Antibiotic resistance genes in surface water and groundwater from mining affected environments

Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics

The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3--N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.

Groundwater resistant gene accumulation in mining-agriculture complex zones: Insights from metagenomic analysis of subterranean mineral and terrestrial agricultural interactions

During the Mining-Agriculture Complex Areas, the mining and agriculture activities could lead to an excessive presence of sulfate content in the regional groundwater. Sulfate exhibits the potential to influence the positive accumulation of RGs, although its mechanisms remain inadequately explored. To address this gap, this study analyzed the RGs buildup mechanisms in the groundwater of the mining-agriculture complex area. Results showed a widespread presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), especially in coal-seams crevice groundwater. And iron and sulfur are primary environmental factors conducive to RGs accumulation through a synergistic interaction. Microbial annotation of gene sets sourced from coal-seams crevice groundwater samples unveiled part of sulfur-metabolizing microorganisms that were hosts of both ARGs and MRGs. Mechanistic insights revealed that iron may stimulates reactive oxygen species (ROS) generation, facilitating RGs accumulation, while adjusting sulfur metabolism and the synthesis of iron-sulfur clusters, thereby augmenting microbial growth which as predominant hosts of RGs, thereby intensifying the buildup of RGs.

Distribution and drivers of co-hosts of antibiotic and metal(loid) resistance genes in the fresh-brackish-saline groundwater

Groundwater is an essential source of drinking water and agricultural irrigation water, and its protection has become a global goal for public health. However, knowledge about heavy metal(loid) resistance genes (MRGs) in groundwater and the potential co-selection of antibiotic resistance genes (ARGs) have seldom been developed. Here, during the wet and dry seasons, we collected 66 groundwater samples (total dissolved solids = 93.9-9530 mg/L) adjacent to Baiyangdian Lake in Northern China, which presented the few metal(loid) and antibiotic contamination. We identified 160 MRGs whose composition exhibited significant seasonal variation, and dissolved metal(loid)s (particularly Ba) played a determinative role in promoting the MRGs proliferation though with relatively low concentrations, suggesting the relatively vulnerable groundwater ecosystems. Moreover, 27.4% of MRG-carrying metagenome-assembled genomes (MAGs) simultaneously carried ARGs, with the most frequently detected MRG types of Cu, Hg, and As, and ARG types of multidrug and bacitracin. Physicochemical variables, variables related to total dissolved solids, metal(loid)s, and antibiotics synthetically shaped the variation of MRG-ARG hosts in groundwater. We found that the increase of MRG-ARG hosts was critically responsible for the spread of MRGs and ARGs in groundwater. Our findings revealed the widespread co-occurrence of MRGs and ARGs in few-contaminated groundwater and highlighted the crucial roles of salinity in their propagation and transmission.

An inclusive study to elucidation the heavy metals-derived ecological risk nexus with antibiotic resistome functional shape of niche microbial community and their carbon substrate utilization ability in serpentine soil

Heavy metals (HMs) contained terrestrial ecosystems are often significantly display the antibiotic resistome in the pristine area due to increasing pressure from anthropogenic activity, is complex and emerging research interest. This study investigated that impact of chromium (Cr), nickel (Ni), cobalt (Co) concentrations in serpentine soil on the induction of antibiotic resistance genes and antimicrobial resistance within the native bacterial community as well as demonstrated their metabolic fingerprint. The full-length 16S-rRNA amplicon sequencing observed an increased abundance of Firmicutes, Actinobacteriota, and Acidobacteriota in serpentine soil. The microbial community in serpentine soil displayed varying preferences for different carbon sources, with some, such as carbohydrates and carboxylic acids, being consistently favored. Notably, 27 potential antibiotic resistance opportunistic bacterial genera have been identified in different serpentine soils. Among these, Lapillicoccus, Rubrobacter, Lacibacter, Chloroplast, Nitrospira, Rokubacteriales, Acinetobacter, Pseudomonas were significantly enriched in high and medium HMs concentrated serpentine soil samples. Functional profiling results illustrated that vancomycin resistance pathways were prevalent across all groups. Additionally, beta-lactamase, aminoglycoside, tetracycline, and vancomycin resistance involving specific bio-maker genes (ampC, penP, OXA, aacA, strB, hyg, aph, tet(A/B), otr(C), tet(M/O/Q), van(A/B/D), and vanJ) were the most abundant and enriched in the HMs-contaminated serpentine soil. Overall, this study highlighted that heavy-metal enriched serpentine soil is potential to support the proliferation of bacterial antibiotic resistance in native microbiome, and might able to spread antibiotic resistance to surrounding environment.

Colistin Resistance Mediated by Mcr-3-Related Phosphoethanolamine Transferase Genes in Aeromonas Species Isolated from Aquatic Environments in Avaga and Pakro Communities in the Eastern Region of Ghana

Purpose

Colistin is classified by the World Health Organization (WHO) as a critically important and last-resort antibiotic for the treatment of infections caused by carbapenem-resistant bacteria. However, colistin resistance mediated by chromosomal mutations or plasmid-linked mobilized colistin resistance (mcr) genes has emerged.

Methods

Thirteen mcr-positive Aeromonas species isolated from water samples collected in Eastern Ghana were analyzed using whole-genome sequencing (WGS). Antimicrobial susceptibility was tested using the broth microdilution method. Resistome analysis was performed in silico using a web-based platform.

Results

The minimum inhibitory concentration (MIC) of colistin for all except three isolates was >4 µg/mL. Nine new sequence types were identified and whole-genome analysis revealed that the isolates harbored genes (mcr-3-related genes) that code for Lipid A phosphoethanolamine transferases on their chromosomes. BLAST analysis indicated that the amino acid sequences of the mcr-3-related genes detected varied from those previously reported and shared 79.04-99.86% nucleotide sequence identity with publicly available mcr-3 variants and mcr-3-related phosphoethanolamine transferases. Analysis of the genetic context of mcr-3-related genes revealed that the genetic environment surrounding mcr-3-related genes was diverse among the different species of Aeromonas but conserved among isolates of the same species. Mcr-3-related-gene-IS-mcr-3-related-gene segment was identified in three Aeromonas caviae strains.

Conclusion

The presence of mcr-3-related genes close to insertion elements is important for continuous monitoring to better understand how to control the mobilization and dissemination of antibiotic resistance genes.

Unveiling the overlooked threat: antibiotic resistance in groundwater near an abandoned sulfuric acid plant in Xingyang, China

Groundwater near a sulfuric acid plant in Xingyang, Henan, China was sampled from seven distinct sites to explore the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Results showed that genes aadA, blaCTX-M, tetA, qnrA, and sul1 were detected with 100% frequency followed by aac(6')-Ib (85.71%), ermB (85.71%), and tetX (71.42%). Most abundant ARGs were sul1 in LSA2 (1.15 × 1011 copies/mL), tetA in LSA6 (4.95 × 1010 copies/mL), aadA in LSA2 (4.56 × 109 copies/mL), blaCTX-M in LSA4 (1.19 × 109 copies/mL), and ermB in LSA5 (1.07 × 109 copies/mL). Moreover, in LSA2, intl1 as a marker of class 1 integron emerged as the most abundant gene as part of MGE (2.25 × 1011 copies/mL), trailed by ISCR1 (1.57 × 109 copies/mL). Environmental factors explained 81.34% of ARG variations, with a strong positive correlation between the intl2 and blaCTX-M genes, as well as the ISCR1 gene and qnrA, tetA, intl2, and blaCTX-M. Furthermore, the intI1 gene had a strong positive connection with the aadA, tetA, and sul1 genes. Moreover, the aac(6')-Ib gene was associated with As, Pb, Mg, Ca, and HCO3-. The intl2 gene was also shown to be strongly associated with Cd. Notably, network analysis highlighted blaCTX-M as the most frequently appearing gene across networks of at least five genera. Particularly, Lactobacillus, Plesiomonas, and Ligilactobacillus demonstrated correlations with aadA, qnrA, blaCTX-M, intI2, and ISCR1. Based on 16S rRNA sequencing, the dominant phyla were Proteobacteria, Firmicutes, Bacteroidota, Acidobacteriota, and Actinobacteriota, with dominant genera including Pseudomonas, Ligilactobacillus, Azoarcus, Vogesella, Streptococcus, Plesiomonas, and Ferritrophicum. These findings enhance our understanding of ARG distribution in groundwater, signaling substantial contamination by ARGs and potential risks to public health.

Heavy Metals as Catalysts in the Evolution of Antimicrobial Resistance and the Mechanisms Underpinning Co-selection

The menace caused by antibiotic resistance in bacteria is acknowledged on a global scale. Concerns over the same are increasing because of the selection pressure exerted by a huge number of different antimicrobial agents, including heavy metals. Heavy metals are non-metabolizable and recalcitrant to degradation, therefore the bacteria can expel the pollutants out of the system and make it less harmful via different mechanisms. The selection of antibiotic-resistant bacteria may be influenced by heavy metals present in environmental reservoirs. Through co-resistance and cross-resistance processes, the presence of heavy metals in the environment can act as co-selecting agents, hence increasing resistance to both heavy metals and antibiotics. The horizontal gene transfer or mutation assists in the selection of mutant bacteria resistant to the polluted environment. Hence, bioremediation and biodegradation are sustainable methods for the natural clean-up of pollutants. This review sheds light on the occurrence of metal and antibiotic resistance in the environment via the co-resistance and cross-resistance mechanisms underpinning co-selection emphasizing the dearth of studies that specifically examine the method of co-selection in clinical settings. Furthermore, it is advised that future research incorporate both culture- and molecular-based methodologies to further our comprehension of the mechanisms underlying bacterial co- and cross-resistance to antibiotics and heavy metals.

Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment

The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.

Comparison of the Antibiotic Resistance of Escherichia coli Populations from Water and Biofilm in River Environments

Antibiotic-resistant, facultative pathogenic bacteria are commonly found in surface water; however, the factors influencing the spread and stabilization of antibiotic resistance in this habitat, particularly the role of biofilms, are not fully understood. The extent to which bacterial populations in biofilms or sediments exacerbate the problem for specific antibiotic classes or more broadly remains unanswered. In this study, we investigated the differences between the bacterial populations found in the surface water and sediment/biofilm of the Mur River and the Drava River in Austria. Samples of Escherichia coli were collected from both the water and sediment at two locations per river: upstream and downstream of urban areas that included a sewage treatment plant. The isolates were subjected to antimicrobial susceptibility testing against 21 antibiotics belonging to seven distinct classes. Additionally, isolates exhibiting either extended-spectrum beta-lactamase (ESBL) or carbapenemase phenotypes were further analyzed for specific antimicrobial resistance genes. E. coli isolates collected from all locations exhibited resistance to at least one of the tested antibiotics; on average, isolates from the Mur and Drava rivers showed 25.85% and 23.66% resistance, respectively. The most prevalent resistance observed was to ampicillin, amoxicillin-clavulanic acid, tetracycline, and nalidixic acid. Surprisingly, there was a similar proportion of resistant bacteria observed in both open water and sediment samples. The difference in resistance levels between the samples collected upstream and downstream of the cities was minimal. Out of all 831 isolates examined, 13 were identified as carrying ESBL genes, with 1 of these isolates also containing the gene for the KPC-2 carbapenemase. There were no significant differences between the biofilm (sediment) and open water samples in the occurrence of antibiotic resistance. For the E. coli populations in the examined rivers, the different factors in water and the sediment do not appear to influence the stability of resistance. No significant differences in antimicrobial resistance were observed between the bacterial populations collected from the biofilm (sediment) and open-water samples in either river. The different factors in water and the sediment do not appear to influence the stability of resistance. The minimal differences observed upstream and downstream of the cities could indicate that the river population already exhibits generalized resistance.

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives

With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.

Environmental concentrations of antibiotics, biocides, and heavy metals fail to induce phenotypic antimicrobial resistance in Escherichia coli

Most anthropogenically affected environments contain mixtures of pollutants from different sources. The impact of these pollutants is usually the combined effect of the individual polluting constituents. However, how these stressors contribute to the development of antimicrobial resistance in environmental microorganisms is poorly understood. Thus, a 30-day exposure experiment to environmental and sub-inhibitory concentrations of oxytetracycline, amoxicillin, zinc, copper, BAC (benzalkonium chloride) 10 and DADMAC (diallyldimethylammonium chloride) 12, was conducted using fully susceptible E. coli ATCC 25922 to ascertain any development of phenotypic or genotypic resistance. Furthermore, wild-type isolates were collected from the same aquatic environment as the stressors, analysed for phenotypic resistance using the disk diffusion method and genotypically through whole genome sequencing. Exposure to the various concentrations and combinations of the stressors did not trigger phenotypic resistance in the experimental bacteria. Furthermore, genotypic analysis of the WGS on the exposed isolates only found the macrolide resistance mdf(A) gene (also present in the control strain) and the disinfectant resistance gene sitABCD. With further analysis for single nucleotide variants (SNV), mutations were detected for 19 genes that encoded for oxidative stress, DNA repair, membrane proteins efflux systems, growth and persister formations except for the robA, a transcription protein subset of the ArcC/XylS family of proteins, which confer multidrug resistance in E. coli. This indicates that exposure to sub-inhibitory concentrations of antibiotics, heavy metals and biocide residues in the aquatic environmental concentrations of the stressors identified in the current study could not induce phenotypic or genotypic resistance but encoded for genes responsible for the development of persistence and tolerance in bacteria, which could be a precursor to the development of resistance in environmental bacteria.

Degradation of sulfamethoxazole and antibiotic resistance genes from surface water in the photocatalyst-loading bionic ecosystems

The behavior and removal of sulfamethoxazole (SMX) and 3 typical corresponding antibiotic resistance genes (ARGs) including sul1, sul2, sul3, and 16S rDNA in surface water were investigated in the photocatalyst-loading bionic ecosystems (PCBEs). Synthesized composite photocatalyst g-C3N4/TiO2 showing higher catalytic activity than Fe/g-C3N4/TiO2 was selected in the PCBEs. Five PCBEs, i.e., A-the control (without bionic grass or photocatalyst), B-bionic grass loaded with 4.12 g/m2 g-C3N4/TiO2, C-bionic grass loaded with 8.25 g/m2 g-C3N4/TiO2, D-bionic grass loaded with 12.37 g/m2 g-C3N4/TiO2, and E-bionic grass loaded with 16.5 g/m2 g-C3N4/TiO2 were constructed and operated in a medium-scale running cyclical flume. SMX could be photolyzed efficiently by g-C3N4/TiO2 with an optimal unit load on the bionic grass of 12.37 g/m2. 3-amino-5-methylisooxazole and p-aminobenzene sulfonamide were selected as main intermediates through the analyses of SMX degradation mechanisms and pathways, and detected in the aqueous phase and bionic grass. The intermediates were higher in the underwater part of the bionic grass than the above-water part. The overall removal of SMX ranged from 31.7 % to 82.3 % in 5 PCBEs, and the removal of sul1and sul2 were 0.2 %- 62.9 % in the aqueous phase and 8.4 %-63.2 % in the sediment. PCBE D might be the best construction when SMX and ARGs' removal was considered comprehensively. Moreover, the microbial structures showed Proteobacteria as the most dominant bacterial species had a relative abundance of 22.2 %-26.6 % and 33.4 %-68.2 % in the aquatic phase and sediment respectively, illustrating that the removal of the antibiotic and ARGs was bound up with the variations of dominant bacteria in the ecosystems. The findings illustrated that ecosystems with bionic grass and photocatalysts could be a promising technology for the removal of typical antibiotics and ARGs from surface water.

Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland

Natural ecosystems can become significant reservoirs and/or pathways for antimicrobial resistance (AMR) dissemination, with the potential to affect nearby microbiological, animal, and ultimately human communities. This is further accentuated in environments that provide direct human exposure, such as drinking water. To date, however, few studies have investigated AMR dissemination potential and the presence of co-selective stressors (e.g., metals/metalloids) in groundwater environments of human health significance. Accordingly, the present study analysed samples from rural (drinking) groundwater supplies (i.e., private wells) in the Republic of Ireland, where land use is dominated by livestock grazing activities. In total, 48 Escherichia coli isolates tested phenotypically for antimicrobial susceptibility in an earlier study were further subject to whole genome sequencing (WGS) and corresponding water samples were further analysed for trace metal/metalloid concentrations. Eight isolates (i.e., 16.7%) were genotypically resistant to antimicrobials, confirming prior phenotypic results through the identification of ten antimicrobial resistance genes (ARGs); namely: aph(3″)-lb (strA; n=7), aph(6)-Id (strA; n = 6), blaTEM (n = 6), sul2 (n = 6), tetA (n = 4), floR (n = 2), dfrA5 (n = 1), tetB (n = 1), and tetY (n = 1). Additional bioinformatic analysis revealed that all ARGs were plasmid-borne, except for two of the six sul2 genes, and that 31.2% of all tested isolates (n = 15) and 37.5% of resistant ones (n = 3) carried virulence genes. Study results also found no significant relationships between metal concentrations and ARG abundance. Additionally, just one genetic linkage was identified between ARGs and a metal resistance gene (MRG), namely merA, a mercury-resistant gene found on the same plasmid as blaTEM, dfrA5, strA, strB, and sul2 in the only isolate of inferred porcine (as opposed to bovine) origin. Overall, findings suggest that ARG (and MRG) acquisition may be occurring prior to groundwater ingress, and are likely a legacy issue arising from agricultural practices.

Graphene Quantum Dots Nonmonotonically Influence the Horizontal Transfer of Extracellular Antibiotic Resistance Genes via Bacterial Transformation

Graphene quantum dots (GQDs) coexist with antibiotic resistance genes (ARGs) in the environment. Whether GQDs influence ARG spread needs investigation, since the resulting development of multidrug-resistant pathogens would threaten human health. This study investigates the effect of GQDs on the horizontal transfer of extracellular ARGs (i.e., transformation, a pivotal way that ARGs spread) mediated by plasmids into competent Escherichia coli cells. GQDs enhance ARG transfer at lower concentrations, which are close to their environmental residual concentrations. However, with further increases in concentration (closer to working concentrations needed for wastewater remediation), the effects of enhancement weaken or even become inhibitory. At lower concentrations, GQDs promote the gene expression related to pore-forming outer membrane proteins and the generation of intracellular reactive oxygen species, thus inducing pore formation and enhancing membrane permeability. GQDs may also act as carriers to transport ARGs into cells. These factors result in enhanced ARG transfer. At higher concentrations, GQD aggregation occurs, and aggregates attach to the cell surface, reducing the effective contact area of recipients for external plasmids. GQDs also form large agglomerates with plasmids and thus hindering ARG entrance. This study could promote the understanding of the GQD-caused ecological risks and benefit their safe application.

Effects of multi-heavy metal composite pollution on microorganisms around a lead-zinc mine in typical karst areas, southwest China

Heavy metal pollution poses a serious hazard to the soil bacterial community. The purpose of this study is to understand the characteristics of soil heavy metal pollution in lead-zinc mines in karst areas and the response of Pb, Zn, Cd, and As-induced composite pollution to soil microorganisms. This paper selected soil samples from the lead-zinc mining area of Xiangrong Mining Co., Ltd., Puding County, Guizhou Province, China. The soil in the mining area is contaminated by multiple heavy metals such as Pb, Zn, Cd and As. The average levels of Pb, Zn, Cd and As in the Pb-Zn mining soil were 14.5, 7.8, 5.5 and 4.4 times higher than the soil background in this area, respectively. Bacterial community structures and functions were analyzed using 16 S rRNA high-throughput sequencing technology and the PICRUSt method. A total of 19 bacterial phyla, 34 classes and 76 orders were detected in the tested soil. At the phylum level, the Proteobacteria are the dominant flora of the soil in the tailings reservoir area of the lead-zinc mine, respectively GWK1 (49.64%), GWK2 (81.89%), GWK3 (95.16%); and for the surrounding farmland soil, the Proteobacteria, Actinobacteriota, Acidobacteriota, Chloroflexi and Firmicutes are the most abundant in five bacterial groups. RDA analyses revealed that the heavy metal pollution of the lead-zinc mining area has a significant impact on the diversity of soil microorganisms. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased, and the bacterial diversity increased. Additionally, various types of heavy metals have different effects on bacterial communities, and soil heavy metal content will also change the bacterial community structure. Proteobacteria positively related to Pb, Cd, and Zn, therefore, Proteobacteria were highly resistant to heavy metals. PICRUSt analysis suggested that heavy metals significantly affect the metabolic function of microorganisms. Microorganisms might generate resistance and enable themselves to survive by increasing the transport of metal ions and excreting metal ions. These results can be used as a basis for the microbial remediation of heavy metal-contaminated farmland in mining areas.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Rhizosphere effect on the relationship between dissolved organic matter and functional genes in contaminated soil

Arsenic contamination in a mining area is a potential threat to the local population. In the context of one-health, biological pollution in contaminated soil should be known and understandable. This study was conducted to clarify the effects of amendments on arsenic species and potential threat factors (e.g., arsenic-related genes (AMGs), antibiotic resistance genes (ARGs) and heavy-metal resistance genes (MRGs)). Ten groups (control (CK), T1, T2, T3, T4, T5, T6, T7, T8, and T9) were set up by adding different ratio of organic fertilizer, biochar, hydroxyapatite and plant ash. The maize crop was grown in each treatment. Compared with CK, the bioavailability of arsenic was reduced by 16.2%-71.8% in the rhizosphere soil treatments, and 22.4%-69.2% in the bulk soil treatments, except for T8. The component 2 (C2), component 3 (C3) and component 5 (C5) of dissolved organic matter (DOM) increased by 22.6%-72.6%, 16.8%-38.1%, 18.4%-37.1%, respectively, relative to CK in rhizosphere soil. A total of 17 AMGs, 713 AGRs and 492 MRGs were detected in remediated soil. The humidification of DOM might directly correlate with MRGs in both soils, while it was influenced directly on ARGs in bulk soil. This may be caused by the rhizosphere effect, which affects the interaction between microbial functional genes and DOM. These findings provide a theoretical basis for regulating soil ecosystem function from the perspective of arsenic contaminated soil.

Spatial distribution of bacterial resistance towards antibiotics of rural sanitation system in China and its potential link with diseases incidence

Chinese government is vigorously promoting toilet renovation in rural areas to reduce the risk of human feces exposure, which would cause infectious diseases, especially antibiotic resistance genes (ARGs) and pathogens. However, the distribution of ARGs in human feces from different regions of China remained ill-defined. It is not yet known how the survival of ARGs after toilet treatment is associated with the regional infection rates. Here, we investigated the prevalence of ARGs in human feces in rural areas of China and their potential relationship with infectious diseases for the first large-scale. The results showed that there were still high ARGs residues in human feces after rural toilet treatment, especially tetM-01 and ermB with average relative abundance as high as 1.21 × 10^-1 (Eastern) and 1.56 × 10^-1 (Northern), respectively. At a large regional scale, the significant differences in human feces resistomes were mainly shaped by the toilet types, TN, NH₃-N, and the bacterial community. A critical finding was that toilets still cannot effectively decrease the pathogenicity risk in human feces. The significant positive relationship (P<0.05) between infectious diseases and ARGs can infer that ARGs in human feces exposure might be a critical path for enhancing the incidence of diseases, as these ARGs hinder the effectiveness of antibiotics.

Effects of biodegradation, biotoxicity and microbial community on biostimulation of sulfolane

To evaluate the effectiveness of biostimulation in remediating soil-free groundwater and groundwater with soil, experiments were conducted using soil and groundwater samples that were contaminated with sulfolane. The main objective was to characterize the differences in sulfolane removal efficiency and biotoxicity between in situ soil-free groundwater and groundwater with soil and different concentrations of dissolved oxygen (1 mg/L and 5 mg/L) and various nutrient salts (in situ and spiked). Optimizing the nutrient salt conditions improved the removal efficiency of sulfolane by 1.8-6.5 that under in situ nutrient salt conditions. Controlling the dissolved oxygen concentration enhanced the efficiency of removal of sulfolane by 1.5-4.5 times over that at the simulated in situ dissolved oxygen concentration, suggesting that the degradation of sulfolane by indigenous microorganisms requires nutrient salts more than it requires dissolved oxygen. Biotoxicity data showed that the luminescence inhibition of Aliivibrio fischeri by sulfolane was lower in the biostimulated samples than in the pre-treated samples. Biostimulation reduced the biotoxicity of the treated samples by 42-51%, revealing that it was effective in removing sulfolane and reducing biotoxicity. Microbial community analysis showed that the biostimulation did not change the dominant species in the original in situ community, and increased the proportion of sulfolane-degraders. The outcome of this study can be used to set parameters for the remediation of groundwater that is contaminated by sulfolane in oil refineries.

Quantification of antibiotic resistance genes (ARGs) in clouds at a mountain site (puy de Dôme, central France)

Antibiotic resistance in bacteria is becoming a major sanitary concern worldwide. The extensive use of large quantities of antibiotics to sustain human activity has led to the rapid acquisition and maintenance of antibiotic resistant genes (ARGs) in bacteria and to their spread into the environment. Eventually, these can be disseminated over long distances by atmospheric transport. Here, we assessed the presence of ARGs in clouds as an indicator of long-distance travel potential of antibiotic resistance in the atmosphere. We hypothesized that a variety of ARGs can reach the altitude of clouds mainly located within the free troposphere. Once incorporated in the atmosphere, they are efficiently transported and their respective concentrations should differ depending on the sources and the geographical origin of the air masses. We deployed high-flow rate impingers and collected twelve clouds between September 2019 and October 2021 at the meteorological station of the puy de Dôme summit (1465 m a.s.l., France). Total airborne bacteria concentration was assessed by flow cytometry, and ARGs subtypes of the main families of antibiotic resistance (quinolone, sulfonamide, tetracycline; glycopeptide, aminoglycoside, β-lactamase, macrolide) including one mobile genetic element (transposase) were quantified by qPCR. Our results indicate the presence of 29 different ARGs' subtypes at concentrations ranging from 1.01 × 10³ to 1.61 × 10⁴ copies m^-3 of air. Clear distinctions could be observed between clouds in air masses transported over marine areas (Atlantic Ocean) and clouds influenced by continental surfaces. Specifically, quinolones (mostly qepA) resistance genes were prevalent in marine clouds (54 % of the total ARGs on average), whereas higher contributions of sulfonamide, tetracycline; glycopeptide, β-lactamase and macrolide were found in continental clouds. This study constitutes the first evidence for the presence of microbial ARGs in clouds at concentrations comparable to other natural environments. This highlights the atmosphere as routes for the dissemination of ARGs at large scale.

Sulfur: a neglected driver of the increased abundance of antibiotic resistance genes in agricultural reclaimed subsidence land located in coal mines with high phreatic water levels

Due to the shallow burial of groundwater in coal mines with a high phreatic water level, a large area of subsidence lakes is formed after the mine collapses. Agricultural and fishery reclamation activities have been carried out, which introduced antibiotics and exacerbated the contamination of antibiotic resistance genes (ARGs), but this has received limited attention. This study analyzed ARG occurrence in reclaimed mining areas, the key impact factors, and the underlying mechanism. The results show that sulfur is the most critical factor impacting the abundance of ARGs in reclaimed soil, which is due to changes in the microbial community. The species and abundance of ARGs in the reclaimed soil were higher than those in the controlled soil. The relative abundances of most ARGs increased with the depth of reclaimed soil (from 0 to 80 cm). In addition, the microbial structures of the reclaimed and controlled soils were significantly different. Proteobacteria, was the most dominant microbial phylum in the reclaimed soil. This difference is likely related to the high abundance of sulfur metabolism functional genes in the reclaimed soil. Correlation analysis showed that the differences in ARGs and microorganisms in the two soil types were highly correlated with the sulfur content. High levels of sulfur promoted the proliferation of sulfur-metabolizing microbial populations such as Proteobacteria and Gemmatimonadetes in the reclaimed soils. Remarkably, these microbial phyla were the main antibiotic-resistant bacteria in this study, and their proliferation created conditions for the enrichment of ARGs. Overall, this study underscores the risk of the abundance and spread of ARGs driven by high-level sulfur in reclaimed soils and reveals the mechanisms.

Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors

The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.

Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources

Antimicrobial resistance is a growing public health problem that requires an integrated approach among human, agricultural, and environmental sectors. However, few studies address all three components simultaneously. We investigated the occurrence of five antibiotic resistance genes (ARGs) and the class 1 integron gene (intI1) in private wells drawing water from a vulnerable aquifer influenced by residential septic systems and land-applied dairy manure. Samples (n = 138) were collected across four seasons from a randomized sample of private wells in Kewaunee County, Wisconsin. Measurements of ARGs and intI1 were related to microbial source tracking (MST) markers specific to human and bovine feces; they were also related to 54 risk factors for contamination representing land use, rainfall, hydrogeology, and well construction. ARGs and intI1 occurred in 5%-40% of samples depending on target. Detection frequencies for ARGs and intI1 were lowest in the absence of human and bovine MST markers (1%-30%), highest when co-occurring with human and bovine markers together (11%-78%), and intermediate when co-occurring with just one type of MST marker (4%-46%). Gene targets were associated with septic system density more often than agricultural land, potentially because of the variable presence of manure on the landscape. Determining ARG prevalence in a rural setting with mixed land use allowed an assessment of the relative contribution of human and bovine fecal sources. Because fecal sources co-occurred with ARGs at similar rates, interventions intended to reduce ARG occurrence may be most effective if both sources are considered.

Meta-analysis addressing the characterization and risk identification of antibiotics and antibiotic resistance genes in global groundwater

Antimicrobial resistance (AMR) is one of the significant global issues to public health. Compared to other aquatic environments, research on AMR in groundwater is scarce. In the study, a meta-analysis was conducted to explore the characteristics and risks of antibiotics and antibiotic resistance genes (ARGs) in global groundwater, using a data set of antibiotic concentrations collected from publications during 2000-2021 and a large-scale metagenomes of groundwater samples (n = 330). The ecotoxicological risks of antibiotics in the global groundwater were evaluated using mixture risk quotient with concentration addition model to consider the synergistic effects of multiple antibiotics. Bioinformatic annotations identified 1413 ARGs belonging to 37 ARG types in the global groundwater, dominated by rifamycin, polyketide, and quinolone resistance genes and including some emerging ARGs such as mcr-family and carbapenem genes. Relatively, the level of ARGs in the groundwater from spring was significantly higher (ANOVA, p < 0.01) than those from the riparian zone, sand and deep aquifer. Similarly, metal resistance genes (MRGs) were prevalent in the global groundwater, and network analysis suggested the MRGs presented non-random co-occurrence with the ARGs in such environments. Taxonomic annotations showed Proteobacteria, Actinobacteria, Eukaryota, Acidobacteria and Thaumarchaeota were the dominant phylum in the groundwater, and the microbial community largely shaped profile of ARGs in the environment. Notably, the ARGs presented co-occurrence with mobile genetic elements, virulence factors and human bacterial pathogens, indicating potential dissemination risk of ARGs in the groundwater. Furthermore, an omics-based approach was used for health risk assessment of antibiotic resistome and screened out 152 risk ARGs in the global groundwater. Comparatively, spring and cold creek presented higher risk index, which deserves more attention to ensure the safety of water supply.

Phytostabilization mitigates antibiotic resistance gene enrichment in a copper mine tailings pond

Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10 cm soil layer by 75 %, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO₄^2- concentration were important physicochemical factors to affect the total ARG abundance, while causal mediation analysis showed that their effects were largely mediated by the changes in ARG mobility and microbial diversity. The increase in ARG diversity associated with phytostabilization was mainly mediated by a small subgroup of ARG hosts, most of which could not be classified at the genus level and deserve further research in the future.

A review of antibiotics and antibiotic resistance genes (ARGs) adsorption by biochar and modified biochar in water

Antibiotics have been used in massive quantities for human and animal medical treatment, and antibiotic resistance genes (ARGs) are of great concern worldwide. Antibiotics and ARGs are exposed to the natural environment through the discharge of medical wastewater, causing great harm to the environment and human health. Biochar has been widely used as a green and efficient adsorbent to remove pollutants. However, pristine and unmodified biochars are not considered sufficient and efficient to cope with the current serious water pollution. Therefore, researchers have chosen to improve the adsorption capacity of biochar through different modification methods. To have a better understanding of the application of modified biochar, this review summarizes the biochar modification methods and their performance, particularly, molecular imprinting and biochar aging are outlined as new modification methods, influencing factors of biochar and modified biochar in adsorption of antibiotics and ARGs and adsorption mechanisms, wherein adsorption mechanism of ARGs on biochar is found to be different than that of antibiotics. After that, the directions of biochar and modified biochar worthy of research and the issues that need attention are proposed. It can be noted that under the current dual carbon policy, biochar may have wider application prospects in future.

The Phenomenon of Antibiotic Resistance in the Polar Regions: An Overview of the Global Problem

The increasing prevalence of antibiotic resistance is a global problem in human and animal health. This leads to a reduction in the therapeutic effectiveness of the measures used so far and to the limitation of treatment options, which may pose a threat to human health and life. The problem of phenomenon of antibiotic resistance affects more and more the polar regions. This is due to the increase in tourist traffic and the number of people staying at research stations, unmodernised sewage systems in inhabited areas, as well as the migration of animals or the movement of microplastics, which may contain resistant bacteria. Research shows that the presence of antibiotic resistance genes is more dominant in zones of human and wildlife influence than in remote areas. In a polluted environment, there is evidence of a direct correlation between human activity and the spread and survival of antibiotic-resistant bacteria. Attention should be paid to the presence of resistance to synthetic and semi-synthetic antibiotics in the polar regions, which is likely to be correlated with human presence and activity, and possible steps to be taken. We need to understand many more aspects of this, such as bacterial epigenetics and environmental stress, in order to develop effective strategies for minimizing the spread of antibiotic resistance genes. Studying the diversity and abundance of antibiotic resistance genes in regions with less anthropogenic activity could provide insight into the diversity of primary genes and explain the historical evolution of antibiotic resistance.

Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance

Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.

Influence of anthropogenic disturbances on antibiotic resistance gene distributions along the Minjiang River in Southeast China

River-reservoir systems have become ubiquitous among modern global aquatic environments due to the widespread construction of dams. However, little is known of antibiotic resistance gene (ARG) distributions in reservoir-river systems experiencing varying degrees of anthropogenic impacts. Here, the diversity, abundance, and spatial distribution of ARGs were comprehensively characterized along the main stem of the Minjiang River, a typical subtropic reservoir-river system in Southeast China using high-throughput quantitative PCR. A total of 252 ARG subtypes were detected from twelve sampling sites that were dominated by aac(3)-Via, followed by czcA, blaTEM, and sul1. Urban river waters (sites S9-S12) harbored more diverse ARGs than did the reservoir waters (sites S1-S7), indicating more serious antibiotic resistance pollution in areas with larger population densities. Dam construction could reduce the richness and absolute abundance of ARGs from upstream (site S7) to downstream (site S8). Urban river waters also harbored a higher proportion of mobile genetic elements (MGEs), suggesting that intensive human activities may promote ARG horizontal gene transfers. The mean relative abundance of Proteobacteria that could promote antibiotic resistance within microbial communities was also highest in urban river waters. Variance partitioning analysis indicated that MGEs and bacterial communities could explain 67.33%, 44.7%, and 90.29% of variation in selected ARGs for the entire watershed, aquaculture waters, and urban river waters, respectively. These results further suggest that urban rivers are ideal media for the acquisition and spread of ARGs. These findings provide new insights into the occurrence and potential mechanisms determining the distributions of ARGs in a reservoir-river system experiencing various anthropogenic disturbances at the watershed scale.

Structure, mechanism, and toxicity in antibiotics metal complexation: Recent advances and perspectives

Antibiotic-metal complexes (AMCs) formed by antibiotics and metal ions have attracted considerable attentions in recent years. Although different removal methods for AMCs have been reported in the literature, very few investigations have focused on the mechanisms and toxic effects of antibiotic-metal coordination. This review briefly describes the structural characteristics of various commonly used antibiotics and the coordination mechanisms with metal ions. Considering the complexity of the real environment, various environmental factors affecting AMC formation are highlighted. The effects of AMCs on microbial community structure and the role of metal ions in influencing resistant genes from the molecular perspective are of interest within this work. The toxicities and mechanisms of AMCs on different species of biota are also discussed. These findings underline the need for more targeted detection and analysis methods and more suitable toxicity markers to verify the combination of antibiotics with metal ions and reveal environmental toxicities in future. This review presents an innovative idea that antibiotics combined with metal ions will change the toxicity and environmental behavior of antibiotics.

Fates of antibiotic resistance genes and bacterial/archaeal communities of activated sludge under stress of copper: Gradient increasing/decreasing exposure modes

Effect of copper (Cu) on antibiotic resistance genes (ARGs) and bacterial/archaeal community of activated sludge under gradient increasing (0.5-10 mg/L) or decreasing exposure (10-0.5 mg/L) modes was explored. Here, 29 genes were detected among 48 selected ARGs and mobile gene elements (MGEs). Two exposure modes showed dissimilar effects on ARGs and distribution was more affected by environmental concentrations of Cu, which promoted transmission of ARGs (multiple drug resistance and sulfonamide). Cellular protection was main resistance mechanism, which was less inhibited than efflux pumps. The tnpA-02, as main MGE, interacted closely with ARGs (sul2, floR, etc.). Gradient increasing exposure mode had more effects on bacterial/archaeal structure and composition. Bacteria were main hosts for specific ARGs and tnpA-02, while archaea carried multiple ARGs (cmx(A), adeA, etc.), and bacteria (24.24 %) contributed more to changes of ARGs than archaea (19.29 %). This study clarified the impacts of Cu on the proliferation and transmission of ARGs.

Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities

Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

The Current Status and Prevention of Antibiotic Pollution in Groundwater in China

The problem of environmental pollution caused by the abuse of antibiotics has received increasing attention. However, only in recent years have antibiotic pollution and its risk assessment to the environment been deeply studied. Although there has been a large number of reports about the input, occurrence, destination, and influence of antibiotics in the past 10 years, systemic knowledge of antibiotics in the groundwater environment is still lacking. This review systematically expounds the sources, migration and transformation, pollution status, and potential risks to the ecological environment of antibiotics in groundwater systems, by integrating 10 years of existing research results. The results showed that 47 kinds of antibiotics in four categories, mainly sulfonamides and fluoroquinolones, have been detected; antibiotics in groundwater species will induce the production of resistance genes and cause ecological harm. In view of the entire process of antibiotics entering groundwater, the current antibiotic control methods at various levels are listed, including the control of the discharge of antibiotics at source, the removal of antibiotics in water treatment plants, and the treatment of existing antibiotic contamination in groundwater. Additionally, the future research direction of antibiotics in groundwater is pointed out, and suggestions and prospects for antibiotic control are put forward.

Associations of typical antibiotic residues with elderly blood lipids and dyslipidemia in West Anhui, China

Growing evidence has indicated the association of clinical antibiotic use with abnormal blood lipid levels; however, no epidemiological study has examined the relationship of antibiotic exposure, probably derived from food chains, with blood lipid levels. This study investigated the relationships of urinary antibiotic levels with blood lipid levels and dyslipidemias in the older population. Baseline data of 960 participants from the Cohort of Elderly Health and Environment Controllable Factors were used in the present study. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was performed to detect antibiotic residues in the urine samples of the participants. Our findings revealed that each 1 μg/g increase in enrofloxacin and ciprofloxacin levels was associated with an increase of 0.084 (95 % confidence interval (CI): 0.030, 0.139) and 0.049 (95 % CI: 0.012, 0.086) in triglyceride levels, respectively. Enrofloxacin was associated with an increased risk of hypertriglyceridemia. Each 1 μg/g increase in the enrofloxacin level corresponded to an increase of 0.052 (95 % CI: 0.006, 0.098) in the low-density lipoprotein cholesterol level. Furthermore, florfenicol exposure increased the risks of both hyperbetalipoproteinemia and hypoalphalipoproteinemia. By contrast, each 1 μg/g increase in sulfaclozine and doxycycline levels was associated with a - 0.062 (95 % CI: -0.111, -0.020), and - 0.083 (95 % CI: -0.160, -0.007) decrease in total cholesterol levels, respectively. Sulfaclozine was closely related to a decreased risk of hypercholesterolemia. Stratification analysis revealed specific differences in the correlation between antibiotic exposure and lipid levels based on the waist circumference (WC) values of the participants. Except for sulfaclozine and doxycycline, other antibiotics exerted adverse effects on lipid levels and increased dyslipidemia prevalence. The older participants with higher WC values were vulnerable to antibiotic exposure. Therefore, an appropriate understanding of the epidemiological attributes of antibiotic residues is indispensable to prevent abdominal obesity in the older population.

Comprehensive insights into profiles and bacterial sources of intracellular and extracellular antibiotic resistance genes in groundwater

Antibiotic resistance genes (ARGs), especially last-resort ARGs (LARGs), are receiving extensive attention as emerging environmental contaminants in groundwater. However, their prevalent intracellular and extracellular patterns and bacterial sources in groundwater remain unclear. Herein, groundwater samples were collected in Tianjin, and characterized based on the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs), as well as the resident bacterial communities and extracellular DNA (eDNA)-releasing bacterial communities. The quantitative real-time PCR assays showed that eARGs presented fewer subtypes than iARGs and generally displayed lower detection frequencies than the corresponding iARGs. Similarly, LARGs exhibited lower detection frequencies than common ARGs, but the total abundance showed no significant differences between them. Genes vanA and bla_VIM were the observed dominant LARGs, and aadA was the observed common ARG independent of location inside or outside the bacteria. Furthermore, the top 10 phyla showed much difference between the main eDNA-releasing bacteria and the dominant resident bacteria. Proteobacteria was the predominant resident bacterial phyla while dominating the source of eDNA in groundwater. Despite representing a minor portion of the abundance in the resident bacteria, Actinobacteriota, Acidobacteriota, and Chloroflex surprisingly accounted for a large majority of eDNA release. Co-occurrence patterns among persistent ARGs, the resident bacteria, and eDNA-releasing bacteria revealed that the dominant common iARG aadA and intracellular LARGs bla_VIM and vanA had significant positive correlations with Methylobacterium_Methylorubrum and Shewanella. Meanwhile, the dominant extracellular LARG bla_VIM may be released by bacteria belonging to at least five genera, including Ellin6067, Bifidobacterium, Blautia, Veillonella, and Dechloromonas. Collectively, the findings of this study extend our understanding regarding the distribution of ARGs and their bacterial sources in groundwater, and indicate the serious pollution of LARGs in groundwater, which poses potential risks to public health.

New insight into the co-adsorption of oxytetracycline and Pb(II) using magnetic metal-organic frameworks composites in aqueous environment: co-adsorption mechanisms and application potentials

The present study aimed to investigate the co-adsorption and application of water stabilized Fe₃O₄@ZIF-8 composite with magnetic cubic crystal structure. This new material was successfully prepared by facile modification strategy and rational design, which was used for simultaneous adsorption of oxytetracycline (OTC) and Pb(II) in aqueous solution. The co-adsorption behavior and mechanism of the composite for OTC and Pb(II) were systematically investigated by characterization techniques and batch experiments, and its application potential was effectively evaluated. The results showed that the synthesized Fe₃O₄@ZIF-8 composite innovatively retained the cubic crystal structure of ZIF-8 and was successfully loaded on the surface of Fe₃O₄ particles with small particle size to form a core-shell structure. The Fe₃O₄@ZIF-8 composite possessed a large specific surface area (1722 m²/g), magnetic separation performance (13.4 emu/g), and rich functional groups. The co-adsorption of OTC and Pb(II) on Fe₃O₄@ZIF-8 had fast reaction kinetics (equilibrium within 90 min) and large adsorption capacity (310.29 mg/g and 276.06 mg/g respectively). The adsorption process for both contaminants followed pseudo-second order kinetics and Langmuir isotherm models and had synergistic and competitive effects at the same time. π-π stacking and electrostatic interaction were the main mechanisms of adsorption. Fe₃O₄@ZIF-8 had good adsorption performance after cyclic adsorption for 4 times and it performed well in the treatment of real waste water. This study provided a new sight for the control of combined pollution of OTC and Pb(II) and proved Fe₃O₄@ZIF-8 composites have great application potentials for complex wastewater treatment.

Antibiotic-resistant bacteria and antibiotic resistance genes in uranium mine: Distribution and influencing factors

Both heavy metals and radiation could affect the proliferation and dissemination of emerging antibiotic resistance pollutants. As an environmental medium rich in radioactive metals, the profile of antibiotic resistance in uranium mine remains largely unknown. A uranium mine in Guangdong province, China was selected to investigate the distribution and influencing factors of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) including intracellular ARGs (iARGs), adsorbed-extracellular ARGs (aeARGs), and free extracellular ARGs (feARGs). The result indicated that sulfonamide and tetracycline ARB could be generally detected in mining area with the absolute concentrations of 7.70 × 10²-5.18 × 10⁵ colony forming unit/g. The abundances of aeARGs in mine soil were significantly higher than those of iARGs (p < 0.05), highlighting the critical contribution of aeARGs to ARGs spread. The feARGs in mine drainage and its receiving river were abundant (3.38 × 10⁴-1.86 × 10⁷ copies/mL). ARB, aeARGs, and iARGs may correlate with nitrogen species and heavy metals (e.g., U and Mn), and feARGs presented a significant correlation with chemical oxygen demand (p < 0.05). These findings demonstrate the occurrence of ARB and ARGs in uranium mine for the first time, thereby contributing to the assessment and control of the ecological risk of antibiotic resistance in radioactive environments.

Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications

Human health is threatened by antibiotic-resistant bacteria and their related infections, which cause thousands of human deaths every year worldwide. Surface waters are vulnerable to human activities and natural processes that facilitate the emergence and spread of antibiotic-resistant bacteria in the environment. This study evaluated the pathways and drivers of antimicrobial resistance (AR) in surface waters. We analyzed antibiotic resistance healthcare-associated infection (HAI) data reported to the CDC's National Healthcare Safety Network to determine the number of antimicrobial-resistant pathogens and their isolates detected in healthcare facilities. Ten pathogens and their isolates associated with HAIs tested resistant to the selected antibiotics, indicating the role of healthcare facilities in antimicrobial resistance in the environment. The analyzed data and literature research revealed that healthcare facilities, wastewater, agricultural settings, food, and wildlife populations serve as the major vehicles for AR in surface waters. Antibiotic residues, heavy metals, natural processes, and climate change were identified as the drivers of antimicrobial resistance in the aquatic environment. Food and animal handlers have a higher risk of exposure to resistant pathogens through ingestion and direct contact compared with the general population. The AR threat to public health may grow as pathogens in aquatic systems adjust to antibiotic residues, contaminants, and climate change effects. The unnecessary use of antibiotics increases the risk of AR, and the public should be encouraged to practice antibiotic stewardship to decrease the risk.

Effects of hematite on the dissemination of antibiotic resistance in pathogens and underlying mechanisms

The dissemination of antibiotic resistance genes (ARGs) in pathogens is becoming a pervasive global health threat, to which the importance of the environment attracts more and more attention. However, how natural minerals affect ARGs transfer in pathogens is still unclear. In this study, the concentration and size effects of hematite on the ARGs conjugative transfer to a common zoonotic pathogen Escherichia coli O157:H7 and underlying mechanisms were explored. Results revealed that bulk hematite reduced the conjugation of resistant plasmids by inhibiting cell growth at any concentration (1-100 mg/L), different from nano-hematite. Low concentrations of nano-hematite (≤ 25 mg/L) induced significant increases in conjugative transfer frequency of 1.83-4.49 folds, while its high concentrations (50 and 100 mg/L) showed no impact, compared with the control group. This low-concentration effect was likely attributed to the increased intracellular ROS level, the reduced intercellular repulsion by increasing the extracellular polymeric substances production and cell surface hydrophobicity, the formation of transfer channels and the increased membrane permeability evidenced by significant changes in gene expression level, and the increased proton motive force by increasing the transmembrane potential of recipients. These findings shed light on potential health risks caused by nano minerals-mediated ARGs dissemination in pathogens in the environment.

Linkage and driving mechanisms of antibiotic resistome in surface and ground water: Their responses to land use and seasonal variation

Antibiotic resistance in the environment, mostly mediated by antibiotic resistance genes (ARGs), has posed a threat to ecological and human health. Contamination of surface water and groundwater with ARGs has become a serious environmental concern. However, the distinctions and similarities across ARG profiles, the various ecological processes associated with ARGs, the driving mechanisms for ARG profiles in surface water and groundwater, and how they respond to land use and seasonal variation remain unknown. To tackle these issues, the contamination of ARGs in surface water and groundwater in central China was investigated using metagenomic technology. The results indicated that seasonal changes in ARG abundance and diversity were inconsistent across surface water and groundwater, and that the relationship between ARGs in surface water and groundwater was stronger during the rainy season. Land use had a greater effect on ARGs in surface water than in groundwater and was stronger during the dry season than during the rainy season. More interestingly, the ideal buffer zones with the greatest impact of land use on the ARGs of surface water and groundwater had distinct radii: 1500 m for both dry and rainy seasons in surface water, and 1000 m for dry season and 500 m for rainy season in groundwater. Furthermore, stochastic mechanisms mediated by mobile gene elements (MGEs) contribute significantly more to ARG assemblages than deterministic processes, particularly in groundwater. Furthermore, our results also showed that ARG enrichment in microbial communities was host- dependent, and the risk of ARGs in groundwater was greater both during the rainy season and dry season. In conclusion, the findings have improved our understanding of the relationship and driving mechanisms of ARGs in surface and ground water, as well as their responses to land use and seasonal variation, which may be beneficial for limiting ARG pollution in a watershed with high levels of anthropogenic activity.

The High Risk of Bivalve Farming in Coastal Areas With Heavy Metal Pollution and Antibiotic-Resistant Bacteria: A Chilean Perspective

Anthropogenic pollution has a huge impact on the water quality of marine ecosystems. Heavy metals and antibiotics are anthropogenic stressors that have a major effect on the health of the marine organisms. Although heavy metals are also associate with volcanic eruptions, wind erosion or evaporation, most of them come from industrial and urban waste. Such contamination, coupled to the use and subsequent misuse of antimicrobials in aquatic environments, is an important stress factor capable of affecting the marine communities in the ecosystem. Bivalves are important ecological components of the oceanic environments and can bioaccumulate pollutants during their feeding through water filtration, acting as environmental sentinels. However, heavy metals and antibiotics pollution can affect several of their physiologic and immunological processes, including their microbiome. In fact, heavy metals and antibiotics have the potential to select resistance genes in bacteria, including those that are part of the microbiota of bivalves, such as Vibrio spp. Worryingly, antibiotic-resistant phenotypes have been shown to be more tolerant to heavy metals, and vice versa, which probably occurs through co- and cross-resistance pathways. In this regard, a crucial role of heavy metal resistance genes in the spread of mobile element-mediated antibiotic resistance has been suggested. Thus, it might be expected that antibiotic resistance of Vibrio spp. associated with bivalves would be higher in contaminated environments. In this review, we focused on co-occurrence of heavy metal and antibiotic resistance in Vibrio spp. In addition, we explore the Chilean situation with respect to the contaminants described above, focusing on the main bivalves-producing region for human consumption, considering bivalves as potential vehicles of antibiotic resistance genes to humans through the ingestion of contaminated seafood.

Shallow-Water Hydrothermal Vents as Natural Accelerators of Bacterial Antibiotic Resistance in Marine Coastal Areas

Environmental contamination by heavy metals (HMs) poses several indirect risks to human health, including the co-spreading of genetic traits conferring resistance to both HMs and antibiotics among micro-organisms. Microbial antibiotic resistance (AR) acquisition is enhanced at sites anthropogenically polluted by HMs, as well as in remote systems naturally enriched in HMs, such as hydrothermal vents in the deep sea. However, to date, the possible role of hydrothermal vents at shallower water depths as hot spots of microbial AR gain and spreading has not been tested, despite the higher potential risks associated with the closer vicinity of such ecosystems to coasts and human activities. In this work, we collected waters and sediments at the Panarea shallow-water hydrothermal vents, testing the presence of culturable marine bacteria and their sensitivity to antibiotics and HMs. All of the bacterial isolates showed resistance to at least one antibiotic and one HM and, most notably, 80% of them displayed multi-AR on average to 12 (min 8, max 15) different antibiotics, as well as multi-HM tolerance. We show that our isolates displayed high similarity (≥99%) to common marine bacteria, affiliating with Actinobacteria, Gammaproteobacteria, Alphaproteobacteria and Firmicutes, and all displayed wide growth ranges for temperature and salinity during in vitro physiological tests. Notably, the analysis of the genomes available in public databases for their closest relatives highlighted the lack of genes for AR, posing new questions on the origin of multi-AR acquisition in this peculiar HM-rich environment. Overall, our results point out that shallow-water hydrothermal vents may contribute to enhance AR acquisition and spreading among common marine bacteria in coastal areas, highlighting this as a focus for future research.

Heavy metal-induced selection and proliferation of antibiotic resistance: A review

Antibiotic resistance is recognized as a global threat to public health. The selection and evolution of antibiotic resistance in clinical pathogens was believed to be majorly driven by the imprudent use of antibiotics. However, concerns regarding the same, through selection pressure by a multitude of other antimicrobial agents, such as heavy metals, are also growing. Heavy metal contamination co-selects antibiotic and metal resistance through numerous mechanisms, such as co-resistance and cross-resistance. Here, we have reviewed the role of heavy metals as antimicrobial resistance driving agents and the underlying concept and mechanisms of co-selection, while also highlighting the scarcity in studies explicitly inspecting the process of co-selection in clinical settings. Prospective strategies to manage heavy metal-induced antibiotic resistance have also been deliberated, underlining the need to find specific inhibitors so that alternate medicinal combinations can be added to the existing therapeutic armamentarium.

Metal(loid)s diffusion pathway triggers distinct microbiota responses in key regions of typical karst non-ferrous smelting assembly

Non-ferrous metal(loid)s in region with karst characteristic are highly diffusible, especially by runoff or atmospheric deposition. However, microbiota in response to the diffusing metal(loid)s is still to be understood. In this study, we focused on microbiota across metal(loid)s diffusion pathways around a non-ferrous smelting assembly. The microbial distribution and metal(loid)s-microbial interactions were analysed by 16S rRNA amplicon and multivariate statistical analysis. Although runoff and atmospheric deposition showed similar metal(loid)s diffusion contribution, different microbial compositions were revealed. The microbiota along the runoff transect (region3) was similar to those within the atmospheric deposition transect (region4), which significantly differed from those closer to the smelting assembly (region1 and region2; R² = 0.3866, p = 0.001). Random forest model indicated the negative impacts of bioavailable metal(loid)s on microbial diversity. Proteobacteria was predominant in region1 while Actinobacteriota dominated in the other regions. Twenty abundant genera were identified in metal(loid)s rich area, such as sulfur metabolizer Sulfurifustis and metal resistant Acinetobacter. Interactions between the geochemical parameters and the dominant taxa indicated that the main drivers were Al, Sb, As and their bioavailable fractions and sulfate. This study provides understandings of microbiota patterns towards different metal(loid)s diffusion pathways around non-ferrous smelting assembly with karst characteristic.

Contribution of enrofloxacin and Cu2+ to the antibiotic resistance of bacterial community in a river biofilm

Pollutants discharged from wastewater are the main cause of the spread of antibiotic resistance in river biofilms. There is controversy regarding the primary contribution of environmental selectors such as antibiotics and heavy metals to the development of antibiotic resistance in bacterial communities. Here, this study compared the effect of environmental safety concentration Cu²⁺ and enrofloxacin (ENR) on the evolution of antibiotic resistance by examining phenotypic characteristics and genotypic profiles of bacterial communities in a river biofilm, and then distinguished the major determinants from a comprehensive perspective. The pollution induced community tolerance in ENR-treated group was significantly higher than that in Cu²⁺-treated group (at concentration levels of 100 and 1000 μg/L). Metagenomic sequencing results showed that ENR significantly increased the number and total abundance of antibiotic resistance genes (ARGs), but there was no significant change in the Cu²⁺- treated group. Compared with Cu²⁺, ENR was the major selective agent in driving the change of taxonomic composition because the taxonomic composition in ENR was the most different from the original biofilm. Comparing and analyzing the prokaryotic composition, the phylum of Proteobacteria was enriched in both ENR and Cu²⁺ treated groups. Among them, Acidovorax and Bosea showed resistance to both pollutants. Linking taxonomic composition to ARGs revealed that the main potential hosts of fluoroquinolone resistance genes were Comamonas, Sphingopyxis, Bradyrhizobium, Afipia, Rhodopseudomonas, Luteimonas and Hoeflea. The co-occurrence of ARGs and metal resistance genes (MRGs) showed that the multidrug efflux pump was the key mechanism connecting MRGs and ARGs. Network analysis also revealed that the reason of Cu²⁺ selected for fluoroquinolones resistant bacterial communities was the coexistence of multidrug efflux gene and MRGs. Our research emphasizes the importance of antibiotics in promoting the development of antibiotic resistant bacterial communities from the perspective of changes in community structure and resistome in river biofilms.