristics in freshwater aquaculture ecosystems of Micropterus salmoides in Zhejiang Province, establishing a foundation on managing antibiotic resistance risks in such aquaculture environments.

Microcosm experiments deciphered resistome coalescence, risks and source-sink relationship of antibiotic resistance in the soil irrigated with reclaimed water

Reclaimed water is widely used in agriculture irrigation to alleviate water scarcity, whereas the dissemination of antibiotic resistance genes (ARGs) in the soil it introduces has attracted widespread attention. Currently, few studies have systematically elucidated the coalescence of the resistome originating from reclaimed water with the soil's native community. Also, the effects and mechanisms of irrigation on the dissemination of ARGs in soils have yet to be demonstrated. To address this gap, microcosm experiments have been conducted in this study to decipher the resistome coalescence, risks and source-sink relationship of ARGs in soils irrigated with reclaimed water. The results show 237 ARGs, 55 mobile genetic elements (MGEs) and 28 virulence factors were identified in the irrigated soils. Irrigation increased the abundance and diversity of ARGs in the soil by introducing antibiotic-resistant bacteria, altering the microbial community and facilitating horizontal transfer of ARGs via MGEs, and ultimately exacerbated resistome risks in the environment. Relatively, a larger volume of irrigation water led to a more complex propagation network of the resistome. Source apportionment analysis suggested reclaimed water contributed less than 15 % of ARGs in the irrigated soils, whereas its contribution proportion increased with a larger volume of irrigation water.

Metagenomic insights into efficiency and mechanism of antibiotic resistome reduction by electronic mediators-enhanced microbial electrochemical system

Electronic mediators are an effective means of enhancing the efficiency of microbial electrochemical electron transfer; however, there are still gaps in understanding the strengthening mechanisms and the efficiency of removing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). This study systematically elucidates the effects of various electron mediators on bioelectrochemical processes, electron transfer efficiency, and the underlying mechanisms that inhibit ARG propagation within sediment microbial fuel cell systems (SMFCs). The results indicate that the addition of electron mediators significantly increased the output voltage (33.3 %-61.1 %) and maximum power density (14 %-106 %) of SMFCs, while also reducing ARB abundance and transmission risk. The enhancement effect follows the order of biochar, nanoscale zero-valent iron, graphene, and carbon nanotubes, with biochar emerging as the most economical and efficient choice for generating electricity and removing human pathogenic bacteria carrying ARGs. Procrustes analysis revealed that electron mediators facilitated the removal of ARGs by altering the structure of the microbiome, particularly the electricity-generating microorganisms (EGMs). Voltage and mobile genetic elements were the primary drivers of ARGs in the SMFCs. The network analysis results show that multiple carbohydrate-active enzymes, cluster of orthologous groups, and EGMs were negatively correlated with ARGs, indicating that the electron mediator-enhanced SMFCs mainly inhibit the spread of ARGs by promoting cell division, carbohydrate metabolism, and electricity generation. This study provides novel insights into how electron mediators affect ARG removal in microbial electrochemistry, which can inform economically viable strategies for sustainable environmental remediation.

Manure application primarily drives changes in antibiotic resistome composition rather than abundance in agricultural soil profile

The prevalence of antibiotic resistance genes (ARGs) in soil has elicited significant concerns about food safety and agricultural sustainability. However, the impact of long-term fertilization on the soil resistome across soil profiles and their associations with both abundant and rare microbial taxa remain unknown. This study employed high-throughput quantitative polymerase chain reaction (HT-qPCR) and 16S rRNA gene sequencing to explore resistome across soil depths under different fertilization regimes (a 12-year field experiment). Compared with the control and chemical-only fertilization, manure amendment increased the ARG richness in the topsoil by 14.1-20 % but had no significant effect on the subsoil. Manure amendment resulted eight unique ARGs into topsoil: sul1, sul2, aadA, aadA2, aadA21, APHA3, ErmY and qacF_H. Compared with the control soil, the manure amendment did not increase the absolute and normalized abundance of ARGs in both top- and subsoil. In addition, abundant microbial taxa exhibited a stronger association with ARGs than rare taxa. Overall, manure amendment had strong and direct impacts on soil ARG composition and indirectly influenced ARG abundance to a limited extent through its effects on soil properties and abundant taxa. These findings strengthen our understanding of the ecological impacts of long-term fertilization and inform sustainable agricultural practices.

Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems

Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.

Deciphering the antibiotic resistome in stratified source water reservoirs in China: Distribution, risk, and ecological drive

The proliferation and dissemination of antibiotic resistance genes (ARGs) in source water reservoirs may pose a threat to human health. This study investigated the antibiotic resistance in stratified reservoirs in China across different seasons and spatial locations. In total, 120 ARG subtypes belonging to 15 ARG types were detected with an abundance ranging from 171.06 to 793.71 × /Gb. Multidrug, tetracycline, aminoglycoside, and bacitracin resistance genes were dominant in the reservoirs. The abundance and transfer potential of ARGs were notably higher, especially during the stratified period, with markedly elevated levels in the bottom layer compared to the surface layer. Metagenomic assembly yielded 1357 ARG-carrying contigs, belonging to 83 resistant bacterial species, of which 13 were identified as human pathogen bacteria (HPB). HPB hosts (Sphingomonas sp., Burkholderiales sp., and Ralstonia sp., etc.) were super carriers of ARGs. Genes including ompR, bacA, golS, and ugd carried on HPB plasmids exhibited higher abundance in the water, warranting attention to the risk of resistance transmission. Environmental pressures have caused a shift in the assembly mechanism of ARGs, transitioning from a random process in surface water to a deterministic process in bottom water. The results of this study will deepen people's understanding of the ARG risk in stratified reservoirs.

Sludge water: a potential pathway for the spread of antibiotic resistance and pathogenic bacteria from hospitals to the environment

Hospitals play an important role in the spread of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR). The ARGs present in hospital wastewater tend to accumulate in activated sludge, with different ARGs exhibiting varying migration rates. As a result, sludge water produced during the activated sludge treatment process may be a significant source of ARGs entering the environment. Despite this, research into the behavior of ARGs during sludge concentration and dewatering remains limited. This study hypothesizes that ARGs might exhibit new behaviors in sludge water during sludge concentration. Using metagenomic analysis, we explored the distribution and migration risks of ARGs and human pathogenic bacteria (HPB) in sludge water, comparing them with those in hospital wastewater. The findings reveal a strong correlation between ARGs in sludge water and hospital wastewater, with subtypes such as arlR, efpA, and tetR showing higher abundance in sludge water. Although the horizontal gene transfer potential of ARGs is greater in hospital wastewater than in sludge water, the resistance mechanisms and migration pathways are similar even when their HPB host associations differ. ARGs in both environments are primarily transmitted through coexisting mobile genetic elements (MGEs). This suggests that sludge water serves as a critical route for the release of hospital-derived ARGs into the environment, posing potential threats to public health and ecological safety.

Resistance to medically important antimicrobials in broiler and layer farms in Cameroon and its relation with biosecurity and antimicrobial use

Introduction

Poultry production accounts for 42% of Cameroonian meat production. However, infectious diseases represent the main hindrance in this sector, resulting in overuse and misuse of antimicrobials that can contribute to the emergence and dissemination of antimicrobial resistance (AMR). This study aimed to evaluate the prevalence of antimicrobial resistance genes (ARGs) conferring resistance to carbapenems (blaVIM-2 and blaNDM ), (fluoro) quinolones (qnrS, qnrA, and qnrB), polymyxins (mcr1 to mcr5), and macrolides (ermA and ermB) in the poultry farm environment. Additionally, the study examined the relationship between these ARGs and biosecurity implementation, as well as farmers' knowledge, attitudes, and practices toward antimicrobial use (AMU) and AMR, including their perception of AMR risk.

Materials and methods

Fecal, drinking water, and biofilm samples from drinking water pipelines were collected from 15 poultry farms and subsequently analyzed by real-time PCR and 16S rRNA NGS.

Results

All samples tested positive for genes conferring resistance to (fluoro) quinolones, 97.8% to macrolides, 64.4% to polymyxins, and 11.1% to carbapenems. Of concern, more than half of the samples (64.4%) showed a multi-drug resistance (MDR) pattern (i.e., resistance to ≥3 antimicrobial classes). Drinking water and biofilm microbial communities significantly differed from the one of the fecal samples, both in term of diversity (α-diversity) and composition (β-diversity). Furthermore, opportunistic pathogens (i.e., Comamonadaceae and Sphingomonadaceae) were among the most abundant bacteria in drinking water and biofilm. The level of biosecurity implementation was intermediate, while the knowledge and attitude of poultry farmers toward AMU were insufficient and unsuitable, respectively. Good practices toward AMU were found to be correlated with a reduction in polymyxins and MDR.

Discussion

This study provides valuable information on resistance to medically important antimicrobials in poultry production in Cameroon and highlights their potential impact on human and environmental health.

Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat

As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.

Antibiotic Resistance as a Functional Characteristic of Urban Dust Particles' Microbial Communities

Urban dust samples were collected in Moscow (Russia) in June 2021. The samples were collected in three functional zones of Moscow (traffic, residential, and recreational) and included air microparticles, leaf dust, and paved dust. Data on the taxonomic composition of bacterial communities were obtained for dust samples, and their functional characteristics were predicted using PICRUSt2 2.5.0 and FAPROTAX 1.8.0 software. The culturable part of the bacterial community was examined for the presence of antibiotic-resistant strains with respect to β-lactams, tetracyclines, amphenicols, and aminoglycosides. The presence of bacteria resistant to ceftazidime, cefepime, and tetracycline was detected in all dust samples. The presence of bacteria resistant to meropenem and amikacin was only observed in the dust collected from leaves in the residential and traffic zones. The overall abundance of cultured antibiotic-resistant bacteria from the total heterotrophs ranged from 0.03% to 1.88%, with the highest percentage observed in dust from the residential zone. Notably, strains resistant to all antibiotics tested were observed in the leaf dust bacterial community.

Fabulous combination therapy: Synergistic antibiotic inhibition of aquatic antibiotic-resistant bacteria via membrane damage and DNA binding by novel nano antimicrobial peptide C-I20

Aquatic microbiota' antibiotic resistance undermines traditional treatment efficacy, posing a severe threat to sustainable water environment. Our study addresses this challenge through a fantastic approach involving novel nano antimicrobial peptide C-I20 and antibiotics. Antibacterial tests demonstrated that C-I20 effectively combated both standard and aquatic pathogenic resistant strains. C-I20 killed drug-resistant bacteria by disrupting membrane structure and binding to DNA. C-I20 bound to DNA, forming precipitates susceptible to rapid degradation by trypsin and DNase I. When combined with chloramphenicol, florfenicol, ampicillin, or enrofloxacin, C-I20 exhibited remarkably higher inhibitory rates against bacteria compared to individual use of C-I20 or antibiotics alone. Continuous passage analysis revealed that co-administration of C-I20 with chloramphenicol, florfenicol, ampicillin, and enrofloxacin delays the emergence and progression of antibiotic resistance. This combination therapy was proved to be highly effective, notably reducing tissue bacterial loads and pathological changes. Evaluation in an Aeromonas hydrophila infection model showed the lowest morbidity rate and bacterial loading in the C-I20 combined with ampicillin group. Antimicrobial susceptibility analysis confirmed that C-I20 supplementation markedly suppresses ampicillin-induced intestinal resistant bacteria. In conclusion, C-I20 in conjunction with antibiotic therapy effectively inhibits infection and drug-resistant bacterial development, offering a promising strategy for managing drug-resistant bacteria in aquatic animals.

Biofilm formation on microplastics and interactions with antibiotics, antibiotic resistance genes and pathogens in aquatic environment

Microplastics (MPs) in aquatic environments easily support biofilm development, which can interact with other environmental pollutants and act as harbors for microorganisms. Recently, numerous studies have investigated the fate and behavior of MP biofilms in aquatic environments, highlighting their roles in the spread of pathogens and antibiotic resistance genes (ARGs) to aquatic organisms and new habitats. The prevalence and effects of MP biofilms in aquatic environments have been extensively investigated in recent decades, and their behaviors in aquatic environments need to be synthesized systematically with updated information. This review aims to reveal the development of MP biofilm and its interactions with antibiotics, ARGs, and pathogens in aquatic environments. Recent research has shown that the adsorption capabilities of MPs to antibiotics are enhanced after the biofilm formation, and the adsorption of biofilms to antibiotics is biased towards chemisorption. ARGs and microorganisms, especially pathogens, are selectively enriched in biofilms and significantly different from those in surrounding waters. MP biofilm promotes the propagation of ARGs through horizontal gene transfer (HGT) and vertical gene transfer (VGT) and induces the emergence of antibiotic-resistant pathogens, resulting in increased threats to aquatic ecosystems and human health. Some future research needs and strategies in this review are also proposed to better understand the antibiotic resistance induced by MP biofilms in aquatic environments.

Research on antibiotic resistance genes in wild and artificially bred green turtles (Chelonia mydas)

Sea turtles, vital to marine ecosystems, face population decline. Artificial breeding is a recovery strategy, yet it risks introducing antibiotic resistance genes (ARGs) to wild populations and ecosystems. This study employed metagenomic techniques to compare the distribution characteristics of ARGs in the guts of wild and artificially bred green turtles (Chelonia mydas). The findings revealed that the total abundance of ARGs in C. mydas that have been artificially bred was significantly higher than that in wild individuals. Additionally, the abundance of mobile genetic elements (MGEs) co-occurring with ARGs in artificially bred C. mydas was significantly higher than in wild C. mydas. In the analysis of bacteria carrying ARGs, wild C. mydas exhibited greater bacterial diversity. Furthermore, in artificially bred C. mydas, we discovered 23 potential human pathogenic bacteria (HPB) that contain antibiotic resistance genes. In contrast, in wild C. mydas, only one type of HPB carrying an antibiotic resistance gene was found. The findings of this study not only enhance our understanding of the distribution and dissemination of ARGs within the gut microbial communities of C. mydas, but also provide vital information for assessing the potential impact of releasing artificially bred C. mydas on the spread of antibiotic resistance.

Microplastics exacerbate the ecological risk of antibiotic resistance genes in wetland ecosystem

Wetlands are vital components of the global ecosystem, significantly influencing the retention and dissemination of microplastics (MPs) and antibiotic resistance genes (ARGs). However, the effects of different types of MPs on the environmental dynamics of ARGs within these ecosystems remain poorly understood. This study focused on the distribution and composition of ARGs associated with two primary types of MPs-polyethylene and polypropylene-within the Poyang Lake wetland, the largest freshwater lake in China, utilizing metagenomic analysis. The findings demonstrated that the bacterial communities and ARG profiles in the plastisphere were markedly distinct from those in the surrounding water. Specifically, thirteen opportunistic pathogens and forty subtypes of ARGs, primarily related to multidrug, bacitracin, and β-lactam resistance, were identified in the plastisphere. Notably, polyethylene exhibited four times more specific ARG subtypes than polypropylene. Procrustes analysis combined with network analysis indicated a lack of strong correlation between ARG abundance and bacterial populations, suggesting potential horizontal transfer of ARGs within the microbiota of the plastisphere. Additionally, three novel and functional β-lactamase genes were identified within this environment. This investigation highlights the role of MPs as reservoirs for ARGs, facilitating their exchange and posing risks to both ecological integrity and human health, thereby underscoring the need for increased attention in future research efforts.

The variation of resistome, mobilome and pathogen in domestic and industrial wastewater treatment systems

Wastewater treatment plants (WWTPs), including both domestic and industrial facilities, are key contributors to antibiotic resistance genes (ARGs) and human pathogens in the environment. However, the characteristics and dissemination mechanisms of ARGs in domestic (SD) and industrial (SI) wastewater treatment systems remain unclear, leading to uncertainties in risk assessment. Based on metagenomic analysis, we observed significant differences in the compositions of resistome (ARGs and metal resistance genes, MRGs), mobilome (mobile genetic elements, MGEs), and bacterial community between SD and SI. SI exhibited lower diversity of ARGs but higher abundance of MRGs compared to SD. The removal efficiency of resistome was lower in the SI than that in the SD. MGEs emerged as the primary driver of ARG dissemination in the WWTPs, followed by the bacterial community. Environmental conditions (physicochemical parameters, heavy metals, and antibiotics) indirectly influenced the variation of resistome. Significantly, environmental conditions and MGEs highly influenced the composition of resistome in the SI, while bacterial community more associated with resistome in the SD. Additionally, we identified 36 human bacterial pathogens as potential hosts of ARGs, MRGs, and MGEs in wastewater samples. This study provides new insights on the dissemination mechanisms and risk assessment of antimicrobial resistance in the different types of WWTPs.

Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach

Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.

Applications of different forms of nitrogen fertilizers affect soil bacterial community but not core ARGs profile

The objective of this study was to investigate the impact of various chemical nitrogen fertilizers on the profile of antibiotic resistance genes (ARGs) in soil. A microcosm experiment was conducted with four treatments, including CK (control with no nitrogen), AN (ammonium nitrogen), NN (nitrate nitrogen), and ON (urea nitrogen), and the abundance of ARGs was assessed over a 30-day period using a metagenomic sequencing approach. The levels of core ARGs varied between 0.16 and 0.22 copies per cell across different treatments over time. The abundance of core ARGs in the ON treatment closely resembled that of the CK treatment, suggesting that environmentally friendly nitrogen fertilizers, particularly those in controlled release formulations, may be preferable. The core ARG abundance in the AN and NN treatments exhibited noticeable fluctuations over time. Overall, chemical nitrogen fertilizers had minimal effects on the core ARG profile as determined by principal component analysis and clustering analyses. Conversely, distinct and significant changes in bacterial communities were observed with the use of different nitrogen fertilizers. However, the influence of nitrogen fertilizers on the core ARGs is limited due to the unaffected potential bacterial hosts. Nitrogen-cycling-related genes (NCRGs), such as those involved in nitrogen-fixing (nifK, nifD, nifH) and denitrification (narG, napA, nirK, norB, nosZ) processes, exhibit a positive correlation with ARGs (rosA, mexF, bacA, vanS), indicating a potential risk of ARG proliferation during intense denitrification activities. This study indicates that the application of chemical nitrogen has a minimal effect on the abundance of ARGs in soil, thereby alleviating concerns regarding the potential accumulation of ARGs due to the use of chemical nitrogen fertilizers.

Prevalence of antibiotic resistance genes in different drinking water treatment processes in a northwest Chinese city

Antibiotic resistance genes (ARGs) are an emerging issue which are receiving increasing concerns in drinking water safety. However, the factors (e.g. treatment processes and water quality) affecting the removal efficiency of ARGs in the drinking water treatment plants (DWTPs) is still unclear. This work investigated the ARG profiles in each treatment process of two DWTPs located in a northwest Chinese city. The results showed that tetracycline and sulfonamide resistance genes were predominant among the 14 targeted ARGs. After the treatment, the Z water treatment plant which demonstrated a higher removal rate of ARGs (ranging from 50 to 80%), compared to the S plant (50-75%). And the average removal rate of tetracycline resistance genes (tetA, tetG, tetQ, tetX) was about 49.18% (S plant) and 67.50% (Z plant), as well as the removal rate of 64.2% and 72.9% for sulfonamide resistance (sul1 and sul2) at S and Z water plants, respectively. It was found that the relative abundance of main microbial communities (such as Bacteroidota, Actinobacteria, Verrucomicrobiota, Roseomonas), α-diversity index, as well as the abundance of pathogenic bacteria were all significantly reduced after different treatment processes. Network co-occurrence analysis revealed that Methylocystis possibly was the potential host for most ARGs, and sul1 was found across a broad spectrum of microorganisms in the drinking water environment. Adonis analysis showed that heavy metals and microbial communities explain solely 44.1% and 35.7% of variances of ARGs within DWTPs. This study provides insights into the contamination status and removal efficiencies of ARGs in DWTPs, offering valuable references for future studies on ARG removal, propagation, and diffusion patterns in drinking water treatment.

Multi-habitat distribution and coalescence of resistomes at the watershed scale based on metagenomics

The characteristics of the resistome distribution in rivers have been extensively studied. However, the distribution patterns of resistomes in multiple habitats and contributions of upstream habitats to the resistome profile in water bodies remains unclear. The current study explored the distribution and coalescence of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) in four habitats (including water bodies, sediments, biofilms, and riparian soils) within the Shichuan River watershed. The results revealed significant variations in the abundances and diversity of resistomes across the four habitats and two seasons. Assembly processes of resistomes were predominated by stochastic processes in summer but deterministic processes in winter. The main source of the resistome in summer water bodies was the movement of genes from upstream water bodies. However, the main sources of resistome in downstream water bodies in winter were the movement of resistomes in upstream sediments and the input of external pollution. The physicochemical properties of winter water bodies significantly influenced the movement of the resistomes across habitats. The current study elucidated the multi-habitat distribution pattern and migration mechanism of the resistome in the river system, providing new insights for effectively monitoring and controlling bacterial resistance.

New Agents Are Coming, and So Is the Resistance

Antimicrobial resistance is a global threat that requires urgent attention to slow the spread of resistant pathogens. The United States Centers for Disease Control and Prevention (CDC) has emphasized clinician-driven antimicrobial stewardship approaches including the reporting and proper documentation of antimicrobial usage and resistance. Additional efforts have targeted the development of new antimicrobial agents, but narrow profit margins have hindered manufacturers from investing in novel antimicrobials for clinical use and therefore the production of new antibiotics has decreased. In order to combat this, both antimicrobial drug discovery processes and healthcare reimbursement programs must be improved. Without action, this poses a high probability to culminate in a deadly post-antibiotic era. This review will highlight some of the global health challenges faced both today and in the future. Furthermore, the new Infectious Diseases Society of America (IDSA) guidelines for resistant Gram-negative pathogens will be discussed. This includes new antimicrobial agents which have gained or are likely to gain FDA approval. Emphasis will be placed on which human pathogens each of these agents cover, as well as how these new agents could be utilized in clinical practice.

Exploring the dynamics of antibiotic resistome on plastic debris traveling from the river to the sea along a representative estuary based on field sequential transfer incubations

The environmental risks arising from ubiquitous microplastics or plastic debris (PD) acting as carriers of antibiotic resistance genes (ARGs) have attracted widespread attention. Enormous amounts of plastic waste are transported by rivers and traverse estuaries into the sea every year. However, changes in the antibiotic resistome within the plastisphere (the biofilms formed on PD) as PD travels through estuaries are largely unknown. In this study, we performed sequential migration incubations for PD along Haihe Estuary to simulate the natural process of PD floating from rivers to the ocean. Metagenomic sequencing and analysis techniques were used to track microbial communities and antibiotic resistome on migrating PD and in seawater representing the marine environment. The total relative gene copies of ARGs on traveling PD remained stable. As migration between greatly varied waters, additional ARG subtypes were recruited to the plastisphere. Above 80 % ARG subtypes identified in the plastisphere were persistent throughout the migration, and over 30 % of these persistent ARGs were undetected in seawater. The bacterial hosts composition of ARGs on PD progressively altered as transported downstream. Human pathogenic bacteria carrying ARGs (HPBs-ARG) exhibited decreasing trends in abundance and species number during transfer. Individual HPBs-ARG persisted on transferred PD and were absent in seawater samples, comprising Enterobacter cloacae, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Vibrio parahaemolyticus. Based on all detected ARGs and HPBs-ARG, the Projection Pursuit model was applied to synthetically evaluate the potential risks of antibiotic resistance on migrating PD. Diminished risks on PD were observed upon the river-to-sea journey but consistently remained significantly higher than in seawater. The potential risks posed to marine environments by drifting PD as dispersal vectors for antibiotic resistance deserve greater attention. Our results provide initial insights into the dynamics or stability of antibiotic resistome on PD crossing distinct aquatic systems in field estuaries.

Spatiotemporal distribution, interactions and toxic effect of microorganisms and ARGs/MGEs from the bioreaction tank in hospital sewage treatment facility

Antibiotic resistance genes (ARGs) can be emitted from wastewater to ambient air and impose unignorable inhalable hazards, which could be exacerbated in antibiotic-concentrated hospital sewage. However, whether the ARG-carrying pathogens are more likely to infect cells remains largely unknown. Here, this study investigated and analyzed the spatiotemporal distribution, interaction, and toxicity of airborne microorganisms and their hosting ARGs in a hospital sewage treatment facility. The average concentration of ARGs/MGEs in sewage of bioreaction tank (BRT-W) was 2.27 × 104 gene copies/L. In the air of bioreaction tank (BRT-A), the average concentration of ARGs/MGEs was 15.86 gene copies/m3. In the four seasons, the ARGs concentration of sewage gradually decreased over time; The concentration of ARGs in the air first decreased and then increased. In spring, the concentration of ARGs/MGEs (qacedelta1-01) in BRT-W was highest (1.05 × 105 gene copies/L); The concentration of ARGs/MGEs (strB) in BRT-A in winter was higher than other seasons (26.18 gene copies/m3). Different from the past, this study also paid attention to the pathogenic potential of ARGs/MGEs in the air. The results of cell experiments showed that the cytotoxicity of drug-resistant Escherichia coli could reach Grade V. This suggested that the longer the drug-resistant E. coli were exposed to cells, the greater the cytotoxicity. Moreover, the cytotoxicity of bacteria increased with the increase in exposure time. In spring, the toxic effect of ARGs/MGEs in sewage of BRT-W was highest. Traceability analysis proved that BRT-W was an essential source of microorganisms and ARGs/MGEs in BRT-A. Furthermore, the combined risk of people exposed to the air of BRT in spring was higher than that in other seasons.

Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa

Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.

Deciphering the dynamics and driving mechanisms of high-risk antibiotic resistome in size-fractionated bacterial community during drinking water chlorination via metagenomic analysis

To reveal the impact of chlorination on the high-risk resistome in size-fractionated bacterial community, we employed metagenomic approaches to decipher dynamics of high-risk antibiotic resistance genes (ARGs) and driving mechanisms in the free-living and particle-associated fractions within a full-scale drinking water treatment system. Our results revealed that chlorination significantly increased the relative abundance of high-risk ARGs in the free-living fraction to 0.33 ± 0.005 copies/cell (cpc), bacitracin and chloramphenicol resistance types were major contributors. Furthermore, chlorination significantly increased the relative abundance of mobile genetic elements (MGEs) in the free-living fraction, while decreasing it in the particle-associated fraction. During chlorination, size-fractionated bacterial communities varied considerably. Multiple statistical analyses highlighted the pivotal role of the bacterial community in altering high-risk ARGs in both the free-living and particle-associated fractions, while MGEs had a more pronounced impact on high-risk ARGs in the free-living fraction. Specifically, the enrichment of pathogenic hosts, such as Comamonas and Pseudomonas, led to an increase in the abundance of high-risk ARGs. Concurrently, MGEs exhibited significant correlations with high-risk ARGs, indicating the potential of horizontal transfer of high-risk ARGs. These findings provide novel insights for mitigating antibiotic resistance risk by considering different bacterial fractions and respective risk ranks in drinking water.

Simultaneous volatile fatty acids promotion and antibiotic resistance genes reduction in fluoranthene-induced sludge alkaline fermentation: Regulation of microbial consortia and cell functions

The impact and mechanism of fluoranthene (Flr), a typical polycyclic aromatic hydrocarbon highly detected in sludge, on alkaline fermentation for volatile fatty acids (VFAs) recovery and antibiotic resistance genes (ARGs) transfer were studied. The results demonstrated that VFAs production increased from 2189 to 4272 mg COD/L with a simultaneous reduction of ARGs with Flr. The hydrolytic enzymes and genes related to glucose and amino acid metabolism were provoked. Also, Flr benefited for the enrichment of hydrolytic-acidifying consortia (i.e., Parabacteroides and Alkalibaculum) while reduced VFAs consumers (i.e., Rubrivivax) and ARGs potential hosts (i.e., Rubrivivax and Pseudomonas). Metagenomic analysis indicated that the genes related to cell wall synthesis, biofilm formation and substrate transporters to maintain high VFAs-producer activities were upregulated. Moreover, cell functions of efflux pump and Type IV secretion system were suppressed to inhibit ARGs proliferation. This study provided intrinsic mechanisms of Flr-induced VFAs promotion and ARGs reduction during alkaline fermentation.

Performance of public drinking water purifiers in control of trihalomethanes, antibiotics and antibiotic resistance genes

Point-of-use water purifiers are widely applied as a terminal treatment device to produce drinking water with high quality. However, concerns are raised regarding low efficiency in eliminating emerging organic pollutants. To enhance our understanding of the reliability and potential risks of water purifiers, the removal of trihalomethanes, antibiotics, and antibiotic resistance genes (ARGs) in four public water purifiers was investigated. In the four public water purifiers in October and November, the removal efficiencies of trichloromethane (TCM) and bromodichloromethane (BDCM) were 15%-69% (averagely 37%) and 6%-44% (averagely 23%). The levels of TCM and BDCM were lowered by all water purifiers in October and November, but accelerated in effluent compared to the influent in one public water purifier in December. The removal efficiencies of twelve antibiotics greatly varied with species and time. Out of twelve sampling cases, the removal efficiencies of total antibiotics were 25%-75% in ten cases. In the other two cases, very low removal efficiency (6%) or higher levels of antibiotics present in effluent compared to the influent were observed. Two public water purifiers effectively remove ARGs from water, with log removal rates of 0.45 log-3.89 log. However, in the other two public water purifiers, the ARG abundance accidently increased in the effluents. Overall, public water purifiers were more effective in removing antibiotics and ARGs compared to household water purifiers, but less or equally effective in removing trihalomethanes. Both public and household water purifiers could be contaminated and release the accumulated micro-pollutants or biofilm-related pollutants into effluent. The production frequency and standing time of water within water purifiers can impact the internal contamination and purification efficacy.

Spatiotemporal Changes of Antibiotic Resistance, Potential Pathogens, and Health Risk in Kindergarten Dust

The microorganisms present in kindergartens are extremely important for children's health during their three-year preschool education. To assess the risk of outdoor dust in kindergartens, the antibiotic resistome and potential pathogens were investigated in dust samples collected from 59 kindergartens in Xiamen, southeast China in both the winter and summer. Both high-throughput quantitative PCR and metagenome analysis revealed a higher richness and abundance of antibiotic resistance genes (ARGs) in winter (P < 0.05). Besides, the bloom of ARGs and potential pathogens was evident in the urban kindergartens. The co-occurrence patterns among ARGs, mobile genetic elements (MGEs), and potential pathogens suggested some bacterial pathogens were potential hosts of ARGs and MGEs. We found a large number of high-risk ARGs in the dust; the richness and abundance of high-risk ARGs were higher in winter and urban kindergartens compared to in summer and peri-urban kindergartens, respectively. The results of the co-occurrence patterns and high-risk ARGs jointly reveal that urbanization will significantly increase the threat of urban dust to human beings and their risks will be higher in winter. This study unveils the close association between ARGs/mobile ARGs and potential pathogens and emphasizes that we should pay more attention to the health risks induced by their combination.

Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach

The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal.

Microbial community of municipal drinking water in Hangzhou using metagenomic sequencing

While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaea, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were non-culturable using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the phyla Proteobacteria and Planctomycetes. Notably, the genus Methylobacterium was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp. Archaeal DNA (Euryarchaeota, Crenarchaeota) was found in trace amounts in some DW samples. Viruses such as rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2 were negative in all DW samples using colloidal gold and real-time reverse transcription polymerase chain reaction (RT‒PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (Ortervirales) and Herpesvirales was found in some DW samples. The metabolic pathways of the entire microbial community involve cell‒cell communication and signal secretion, contributing to cooperation between different microbial populations in the water. This study provides insight into the microbial community and metabolic process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.

Free-living lifestyle preferences drive the antibiotic resistance promotion during drinking water chlorination

The risk associated with antibiotic resistance genes (ARGs) in size-fractionated bacterial community during drinking water chlorination remains unclear, and is of paramount importance for risk mitigation through process selection and optimization. This study employed metagenomic approaches to reveal the alterations of ARGs, their potential functions and hosts within the free-living and particle-associated fractions. The total relative abundance of ARGs, mobile genetic elements (MGEs), and virulence factor genes (VFGs) significantly increased in the free-living fraction after chlorination. The contribution of the free-living fraction to the ARG relative abundance rose from 16.40 ± 1.31 % to 93.62 ± 0.47 % after chlorination. Multidrug resistance genes (e.g. mexF and mexW) were major contributors, and their co-occurrence with MGEs in the free-living fraction was enhanced after chlorination. Considering multiple perspectives, including presence, mobility, and pathogenicity, chlorination led to a significant risk of the antibiotic resistome in the free-living fraction. Moreover, potential functions of ARGs, such as cell wall/membrane/envelope biogenesis, defense mechanisms, and transcription in the free-living fraction, were intensified following chlorination. Potential pathogens, including Pseudomonas aeruginosa, Pseudomonas alcaligenes, and Acinetobacter junii, were identified as the predominant hosts of multidrug resistance genes, with their increased abundances primarily contributing to the rise of the corresponding ARGs. Overall, alterations of hosts as well as enhancing mobility and biological functions could collectively aid the proliferation and spread of ARGs in the free-living fraction after chlorination. This study provides novel insights into antibiotic resistance evolution in size-fractionated bacteria community and offers a management strategy for microbiological safety in drinking water.

Assessing impacts of municipal wastewater treatment plant upgrades on bacterial hazard contributions to the receiving urban river using SourceTracker

Upgrading municipal wastewater treatment plants (MWTPs) has been implemented in many megacities of China to reduce the discharges of nutrients and other pollutants and improve water quality of highly urbanized rivers. However, the contribution of MWTP discharge to bacterial hazards in the receiving rivers after upgrades has been largely unknown. In this study, high-throughput sequencing and shotgun metagenomics were applied to investigate the changes in the abundance, composition, potential risks, and contributions of bacteria and antibiotic resistance genes (ARGs) from effluent to receiving river after upgrading the third-largest MWTP in China with denitrification biofilters, ultrafiltration, ozonation, and disinfection processes. The annual loadings of total nitrogen and 27 types of pharmaceuticals were reduced by 42.4% ± 13.2% and 46.2% ± 15.4%, respectively. Bacterial biomass decreased from (3.58 ± 0.49) to (1.23 ± 0.27) × 107 16S rRNA gene copies/mL, and identified biomarkers in effluent and downstream shifted due to the adopted processes. Opportunistic pathogen bacteria downstream were also reduced. Although the relative abundance of total ARGs in MWTP effluent increased from 1.10 ± 0.02 to 2.19 ± 0.03 copies/16S rRNA gene after upgrades, that of total and high-risk ARGs downstream showed no significant difference. More importantly, the Bayesian-based SourceTracker method provided valuable insight by revealing that the contributions of MWTP discharge to downstream bacteria (from 44.2% ± 1.5%-31.4% ± 0.9%) and ARGs (from 61.2% ± 5.3%-47.6% ± 4.1%) were significantly reduced following the upgrades, indicating upgrading MWTP showed integrated benefits to the bacterial hazards in the receiving river. This study provides useful information for better control of bacterial hazard risks and operational strategy for the improvement of the urban aquatic ecosystem.

Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly

Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.

Effect of booster disinfection on the prevalence of microbial antibiotic resistance and bacterial community in a simulated drinking water distribution system

Booster disinfection was often applied to control the microorganism's growth in long-distance water supply systems. The effect of booster disinfection on the changing patterns of antibiotic resistance and bacterial community was investigated by a simulated water distribution system (SWDS). The results showed that the antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) were initially removed after dosing disinfectants (chlorine and chloramine), but then increased with the increasing water age. However, the relative abundance of ARGs significantly increased after booster disinfection both in buck water and biofilm, then decreased along the pipeline. The pipe materials and disinfectant type also affected the antibiotic resistance. Chlorine was more efficient in controlling microbes and ARGs than chloramine. Compared with UPVC and PE pipes, SS pipes had the lowest total bacteria, ARB concentration, and ARB percentage, mainly due to higher disinfectant residuals and a smoother surface. The significant correlation (rs = 0.77, p < 0.001) of the 16S rRNA genes was observed between buck water and biofilm, while the correlations of targeted ARGs were found to be weak. Bray-Curtis similarity index indicated that booster disinfection significantly changed the biofilm bacterial community and the disinfectant type also had a marked impact on the bacterial community. At the genus level, the relative abundance of Pseudomonas, Sphingomonas, and Methylobacterium significantly increased after booster disinfection. Mycobacterium increased after chloramination while decreased after chlorination, indicating Mycobacterium might resist chloramine. Pseudomonas, Methylobacterium, and Phreatobacter were found to correlate well with the relative abundance of ARGs. These results highlighted antibiotic resistance shift and bacterial community alteration after booster disinfection, which may be helpful in controlling potential microbial risk in drinking water.

Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere

The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.

Microcosm experiments revealed resistome coalescence of sewage treatment plant effluents in river environment

Sewage treatment plant (STP) effluents are important contributors of antibiotic resistance (AR) pollution in rivers. Effluent discharging into rivers causes resistome coalescence. However, their mechanisms and dynamic processes are poorly understood, especially for the effects of dilution, diffusion, and sunlight-induced attenuation on coalescence. In this study, we have constructed microcosmic experiments based on in-situ investigation to explore these issues. The first batch experiment revealed the effects of dilution and diffusion. The coverage of water coalesced resistomes ranged 66.26∼152.18 × /Gb and was positively correlated with effluent volume (Mann-Kendall test, p < 0.01). Principal coordinate analysis (PCoA) and source tracking analysis demonstrated that dilution and diffusion stepwise reduced AR pollution. The second batch experiment explored the temporal dynamics and sunlight attenuation on coalesced resistomes. Under natural light, the coverage and diversity of water resistomes posed decreasing trends, primarily attributed to drastic erasure of effluent traces. The proportion of effluent-specific ARGs in coalesced resistomes significantly declined over time (Spearman's r = -0.83 and -0.94 in coverage and richness). While under dark condition, the coverage and diversity increased. Sunlight radiation intensified the interactions between water and sediment resistomes, as evidenced by more shared ARGs and less dissimilarities across niches. Network analysis, metagenome-assembled genome (MAG) analysis and variation partitioning analysis (VPA) showed that microbiome controlled resistome coalescence, explaining 56.5% and 58.4% of resistomes in water and sediment, respectively. Biotic and abiotic factors synergistically explained 40% of water resistomes. This study offers a comprehensive understanding of AR transmission and provides theoretical bases for grasping AR pollution and developing effective suppression strategies.

Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater

Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.

The honeybee gut resistome and its role in antibiotic resistance dissemination

There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.

Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking

Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10-4 to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.

Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities

Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R2 = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.

The Impact of Bamboo Consumption on the Spread of Antibiotic Resistance Genes in Giant Pandas

The spread of antibiotic resistance genes (ARGs) in the environment exacerbates the contamination of these genes; therefore, the role plants play in the transmission of resistance genes in the food chain requires further research. Giant pandas consume different bamboo parts at different times, which provides the possibility of investigating how a single food source can affect the variation in the spread of ARGs. In this study, metagenomic analysis and the Comprehensive Antibiotic Resistance Database (CARD) database were used to annotate ARGs and the differences in gut microbiota ARGs during the consumption of bamboo shoots, leaves, and culms by captive giant pandas. These ARGs were then compared to investigate the impact of bamboo part consumption on the spread of ARGs. The results showed that the number of ARGs in the gut microbiota of the subjects was highest during the consumption of bamboo leaves, while the variety of ARGs was highest during the consumption of shoots. Escherichia coli, which poses a higher risk of ARG dissemination, was significantly higher in the leaf group, while Klebsiella, Enterobacter, and Raoultella were significantly higher in the shoot group. The ARG risk brought by bamboo shoots and leaves may originate from soil and environmental pollution. It is recommended to handle the feces of giant pandas properly and regularly monitor the antimicrobial and virulence genes in their gut microbiota to mitigate the threat of antibiotic resistance.

Prevalence of antimicrobial resistance in a full-scale drinking water treatment plant

Antibiotic resistance in drinking water has received increasing attention in recent years. In this study, the occurrence and abundance of antibiotic resistance genes (ARGs) in a drinking water treatment plant (DWTP) was comprehensively investigated using metagenomics. Bioinformatics analysis showed that 381 ARG subtypes belonging to 15 ARG types were detected, and bacitracin had the highest abundance (from 0.26 × 10-2 to 0.86 copies/cell), followed by multidrug (from 0.57 × 10-1 to 0.47 copies/cell) and sulfonamide (from 0.83 × 10-2 to 0.35 copies/cell). Additionally, 933 ARG-carrying contigs (ACCs) were obtained from the metagenomic data, among which 153 contigs were annotated as pathogens. The most abundant putative ARG host was Staphylococcus (7.9%), which most frequently carried multidrug ARGs (43.2%). Additionally, 38 high-quality metagenome-assembled genomes (MAGs) were recovered, one of which was identified as Staphylococcus aureus (Bin.624) and harboured the largest number of ARGs (n = 16). Using the cultivation technique, 60 isolates were obtained from DWTP samples, and Staphylococcus spp. (n = 11) were found to be dominant in all isolates, followed by Bacillus spp. (n = 17). Antimicrobial susceptibility testing showed that most Staphylococcus spp. were multidrug resistant (MDR). These results deepen our understanding of the distribution profiles of ARGs and antibiotic resistant bacteria (ARB) in DWTPs for potential health risk evaluation. Our study also highlights the need for new and efficient water purification technologies that can be introduced and applied in DWTPs.

Antibiotic resistance genes and the association with bacterial community in biofilms occurring during the drinking water granular activated carbon (GAC) sandwich biofiltration

The granular activated carbon (GAC) sandwich modification to slow sand filtration could be considered as a promising technology for improved drinking water quality. Biofilms developed on sand and GAC surfaces are expected to show a functional diversity during the biofiltration. Bench-scale GAC sandwich biofilters were set-up and run continuously with and without antibiotic exposure. Surface sand (the schmutzdecke) and GAC biofilms were sampled and subject to high-throughput qPCR for antibiotic resistance gene (ARG) analysis and 16 S rRNA amplicon sequencing. Similar diversity of ARG profile was found in both types of biofilms, suggesting that all ARG categories decreased in richness along the filter bed. In general, surface sand biofilm remained the most active layer with regards to the richness and abundance of ARGs, where GAC biofilms showed slightly lower ARG risks. Network analysis suggested that 10 taxonomic genera were implicated as possible ARG hosts, among which Nitrospira, Methyloversatilis and Methylotenera showed the highest correlation. Overall, this study was the first attempt to consider the whole structure of the GAC sandwich biofilter and results from this study could help to further understand the persistence of ARGs and their association with the microbial community in drinking water biofiltration system.

Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts

Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.

Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes

Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.

Metagenomic analysis reveals antibiotic resistance profiles in tissue samples from patients with diabetic foot infections

OBJECTIVES

Treating patients with diabetic foot infection (DFI) is challenging because of high rates of antibiotic resistance. Therefore, to administer a suitable antibiotic treatment, it is necessary to know the antibiotic resistance patterns in DFIs.

METHODS

To explore this question, we selected metagenomic data of 36 tissue samples from patients with DFI in the National Center for Biotechnology Information Sequence Read Archive database.

RESULTS

A total of 229 antibiotic-resistant gene (ARG) subtypes belonging to 20 ARG types were detected. The antibiotic resistome of 229 different genes in the tissue samples of patients with DFI comprised 24 core and 205 accessory resistance genes. Among the core antibiotic resistome, multidrug, tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam resistance genes were the dominant categories. Procrustes analysis indicated that both the microbial community composition and mobile genetic elements (MGEs) were determinants of the ARGs. In the network analysis, 29 species were speculated to be potential hosts of 28 ARGs based on the co-occurrence results. Plasmids and transposons were the most common elements that co-occurred with ARGs.

CONCLUSIONS

Our study provided detailed information about antibiotic resistance patterns in DFI, which has practical implications for suggesting a more specific antibiotic choice.

Impact of the microbiome on human, animal, and environmental health from a One Health perspective

The microbiome encompasses the genomes of the microorganisms that inhabit specific environments. One Health is an emerging concept, recognised as a cohesive, harmonising approach aimed at sustainably improving the well-being of humans, animals, and the environment. The microbiome plays a crucial role in the One Health domain, facilitating interactions among humans, animals, and the environment, along with co-evolution, co-development, co-metabolism, and co-regulation with their associated humans and animals. In addition, the microbiome regulates environmental health through interactions with plant microbiota, which actively participate in substance cycling (particularly the carbon and nitrogen cycles) and influence the overall energy flow in the biosphere. Moreover, antibiotic resistance genes present in microbiota can lead to widespread drug resistance in both humans and animals. This review explores the impact of the microbiome on humans, animals, and the environment, highlighting the significance of focusing on this field in One Health research.

Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly

Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.