Occurrence of antibiotic resistance genes and microbial source tracking markers in the water of a karst spring in Germany

A rapid approach with machine learning for quantifying the relative burden of antimicrobial resistance in natural aquatic environments

The massive use and discharge of antibiotics have led to increasing concerns about antimicrobial resistance (AMR) in natural aquatic environments. Since the dose-response mechanisms of pathogens with AMR have not yet been fully understood, and the antibiotic resistance genes and bacteria-related data collection via field sampling and laboratory testing is time-consuming and expensive, designing a rapid approach to quantify the burden of AMR in the natural aquatic environment has become a challenge. To cope with such a challenge, a new approach involving an integrated machine-learning framework was developed by investigating the associations between the relative burden of AMR and easily accessible variables (i.e., relevant environmental variables and adjacent land-use patterns). The results, based on a real-world case analysis, demonstrate that the quantification speed has been reduced from 3-7 days, which is typical for traditional measurement procedures with field sampling and laboratory testing, to approximately 0.5 hours using the new approach. Moreover, all five metrics for AMR relative burden quantification exceed the threshold level of 85%, with F1-score surpassing 0.92. Compared to logistic regression, decision trees, and basic random forest, the adaptive random forest model within the framework significantly improves quantification accuracy without sacrificing model interpretability. Two environmental variables, dissolved oxygen and resistivity, along with the proportion of green areas were identified as three key feature variables for the rapid quantification. This study contributes to the enrichment of burden analyses and management practices for rapid quantification of the relative burden of AMR without dose-response information.

Do storm overflows influence AMR in the environment and is this relevant to human health? A UK perspective on a global issue

Antimicrobial resistance (AMR) is a global public health threat, and the environment has been identified as an important reservoir for resistant microorganisms and genes. Storm overflows (SOs) discharge wastewater and stormwater, and are found throughout many wastewater networks. While there are no data currently showing the impact of SOs on the environment with respect to AMR in the UK, there is a small but growing body of evidence globally highlighting the potential role of SOs on environmental AMR. This review aims to provide an overview of the current state of SOs, describe global data investigating the impact of SOs on environmental AMR, and discuss the implications of SOs regarding AMR and human health. In addition, the complexities of studying the effects of SOs are discussed and a set of priority research questions and policy interventions to tackle a potentially emerging threat to public health are presented.

Leaching of antibiotic resistance genes and microbial assemblages following poultry litter applications in karst and non-karst landscapes

Antibiotic resistance is increasingly recognized as a critical challenge affecting human, animal, and environmental health. Yet, environmental dynamics and transport of antibiotic resistance genes (ARGs) and microbial communities in karst and non-karst leachate following poultry litter land applications are not well understood. This study investigates impacts of broiler poultry litter application on the proliferation of ARGs (tetW, qnrS, ermB, sulI, and blaCTX-M-32), class 1 integron (intI1 i), and alterations in microbial communities (16S rRNA) within karst derived soils, which are crucial and under-researched systems in the global hydrological cycle, and non-karst landscapes. Using large, intact soil columns (45 cm diam. × 100 cm depth) from karst and non-karst landscapes, the role of preferential flow and ARG transport in leachate was enumerated following surface application of poultry litter and simulated rain events. This research demonstrated that in poultry litter amended karst soils, ARG (i.e., ermB and tetW) abundance in leachate increased 1.5 times compared to non-karst systems (p < 0.05), highlighting the influence of geological factors on ARG proliferation. Notably, microbial communities in karst soil leachate exhibited increased diversity and abundance, suggesting a potential linkage between microbial composition and ARG presence. Further, our correlation and network analyses identified relationships between leachate ARGs, microbial taxa, and physicochemical properties, underscoring the complex interplay in these environmentally sensitive areas. These findings illuminate the critical role of karst systems in shaping ARG abundance and pollutant dispersal and microbial community dynamics, thus emphasizing the need for landscape-specific approaches in managing ARG dissemination to the environment. This study provides a deeper understanding of hydrogeological ARG dynamics but also lays the groundwork for future research and strategies to mitigate ARG dissemination through targeted manure applications across agricultural landscapes.

Quantification of β-lactamase producing bacteria in German surface waters with subsequent MALDI-TOF MS-based identification and β-lactamase activity assay

Environmental oligotrophic bacteria are suspected to be highly relevant carriers of antimicrobial resistance (AMR). However, there is a lack of validated methods for monitoring in the aquatic environment. Since extended-spectrum β-lactamases (ESBLs) play a particularly important role in the clinical sector, a culturing method based on R2A-medium spiked with different combinations of β-lactams was applied to quantify β-lactamase-producing environmental bacteria from surface waters. In German surface water samples (n = 28), oligotrophic bacteria ranging from 4.0 × 103 to 1.7 × 104 CFU per 100 mL were detected on the nutrient-poor medium spiked with 3rd generation cephalosporins and carbapenems. These numbers were 3 log10 higher compared to ESBL-producing Enterobacteriales of clinical relevance from the same water samples. A MALDI-TOF MS identification of the isolates demonstrated, that the method leads to the isolation of environmentally relevant strains with Pseudomonas, Flavobacterium, and Janthinobacterium being predominant β-lactam resistant genera. Subsequent micro-dilution antibiotic susceptibility tests (Micronaut-S test) confirmed the expression of β-lactamases. The qPCR analysis of surface waters DNA extracts showed the presence of β-lactamase genes (blaTEM, blaCMY-2, blaOXA-48, blaVIM-2, blaSHV, and blaNDM-1) at concentrations of 3.7 (±1.2) to 1.0 (±1.9) log10 gene copies per 100 mL. Overall, the results demonstrate a widespread distribution of cephalosporinase and carbapenemase enzymes in oligotrophic environmental bacteria that have to be considered as a reservoir of ARGs and contribute to the spread of antibiotic resistance.

Fate and transport modelling for evaluating antibiotic resistance in aquatic environments: Current knowledge and research priorities

Antibiotics have revolutionised medicine in the last century and enabled the prevention of bacterial infections that were previously deemed untreatable. However, in parallel, bacteria have increasingly developed resistance to antibiotics through various mechanisms. When resistant bacteria find their way into terrestrial and aquatic environments, animal and human exposures increase, e.g., via polluted soil, food, and water, and health risks multiply. Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. The conceptual understanding of sources and pathways of antibiotics, ARB, and ARGs from society to the water environments is essential for setting the scene and developing an appropriate framework for modelling. Various factors and processes associated with hydrology, ecology, and climate change can significantly affect the fate and transport of ARB and ARGs in natural environments. This article reviews current knowledge, research gaps, and priorities for developing water quality models to assess the fate and transport of ARB and ARGs. The paper also provides inputs on future research needs, especially the need for new predictive models to guide risk assessment on AR transmission and spread in aquatic environments.

Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi

Introduction

Understanding the gut microbiota and antibiotic resistance gene (ARG) profiles in non-human primates (NHPs) is crucial for evaluating their potential impact on human health and the environment.

Methods

In this study, we performed metagenomic analysis of 203 primate fecal samples, including nine NHP species and humans, to comprehensively characterize their gut microbiota and ARGs.

Results

Our study reveals the prevailing phyla in primates as Firmicutes, Bacteroidetes, Euryarchaeota, and Proteobacteria. The captive NHPs exhibited higher ARG abundance compared to their wild counterparts, with tetracycline and beta-lactam resistance genes prevailing. Notably, ARG subtypes in Trachypithecus leucocephalus (T. leucocephalus) residing in karst limestone habitats displayed a more dispersed distribution compared to other species. Interestingly, ARG profiles of NHPs clustered based on geographic location and captivity status. Co-occurrence network analysis revealed intricate correlations between ARG subtypes and bacterial taxa. Procrustes analysis unveiled a significant correlation between ARGs and microbial phylogenetic community structure. Taxonomic composition analysis further highlighted differences in microbial abundance among NHPs and humans.

Discussion

Our study underscores the impact of lifestyle and geographical location on NHP gut microbiota and ARGs, providing essential insights into the potential risks posed by NHPs to antibiotic resistance dissemination. This comprehensive analysis enhances our understanding of the interplay between NHPs and the gut resistome, offering a critical reference for future research on antibiotic resistance and host-microbe interactions.

Meta-analysis of microbial source tracking for the identification of fecal contamination in aquatic environments based on data-mining

Microbial source tracking (MST) technology represents an innovative approach employed to trace fecal contamination in environmental water systems. The performance of primers may be affected by amplification techniques, target primer categories, and regional differences. To investigate the influence of these factors on primer recognition performance, a meta-analysis was conducted on the application of MST in water environments using three databases: Web of Science, Scopus, and PubMed (n = 2291). After data screening, 46 studies were included in the final analysis. The investigation encompassed Polymerase Chain Reaction (PCR)/quantitative PCR (qPCR) methodologies, dye-based (SYBR)/probe-based (TaqMan) techniques, and geographical differences of a human host-specific (HF183) primer and other 21 additional primers. The results indicated that the primers analyzed were capable of differentiating host specificity to a certain degree. Nonetheless, by comparing sensitivity and specificity outcomes, it was observed that virus-based primers exhibited superior specificity and recognition capacity, as well as a stronger correlation with human pathogenicity in water environments compared to bacteria-based primers. This finding highlights an important direction for future advancements. Moreover, within the same category, qPCR did not demonstrate significant benefits over conventional PCR amplification methods. In comparing dye-based and probe-based techniques, it was revealed that the probe-based method's advantage lay primarily in specificity, which may be associated with the increased propensity of dye-based methods to produce false positives. Furthermore, the heterogeneity of the HF183 primer was not detected in China, Canada, and Singapore respectively, indicating a low likelihood of regional differences. The variation among the 21 other primers may be attributable to regional differences, sample sources, detection techniques, or alternative factors. Finally, we identified that economic factors, climatic conditions, and geographical distribution significantly influence primer performance.

Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination

Karst aquifers are important water resources for drinking water supplies worldwide. Although they are susceptible to anthropogenic contamination due to their high permeability, there is a lack of detailed knowledge on the stable core microbiome and how contamination may affect these communities. In this study, eight karst springs (distributed across three different regions in Romania) were sampled seasonally for one year. The core microbiota was analysed by 16S rRNA gene amplicon sequencing. To identify bacteria carrying antibiotic resistance genes and mobile genetic elements, an innovative method was applied, consisting of high-throughput antibiotic resistance gene quantification performed on potential pathogen colonies cultivated on Compact Dry™ plates. A taxonomically stable bacterial community consisting of Pseudomonadota, Bacteroidota, and Actinomycetota was revealed. Core analysis reaffirmed these results and revealed primarily freshwater-dwelling, psychrophilic/psychrotolerant species affiliated to Rhodoferax, Flavobacterium, and Pseudomonas genera. Both sequencing and cultivation methods indicated that more than half of the springs were contaminated with faecal bacteria and pathogens. These samples contained high levels of sulfonamide, macrolide, lincosamide and streptogramins B, and trimethoprim resistance genes spread primarily by transposase and insertion sequences. Differential abundance analysis found Synergistota, Mycoplasmatota, and Chlamydiota as suitable candidates for pollution monitoring in karst springs. This is the first study highlighting the applicability of a combined approach based on high-throughput SmartChip™ antibiotic resistance gene quantification and Compact Dry™ pathogen cultivation for estimating microbial contaminants in karst springs and other challenging low biomass environments.

Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework

Introduction

Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined.

Methods

To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region.

Results

A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km.

Discussion

Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.

Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study

With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.

Occurrence and prevalence of antimicrobial resistance in urban karst groundwater systems based on targeted resistome analysis

Antimicrobial resistance (AMR) is a global crisis threatening human, animal, and environmental health. The natural environment, specifically water resources, has been recognized as a reservoir and dissemination pathway for AMR; however, urban karst aquifer systems have been overlooked. This is a concern as these aquifer systems provide drinking water to about 10 % of the global population; yet, the urban influence on the resistome in these vulnerable aquifers is sparingly explored. This study used high-throughput qPCR to determine the occurrence and relative abundance of antimicrobial resistant genes (ARG) in a developing urban karst groundwater system in Bowling Green, KY. Ten sites throughout the city were sampled weekly and analyzed for 85 ARGs, as well as seven microbial source tracking (MST) genes for human and animal sources, providing a spatiotemporal understanding of the resistome in urban karst groundwater. To further understand ARGs in this environment, potential drivers (landuse, karst feature type, season, source of fecal pollution) were considered in relation to the resistome relative abundance. The MST markers highlighted a prominent human influence to the resistome in this karst setting. The concentration of targeted genes varied between the sample weeks, but all targeted ARGs were prevalent throughout the aquifer regardless of karst feature type or season, with high concentrations captured for sulfonamide (sul1), quaternary ammonium compound (qacE), and aminoglycoside (strB) antimicrobial classes. Higher prevalence and relative abundance were detected during the summer and fall seasons, as well as at the spring features. Linear discriminant analysis suggested that karst feature type had higher influence on ARGs in the aquifer compared to season and the source of fecal pollution had the least influence. These findings can contribute to the development of effective management and mitigation strategies for AMR.

Prevalence and whole-genome sequencing characterization of Salmonella in urban karst groundwater and predominantly groundwater-fed surface waters for serotypes and antimicrobial resistance

Karst aquifers provide a significant source of drinking water around the world; however, they are prone to bacterial contamination. We investigated the prevalence, serotypes, and antimicrobial resistance genes (ARGs) of Salmonella in urban karst groundwater and groundwater-fed surface waters. Weekly water samples (n = 443) were collected from nine groundwater sites and the Barren River in Bowling Green, KY. Additionally, cross-sectional samples were collected from 45 sites, including groundwaters and two rivers, in Tampa, FL. Salmonella was detected in 14.5% of Bowling Green samples resulting in 176 isolates representing 18 serotypes. Two (4.4%) of the Tampa samples were positive yielding eight isolates representing two serotypes. In Bowling Green, Salmonella prevalence varied by sampling site, week, month, and season, with the highest prevalence in surface water in the month of November and during summer. Salmonella Newport was the most common serotype detected. Nine of the serotypes detected in the study were among the top 20 serotypes commonly associated with human infections in the United States. Isolates were clustered with human clinical isolates, or isolates obtained from food animals, suggesting the importance of humans and agricultural practices as a source of water contamination. ARGs were detected in 12.5% (n = 176) of the Bowling Green isolates; overall, 81.8% (n = 22) of these were multidrug-resistant (resistance to ≥3 antimicrobial classes). Notably, the four Salmonella Agona isolates were resistant to four antimicrobial classes, mercury, and quaternary ammonium compounds. Seasonality and the widespread occurrence of Salmonella both in the groundwater and groundwater-fed surface waters is a potential risk to public health.

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.

Antibiotic resistome in groundwater and its association with mountain springs and river

The distribution of antibiotic resistance genes (ARGs) in water sources potentially threatens drinking water safety. However, the sources of antibiotic resistome in groundwater are still under-investigated. Here, we evaluated the profiles of antibiotic resistome in peri-urban groundwater and its associated water sources (river and mountain spring) to characterize the antibiotic resistome from natural water sources on groundwater resistome. A total of 261 antibiotic resistome were detected in groundwater, mountain spring, and river samples. The relative abundances of ARGs and mobile genetic elements (MGEs) were significantly higher in the river samples than in spring water and groundwater samples. The resistome profiles were similar between groundwater and spring water but differed from the river samples. According to source tracking results, the groundwater resistome was likely to be derived from springs (28.0%-50.0%) and rivers (28.6%-48.6%), which share the same trend for the source tracking of bacterial communities. Bacterial α-diversity, bacterial β-diversity, and MGEs directly or indirectly affected the ARGs in groundwater samples. Although the abundance of groundwater resistome was not elevated by river and spring water, groundwater resistomes were diverse and may be derived from both river and spring water. We highlight the importance of groundwater resistome and its association with potential water sources, providing a better understanding and basis for the effective control of the ARG proliferation and dissemination in groundwater from exogenous water bodies in the future.

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.

Antimicrobial resistomes in food chain microbiomes

The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.

Antibiotics, antibiotic resistance and associated risk in natural springs from an agroecosystem environment

This study investigates the occurrence, transport, and risks associated to antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic resistant Escherichia coli (AR-E. coli) in eleven natural springs in an agroecosystem environment with intense livestock production, where groundwater nitrate concentration usually sets above 50 mg L^-1. Out of 23 multiple-class antibiotics monitored, tetracycline and sulfonamide residues were the most ubiquitous, and they were detected at concentrations ranging from ng L^-1 to μg L^-1. Five ARGs were monitored, conferring resistance to the antibiotic classes of major use in livestock production. Thus, genes conferring resistance to sulfonamides (sul1 and sul2) and tetracyclines (tetW) as well as a gene proxy for anthropogenic pollution (intI1) were present in most springs. sul1 was the most abundant, with absolute concentrations ranging from 4 × 10² to 5.6 × 10⁶ gene copies L^-1 water. AR-E. coli showing resistance to sulfonamides and tetracyclines was also detected, with a prevalence up to approximately 40 % in some sites but with poor correlations with the concentration of antibiotic residues and ARGs. The occurrence of antibiotics, ARGs and AR-E. coli was characterized by large seasonal variations which were mostly associated to both hydrological factors and reactive transport processes. Finally, a risk assessment approach pointed out towards low risk for both the groundwater environment and human health, when spring water is used for direct human consumption, associated with the occurrence of antibiotics, ARGs and AR-E. coli. However, long-term effects cannot be neglected, and proper actions must be taken to preserve groundwater quality.

A Low-Cost Electrochemical Method for the Determination of Sulfadiazine in Aquaculture Wastewater

As the concept of green development spreads worldwide, environmental protection awareness for production and life has been continuously strengthened. Antibiotic residues in aquaculture wastewaters aggravate environmental pollution and threaten human health. Therefore, the detection of residual antibiotics in wastewater is crucial. In this paper, a new, simple, and low-cost method based on the glassy carbon electrode electrochemical sensor for the detection of sulfadiazine in aquaculture wastewater was developed without using complex materials to modify the electrode surface, to detect sulfadiazine which electrochemically oxidizes directly. The electrochemical performance of the sensor was studied and optimized with differential pulse voltammetry and cyclic voltammetry in the three-electrode system. The optimal electrolyte was acetic acid-sodium acetate buffer, and the optimal pH was 4.0. Finally, based on the optimized conditions, the newly established method showed satisfactory results for detecting sulfadiazine in aquaculture wastewater. The concentration of sulfadiazine and the peak current intensity showed a linear relationship in the range of 20 to 300 μmol/L, and the limit of detection was 6.14 μmol/L, the recovery rate of standard addition was 87-95%, with satisfactory reproducibility and low interference.

Fecal pollution source characterization in the surface waters of recharge and contributing zones of a karst aquifer using general and host-associated fecal genetic markers

Fecal pollution of surface waters in the karst-dominated Edwards aquifer is a serious concern as contaminated waters can rapidly transmit to groundwaters, which are used for domestic purposes. Although microbial source tracking (MST) detects sources of fecal pollution, integrating data related to environmental processes (precipitation) and land management practices (septic tanks) with MST can provide better understanding of fecal contamination fluxes to implement effective mitigation strategies. Here, we investigated fecal sources and their spatial origins at recharge and contributing zones of the Edwards aquifer and identified their relationship with nutrients in different environmental/land-use conditions. During March 2019 to March 2020, water samples (n = 295) were collected biweekly from 11 sampling sites across four creeks and analyzed for six physico-chemical parameters and ten fecal indicator bacteria (FIB) and MST-based qPCR assays targeting general (E. coli, Enterococcus, and universal Bacteroidales), human (BacHum and HF183), ruminant (Rum2Bac), cattle (BacCow), canine (BacCan), and avian (Chicken/Duck-Bac and GFD) fecal markers. Among physico-chemical parameters, nitrate-N (NO₃-N) concentrations at several sites were higher than estimated national background concentrations for streams. General fecal markers were detected in the majority of water samples, and among host-associated MST markers, GFD, BacCow, and Rum2Bac were more frequently detected than BacCan, BacHum, and HF183, indicating avian and ruminant fecal contamination is a major concern. Cluster analysis results indicated that sampling sites clustered based on precipitation and septic tank density showed significant correlation (p < 0.05) between nutrients and FIB/MST markers, indicating these factors are influencing the spatial and temporal variations of fecal sources. Overall, results emphasize that integration of environmental/land-use data with MST is crucial for a better understanding of nutrient loading and fecal contamination.

Predictive modeling of microbiological seawater quality in karst region using cascade model

This paper presents an in-depth analysis of seawater quality measurements during the bathing seasons from year 2009 to 2020 in the city of Rijeka, Croatia. Due to rare occurrences of measurements with less than excellent water quality, considered dataset is deeply imbalanced. Additionally, it incorporates measurements under the influence of submerged groundwater discharges (SGD), which were observed in some bathing locations. These discharges were previously thought to dry up during the summer season and are now suspected to be one of the causes of increased Escherichia coli values. Consequently, and in view of the fact that the accuracy of prediction models can be significantly influenced by temporal and spatial variation of the input data, a novel cascade prediction modeling strategy was proposed. It consists of a sequence of prediction models which tend to identify general environmental conditions which confidently lead to excellent bathing water quality. The proposed model uses environmental features which can rather easily be estimated or obtained from the weather forecast. The model was trained on a highly biased dataset, consisting of data from locations with and without SGD influence, and for the time period spanning extremely dry and warm seasons, extremely wet seasons, as well as normal seasons. To simulate realistic application, the model was tested using temporal and spatial stratification of data. The cascade strategy was shown to be a good approach for reliably detecting environmental parameters which produce excellent water quality. Proposed model is designed as a filter method, where instances classified as less-than-excellent water quality require further analysis. The cascade model provides great flexibility as it can be customized to the particular needs of the investigated area and dataset specifics.

Distribution and correlation between antibiotic resistance genes and host-associated markers before and after swine fever in the longjiang watershed

Antibiotic resistance genes (ARGs) are abundantly shed in feces. Thus, it is crucial to identify their host sources so that ARG pollution can be effectively mitigated and aquatic ecosystems can be properly conserved. Here, spatiotemporal variations and sources of ARGs in the Longjiang watershed of South China were investigated by linking them with microbial source tracker (MST) indicators. The most frequently detected ARGs (>90%) were sulI, sulII, bla_TEM, tetW, ermF, and the mobile element intI1. Spatial distribution analyses showed that tributaries contributed significantly more sulI, sulII, and ermF contamination to the Longjiang watershed than the main channel. MST indicator analysis revealed that the Longjiang watershed was contaminated mainly by human fecal pollution. Livestock- and poultry-associated fecal pollution significantly declined after the swine fever outbreak. The occurrence of most ARGs is largely explained by human fecal pollution. In contrast, pig fecal pollution might account for the prevalence of tetO. Moreover, combined human-pig fecal pollution contributed to the observed bla_NDM-1 distribution in the Longjiang watershed. Subsequent analysis of the characteristics of MST markers disclosed that the relatively lower specificities of BacHum and Rum-2-Bac may lead to inaccurate results of tracking ARG pollution source. The present study determined spatiotemporal variations and ARG origins in the Longjiang watershed by combining MST markers. It also underscored the necessity of using multiple MST markers simultaneously to identify and characterize ARG pollution sources accurately.

Fecal indicators and antibiotic resistance genes exhibit diurnal trends in the Chattahoochee River: Implications for water quality monitoring

Water bodies that serve as sources of drinking or recreational water are routinely monitored for fecal indicator bacteria (FIB) by state and local agencies. Exceedances of monitoring thresholds set by those agencies signal likely elevated human health risk from exposure, but FIB give little information about the potential source of contamination. To improve our understanding of how within-day variation could impact monitoring data interpretation, we conducted a study at two sites along the Chattahoochee River that varied in their recreational usage and adjacent land-use (natural versus urban), collecting samples every 30 min over one 24-h period. We assayed for three types of microbial indicators: FIB (total coliforms and Escherichia coli); human fecal-associated microbial source tracking (MST) markers (crAssphage and HF183/BacR287); and a suite of clinically relevant antibiotic resistance genes (ARGs; blaCTX-M, blaCMY, MCR, KPC, VIM, NDM) and a gene associated with antibiotic resistance (intl1). Mean levels of FIB and clinically relevant ARGs (blaCMY and KPC) were similar across sites, while MST markers and intI1 occurred at higher mean levels at the natural site. The human-associated MST markers positively correlated with antibiotic resistant-associated genes at both sites, but no consistent associations were detected between culturable FIB and any molecular markers. For all microbial indicators, generalized additive mixed models were used to examine diurnal variability and whether this variability was associated with environmental factors (water temperature, turbidity, pH, and sunlight). We found that FIB peaked during morning and early afternoon hours and were not associated with environmental factors. With the exception of HF183/BacR287 at the urban site, molecular MST markers and intI1 exhibited diurnal variability, and water temperature, pH, and turbidity were significantly associated with this variability. For blaCMY and KPC, diurnal variability was present but was not correlated with environmental factors. These results suggest that differences in land use (natural or urban) both adjacent and upstream may impact overall levels of microbial contamination. Monitoring agencies should consider matching sample collection times with peak levels of target microbial indicators, which would be in the morning or early afternoon for the fecal associated indicators. Measuring multiple microbial indicators can lead to clearer interpretations of human health risk associated with exposure to contaminated water.

The Sources and Potential Hosts Identification of Antibiotic Resistance Genes in the Yellow River, Revealed by Metagenomic Analysis

The fate of antibiotic resistance genes (ARGs) has been revealed in various environmental media in recent years. Namely, the emergence of genes that resist colistin and carbapenems has attracted wide attention. However, the pollution condition of ARGs and sources in the Yellow River is still little understood, despite the river being the second longest in China. The present study determined the levels of ARG pollution in the Henan section of the Yellow River and evaluated the role of the aquaculture industry in the spread of ARGs. As revealed by the results, a total of 9 types of ARGs were detected in the sediments of the Yellow River, and the total ARG content in the Yellow River ranges from 7.27 to 245.45 RPKM. Sul1 and sul2 are the dominant ARGs, and the huge usage of sulfonamides, horizontal gene transfer, and wide bacteria host contribute to the prevalence of these two genes. The results of Spearman correlation analysis indicate that the breeding industry has little influence on ARGs in the Yellow River. Network analysis reveals that the opportunistic pathogen Pseudomonas is the potential host of sul1, tetG, and ANT(3'')-IIa, which can pose a risk to human health.

Cascade Filtration With PCR Detection and Field-Flow-Fractionation Online With ICP-MS for the Characterization of DNA Interaction With Suspended Particulate Matter

The variety of applied antibiotics in animal and human medicine results in the release, development, and spread of relevant numbers of antibiotic resistance genes (ARGs) in the environment. The majority of ARGs are present in intracellular forms (in bacteria). Neglected aspects are extracellular variants of ARGs (eARGs) and their fragments, which have been detected in surface-water samples and sediments. The stability of eARGs is expected to be low; however, binding to particulate matter is likely to improve their stability and also affect their transport and dissemination behavior. Few studies have investigated DNA particle interactions, mostly via indirect characterization of adduct formation in model systems but not in real environmental matrices. Therefore, our study aims at a novel approach for direct characterization of desoxyribonucleic acid (DNA) particle interactions using both cascade filtration and field-flow fractionation. Cascade filtration with quantitative polymerase chain reaction (qPCR) detection indicated retention of ARGs on filters with much larger pore sizes supporting the hypothesis of ARG-particle interactions. However, artifacts from membrane clogging or DNA–membrane interaction cannot be excluded. Consequently, asymmetric flow field-flow fractionation was investigated as an alternative separation technique with the advantage of particle separation in a thin channel, reducing the risk of artifacts. The key method parameters, membrane composition, molecular weight cut off, and carrier composition, were systematically investigated using a calf-thymus DNA-spiked surface-water sample as a model. The results clearly showed a shift in the elution time of clay particles suggesting the presence of DNA–clay adducts. Multi-element detection by inductively coupled plasma mass spectrometry (ICP-MS) enabled monitoring of clay via the Al, Fe, and Si signals and DNA via the P signal. Matching peak profiles for the new fraction in the fractograms of the ARG and DNA-spiked water sample support adduct formation. Further evidence was provided by a novel post-channel filtration approach for the separation of free DNA from DNA–clay adducts.

An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments

Fecal contamination of water constitutes a serious health risk to humans and environmental ecosystems. This is mainly due to the fact that fecal material carries a variety of enteropathogens, which can enter and circulate in water bodies through fecal pollution. In this respect, the prompt identification of the polluting source(s) is pivotal to guiding appropriate target-specific remediation actions. Notably, microbial source tracking (MST) is widely applied to determine the host origin(s) contributing to fecal water pollution through the identification of zoogenic and/or anthropogenic sources of fecal environmental DNA (eDNA). A wide array of host-associated molecular markers have been developed and exploited for polluting source attribution in various aquatic ecosystems. This review is intended to provide the most up-to-date overview of genetic marker-based MST studies carried out in different water types, such as freshwaters (including surface and groundwaters) and seawaters (from coasts, beaches, lagoons, and estuaries), as well as drinking water systems. Focusing on the latest scientific progress/achievements, this work aims to gain updated knowledge on the applicability and robustness of using MST for water quality surveillance. Moreover, it also provides a future perspective on advancing MST applications for environmental research.

Transport-based source tracking of contaminants in a karst aquifer: Model implementation, proof of concept, and application to event-based field data

Identification and location of contamination sources is crucial for water resource protection - especially in karst aquifers which provide 25% of the world´s population with water but are highly vulnerable to contamination. Transport-based source tracking is proposed and verified here as a complementary approach to microbial and chemical source tracking in karst aquifers for identifying and locating such sources of contamination and for avoiding ambiguities that might arise from using one method alone. The transport distance is inversely modelled from contaminant breakthrough curves (BTC), based on analytical solutions of the 1D two-region non-equilibrium advection dispersion equation using GNU Octave. Besides the BTC, the model requires reliable estimates of transport velocity and input time. The model is shown to be robust, allows scripted based, automated 2D sensitivity analyses (interplay of two parameters), and can be favourable when distributed numerical models are inappropriate due to insufficient data. Sensitivity analyses illustrate that the model is highly sensitive to the input time, the flow velocity, and the fraction of the mobile fluid region. A conclusive verification approach was performed by applying the method to synthetic data, tracer tests, and event-based field data. Transport distances were correctly modelled for a set of artificial tracer tests using a discharge-velocity relationship that could be established for the respective karst catchment. For the first time such an approach was shown to be applicable to estimate the maximum distance to the contamination source for coliform bacteria in karst spring water combined with microbial source tracking. However, prediction intervals for the transport distance can be large even in well-studied karst catchments mainly related to uncertainties in the flow velocity and the input time. Using a maximum transport distance is proposed to account for less permeable, "slower" pathways. In general, transport-based source tracking might be used wherever transport can be described by the 1D two-region non-equilibrium model, e.g. rivers and fractured or porous aquifers.

Occurrence of Antimicrobial Resistance in the Environment in Germany, Austria, and Switzerland: A Narrative Review of Existing Evidence

(1) Background: This study summarizes the current research on antibiotic resistance (AR) in the environment conducted in Austria, Germany, and Switzerland; (2) Methods: A narrative systematic literature review of epidemiological studies based on searches in EMBASE and CAB abstracts (up to 16 June2021) was conducted. Environmental reservoirs included water sources, wastewater, animal husbandry, wildlife, soil, and sediment; (3) Results: Four hundred and four records were screened, and 52 studies were included. Thirteen studies examined aquatic environments, and eleven investigated wastewater. Eight studies investigated both wildlife and animal husbandry. Less evidence was available for sediments, soil, and air. Considerable heterogeneity in research focus, study design, sampling, and measurement of resistance was observed. Resistance to all categories of antimicrobials in the WHO CIA list was identified. Resistance to critically important and highly important substances was reported most frequently; (4) Conclusions: The current research scope presents data-gathering efforts. Usage of a unified protocol for isolate collection, selecting sampling sites, and susceptibility testing is required to provide results that can be compared between the studies and reservoirs. Epidemiological, environmental, and ecological factors should be considered in surveys of the environmental dissemination of AR. Systematic epidemiological studies investigating AR at the interface of human, animal, and environmental health are needed.

Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén

Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.

Occurrence of Antibiotic Resistant Bacteria in Urban Karst Groundwater Systems

Antibiotic resistance is a global concern for human, animal, and environmental health. Many studies have identified wastewater treatment plants and surface waters as major reservoirs of antibiotic resistant bacteria (ARB) and genes (ARGs). Yet their prevalence in urban karst groundwater systems remains largely unexplored. Considering the extent of karst groundwater use globally, and the growing urban areas in these regions, there is an urgent need to understand antibiotic resistance in karst systems to protect source water and human health. This study evaluated the prevalence of ARGs associated with resistance phenotypes at 10 urban karst features in Bowling Green, Kentucky weekly for 46 weeks. To expand the understanding of prevalence in urban karst, a spot sampling of 45 sites in the Tampa Bay Metropolitan area, Florida was also conducted. Specifically, this study considered tetracycline and extended spectrum beta-lactamase (ESBLs) producing, including third generation cephalosporin, resistant E. coli, and tetracycline and macrolide resistant Enterococcus spp. across the 443 Kentucky and 45 Florida samples. A consistent prevalence of clinically relevant and urban associated ARGs were found throughout the urban karst systems, regardless of varying urban development, karst geology, climate, or landuse. These findings indicate urban karst groundwater as a reservoir for antibiotic resistance, potentially threatening human health.

Occurrence and distribution of antibiotics in groundwater, surface water, and sediment in Xiong'an New Area, China, and their relationship with antibiotic resistance genes

The emergence and pollution of antibiotics in surface water in various regions have drawn widespread concern because of the harm to aquatic ecosystems and human health. In this study, we aim to first investigate contamination and ecological risks of 39 antibiotics in Xiong'an New Area (XANA), China, and then illuminate relative abundances of antibiotic resistance genes (ARGs) and their correlations with antibiotics. The sum of antibiotic concentrations in the water circulation system, including surface water, groundwater, and sediment was 12.71-260.56 ng/L, ND-196.12 ng/L, and 38.03-406.31 ng/g, respectively. In surface water and sediment, cephalosporins and quinolones were the primary antibiotics, accounting for 45% and 16% of the total antibiotic concentrations in surface water and for 62% and 32% of the total antibiotic concentrations in sediment; this suggests a significant interaction between the two media. The antibiotic concentration was the highest in shallow groundwater at depths of <50 m (mean concentration of 79.22 ± 56.46 ng/L), indicating that surface water was a possible source of antibiotic contamination in groundwater. AMX presented the highest risk in both surface and groundwater and should be controlled as a priority. Moreover, the selection pressure of antibiotics on ARGs was discovered in the sediment in XANA, because the enrichment of sulA was significantly correlated with spiramycin and lincomycin and the enrichment of bla_OXA-1 was significantly correlated with roxithromycin, ciprofloxacin, ofloxacin, and sulfapyridine. Thus, our investigation revealed potential antibiotic contamination in multiple environmental media in XANA, which should be addressed to prevent more serious pollution.

Impact of sewer overflow on public health: A comprehensive scientometric analysis and systematic review

Sewer overflow (SO), which has attracted global attention, poses serious threat to public health and ecosystem. SO impacts public health via consumption of contaminated drinking water, aerosolization of pathogens, food-chain transmission, and direct contact with fecally-polluted rivers and beach sediments during recreation. However, no study has attempted to map the linkage between SO and public health including Covid-19 using scientometric analysis and systematic review of literature. Results showed that only few countries were actively involved in SO research in relation to public health. Furthermore, there are renewed calls to scale up environmental surveillance to safeguard public health. To safeguard public health, it is important for public health authorities to optimize water and wastewater treatment plants and improve building ventilation and plumbing systems to minimize pathogen transmission within buildings and transportation systems. In addition, health authorities should formulate appropriate policies that can enhance environmental surveillance and facilitate real-time monitoring of sewer overflow. Increased public awareness on strict personal hygiene and point-of-use-water-treatment such as boiling drinking water will go a long way to safeguard public health. Ecotoxicological studies and health risk assessment of exposure to pathogens via different transmission routes is also required to appropriately inform the use of lockdowns, minimize their socio-economic impact and guide evidence-based welfare/social policy interventions. Soft infrastructures, optimized sewer maintenance and prescreening of sewer overflow are recommended to reduce stormwater burden on wastewater treatment plant, curtail pathogen transmission and marine plastic pollution. Comprehensive, integrated surveillance and global collaborative efforts are important to curtail on-going Covid-19 pandemic and improve resilience against future pandemics.

High Prevalence and Factors Associated With the Distribution of the Integron intI1 and intI2 Genes in Scottish Cattle Herds

Integrons are genetic elements that capture and express antimicrobial resistance genes within arrays, facilitating horizontal spread of multiple drug resistance in a range of bacterial species. The aim of this study was to estimate prevalence for class 1, 2, and 3 integrons in Scottish cattle and examine whether spatial, seasonal or herd management factors influenced integron herd status. We used fecal samples collected from 108 Scottish cattle herds in a national, cross-sectional survey between 2014 and 2015, and screened fecal DNA extracts by multiplex PCR for the integrase genes intI1, intI2, and intI3. Herd-level prevalence was estimated [95% confidence interval (CI)] for intI1 as 76.9% (67.8-84.0%) and intI2 as 82.4% (73.9-88.6%). We did not detect intI3 in any of the herd samples tested. A regional effect was observed for intI1, highest in the North East (OR 11.5, 95% CI: 1.0-130.9, P = 0.05) and South East (OR 8.7, 95% CI: 1.1-20.9, P = 0.04), lowest in the Highlands. A generalized linear mixed model was used to test for potential associations between herd status and cattle management, soil type and regional livestock density variables. Within the final multivariable model, factors associated with herd positivity for intI1 included spring season of the year (OR 6.3, 95% CI: 1.1-36.4, P = 0.04) and watering cattle from a natural spring source (OR 4.4, 95% CI: 1.3-14.8, P = 0.017), and cattle being housed at the time of sampling for intI2 (OR 75.0, 95% CI: 10.4-540.5, P < 0.001). This study provides baseline estimates for integron prevalence in Scottish cattle and identifies factors that may be associated with carriage that warrant future investigation.

Vertical and horizontal distributions of clinical antibiotic resistance genes and bacterial communities in Danjiangkou Reservoir, China

The Danjiangkou Reservoir is an important water source for the middle route of the South-to-North Water Diversion Project in China. The current anthropogenic pollution of this reservoir is a great public health concern. Therefore, the horizontal and vertical distributions of seven clinical antibiotic resistance genes (ARGs) and bacterial communities in the Danjiangkou Reservoir were investigated using qPCR and next-generation sequencing, respectively. The average relative abundance of ARGs was 3.01 × 10^-4 to 1.90 × 10^-3 and 4.66 × 10^-4 to 1.85 × 10^-3 in horizontal and vertical profiles, respectively. There was a significant difference in the vertical composition of ARGs, which was caused by different media (i.e. water column vs. sediment). No significant differences in the composition of ARGs were found in the horizontal profile. Proteobacteria was the most abundant phylum, followed by Actinobacteria in the Danjiangkou Reservoir. The beta diversity pattern of the microbial communities in the vertical profile was consistent with that of the ARGs. Moreover, a significant difference in the horizontal composition of the bacterial communities among these water columns was found. All of these factors have resulted in noticeably different co-occurrence patterns of ARGs and bacterial communities between water columns and surface sediment samples. ARGs were closely associated with Proteobacteria and Chloroflexi in the sediment samples, indicating potential anthropogenic pollution in the Danjiangkou Reservoir. Although there was no significant correlation between the occurrence of ARGs and 11 opportunistic pathogens, our results point to potential risks for the development of multi-resistant pathogens due to the simultaneous presence of ARGs and pathogens in the study area. These results provide a good basis for thorough ecological evaluation and remediation of the Danjiangkou Reservoir.

Antibiotics adaptation costs alter carbon sequestration strategies of microorganisms in karst river

Karst ecosystems make an important contribution to the global carbon cycle, in which carbon-fixing microorganisms play a vital role. However, the healthy functioning of karst ecosystems is threatened because pollutants easily diffuse and spread through them due to their strong hydraulic connectivity. The microbiome of a karst river contaminated with antibiotics was studied. Through co-occurrence network analysis, six ecological clusters (MOD 1-MOD 6) with different distribution characteristics were determined, of which four were significantly correlated with antibiotics. The carbon fixation pathways in different ecological clusters were varied, and the dominant hydroxypropionate-hydroxybutyrate cycle and reductive acetyl-CoA pathway were negatively and positively correlated with antibiotics, respectively. Long-term antibiotic contamination altered the selection of carbonic anhydrase (CA) encoding genes in some of the CA-producing mineralization microorganisms. The selection of different carbon fixation pathways is a possible strategy for the microbial community to compensate for the adaptation costs associated with the pressure of antibiotics contamination and emergence of antibiotics resistance. Bayesian network analysis revealed that some carbon sequestration functions (such as β-CA and reductive acetyl-CoA pathway) surpassed certain antibiotic resistance genes in the regulation of environmental factors and microbial networks. An ecological cluster (MOD5) that possibly homologous to antibiotic contamination was the final node of the microbial community in karst river, which indicated that ecological clusters were not only selected by antibiotics, but were also regulated by multiple environmental factors in the karst river system. The carbon sequestration pathway was more directly reflected in the abundance of ecological groups than in the influence of CA. This study provides new insights into the feedback effect of karst system on typical pollutants generated from human activities.

Molecular Epidemiology, Virulence Traits and Antimicrobial Resistance Signatures of Aeromonas spp. in the Critically Endangered Iberochondrostoma lusitanicum Follow Geographical and Seasonal Patterns

Despite the fact that freshwater fish populations are experiencing severe declines worldwide, our knowledge on the interaction between endangered populations and pathogenic agents remains scarce. In this study, we investigated the prevalence and structure of Aeromonas communities isolated from the critically endangered Iberochondrostoma lusitanicum, a model species for threatened Iberian leuciscids, as well as health parameters in this species. Additionally, we evaluated the virulence profiles, antimicrobial resistance signatures and genomic relationships of the Aeromonas isolates. Lesion prevalence, extension and body condition were deeply affected by location and seasonality, with poorer performances in the dry season. Aeromonas composition shifted among seasons and was also different across river streams. The pathogenic potential of the isolates significantly increased during the dry season. Additionally, isolates displaying clinically relevant antimicrobial resistance phenotypes (carbapenem and fluroquinolone resistance) were detected. As it inhabits intermittent rivers, often reduced to disconnected pools during the summer, the dry season is a critical period for I. lusitanicum, with lower general health status and a higher potential of infection by Aeromonas spp. Habitat quality seems a determining factor on the sustainable development of this fish species. Also, these individuals act as reservoirs of important antimicrobial resistant bacteria with potential implications for public health.

Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow

Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except bla_VIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.

Antimicrobial resistance genes are enriched in aerosols near impacted urban surface waters in La Paz, Bolivia

Antibiotic resistance poses a major global health threat. Understanding emergence and dissemination of antibiotic resistance in environmental media is critical to the design of control strategies. Because antibiotic resistance genes (ARGs) may be aerosolized from contaminated point sources and disseminated more widely in localized environments, we assessed ARGs in aerosols in urban La Paz, Bolivia, where wastewater flows in engineered surface water channels through the densely populated urban core. We quantified key ARGs and a mobile integron (MI) via ddPCR and E. coli spp. as a fecal indicator by culture over two years during both the rainy and dry seasons in sites near wastewater flows. ARG targets represented major antibiotic groups-tetracyclines (tetA), fluoroquinolines (qnrB), and beta-lactams (blaTEM)-and an MI (intI1) represented the potential for mobility of genetic material. Most air samples (82%) had detectable targets above the experimentally determined LOD: most commonly blaTEM and intI1 (68% and 47% respectively) followed by tetA and qnrB (17% and 11% respectively). ARG and MI densities in positive air samples ranged from 1.3 × 101 to 6.6 × 104 gene copies/m3 air. Additionally, we detected culturable E. coli in the air (52% of samples <1 km from impacted surface waters) with an average density of 11 CFU/m3 in positive samples. We observed decreasing density of blaTEM with increasing distance up to 150 m from impacted surface waters. To our knowledge this is the first study conducting absolute quantification and a spatial analysis of ARGs and MIs in ambient urban air of a city with contaminated surface waters. Environments in close proximity to urban wastewater flows in this setting may experience locally elevated concentrations of ARGs, a possible concern for the emergence and dissemination of antimicrobial resistance in cities with poor sanitation.

Using Isotopic and Hydrochemical Indicators to Identify Sources of Sulfate in Karst Groundwater of the Niangziguan Spring Field, China

Karst groundwater in the Niangziguan spring fields is the main source to supply domestic and industrial water demands in Yangquan City, China. However, the safety of water supply in this region has recently suffered from deteriorating quality levels. Therefore, identifying pollution sources and causes is crucial for maintaining a reliable water supply. In this study, a systematic sample collection for the karst groundwater in the Niangziguan spring fields was implemented to identify hydrochemical characteristics of the karst groundwater through comprehensive analyses of hydrochemistry (piper diagram, and ion ratios,) and stable isotopes (S and H-O). The results show that the karst groundwater in the Niangziguan spring fields was categorized as SO4·HCO3-Ca·Mg, HCO3·SO4-Ca·Mg, and SO4-Ca types. K+, Cl-, and Na+ are mainly sourced from urban sewage and coal mine drainage. In addition, SO42− was mainly supplied by the dissolution of gypsum and the oxidation of FeS2 in coal-bearing strata. It is noteworthy that, based on H-O and S isotopes, 75% of the karst groundwater was contaminated by acidic water in coal mines at different degrees. In the groundwater of the Niangziguan spring field, the proportions of SO42− derived from FeS2 oxidation were 60.6% (N50, Chengxi spring), 30.3% (N51, Wulong spring), and 26.0% (N52, Four springs mixed with water). Acid mine drainage directly recharges and pollutes karst groundwater through faults or abandoned boreholes, or discharges to rivers, and indirectly pollutes karst groundwater through river infiltration in carbonate exposed areas. The main source of rapid increase of sulfate in karst groundwater is acid water from abandoned coal mines.

New plastic formations in the Anthropocene

Plastic pollution is one of the major challenges in the Anthropocene. Upon reaching the marine environment, plastic debris is subject to anthropogenic and environmental conditions that result in novel items that vary in composition, physical and chemical characteristics. Here, we reviewed and discussed the potential fate and threat to the environment of four recently described plastic formations: Plastiglomerates, pyroplastics, plasticrusts, and anthropoquinas. The threats identified were mostly related to the release of toxic chemicals and plastic ingestion. Transportation of alien invasive species or microbial pathogens and fragmentation of larger plastics into microplastics (<5 mm), potentially reaching marine trophic webs, are suspected as potential impacts based on the characteristics of these plastic formations. Some plastic forms may persist in the environment and voyage across the ocean, while others are denser and less likely to enter the plastic cycle or interact with biota. In the latter case, plastics are expected to become buried in the sediment and incorporate into the geological record. It is necessary to establish sampling protocols or standards that are specific to each plastic formation and start reporting the occurrence of these new plastic categories as such to avoid underestimating plastic pollution in marine environments. It is suggested that monitoring plans include these categories and identify potential sources. Further research must focus on investigating whether the suspected impacts are a matter of concern. In this sense, we have suggested research questions to address the knowledge gaps and have a better understanding of the impacts and distribution of the new plastic forms.

Performance of Layer-by-Layer-Modified Multibore® Ultrafiltration Capillary Membranes for Salt Retention and Removal of Antibiotic Resistance Genes

Polyether sulfone Multibore^® ultrafiltration membranes were modified using polyelectrolyte multilayers via the layer-by-layer (LbL) technique in order to increase their rejection capabilities towards salts and antibiotic resistance genes. The modified capillary membranes were characterized to exhibit a molecular weight cut-off (at 90% rejection) of 384 Da. The zeta-potential at pH 7 was −40 mV. Laboratory tests using single-fiber modified membrane modules were performed to evaluate the removal of antibiotic resistance genes; the LbL-coated membranes were able to completely retain DNA fragments from 90 to 1500 nt in length. Furthermore, the pure water permeability and the retention of single inorganic salts, MgSO₄, CaCl₂ and NaCl, were measured using a mini-plant testing unit. The modified membranes had a retention of 80% toward MgSO₄ and CaCl₂ salts, and 23% in case of NaCl. The modified membranes were also found to be stable against mechanical backwashing (up to 80 LMH) and chemical regeneration (in acidic conditions and basic/oxidizing conditions).