The impact of WWTP size and sampling season on the prevalence of antibiotic resistance genes in wastewater and the river system

An unignorable human health risk posed by antibiotic resistome and microbiome in urban rivers: Insights from Beijing, China

Urban rivers are the main water bodies humans frequently come into contact with, so the risks posed are closely monitored. Antibiotic resistance genes (ARGs) residues in reclaimed water pose serious risks to human health. There are urgent needs to improve the understanding of distribution of and risks posed by ARGs in urban rivers. In this study, shotgun metagenomic approach was used to characterize ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) in water and sediment from Xinfeng River in Beijing and to identify microbes, potential antibiotic resistant bacteria, and human pathogens (HPs). MGE, microbial community, VF, and ARG co-occurrences were used to assess the environmental risks posed by ARGs. The results indicated that quinolone was the most abundant ARG type and that tufA and fusA were the two dominant ARG subtypes. Wetland effluent increased ARG abundance in the river, and the effect was detected even 50 m downstream. ARG abundances and distribution in the river had difference in different seasons. The dominant bacteria in the river were Proteobacteria, Bacteroidetes, and Actinobacteria, and 59 HPs were detected. In total, 69 MGEs and 19 VFs were found. Co-occurrence networks indicated that potential antibiotic resistant bacteria, MGEs, VFs, and ARGs in the river significantly correlated, indicating the potential risks posed by ARGs. The results improve our understanding of ARG distribution and environmental risks in urban river water. More attention should be paid to controlling environmental risks posed by ARGs in urban river and reclaimed water.

Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic

Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.

Antibiotic resistance and pathogen spreading in a wastewater treatment plant designed for wastewater reuse

Climate change significantly contributes to water scarcity in various regions worldwide. While wastewater reuse is a crucial strategy for mitigating water scarcity, it also carries potential risks for human health due to the presence of pathogenic and antibiotic resistant bacteria (ARB). Antibiotic resistance represents a Public Health concern and, according to the global action plan on antimicrobial resistance, wastewater role in selecting and spreading ARB must be monitored. Our aim was to assess the occurrence of ARB, antibiotic resistance genes (ARGs), and potential pathogenic bacteria throughout a wastewater treatment plant (WWTP) designed for water reuse. Furthermore, we aimed to evaluate potential association between ARB and ARGs with antibiotics and heavy metals. The results obtained revealed the presence of ARB, ARGs and pathogenic bacteria at every stage of the WWTP. Notably, the most prevalent ARB and ARG were sulfamethoxazole-resistant bacteria (up to 7.20 log CFU mL-1) and sulII gene (up to 5.91 log gene copies mL-1), respectively. The dominant pathogenic bacteria included Arcobacter, Flavobacterium and Aeromonas. Although the abundance of these elements significantly decreased during treatment (influent vs. effluent, p < 0.05), they were still present in the effluent designated for reuse. Additionally, significant correlations were observed between heavy metal concentrations (copper, nickel and selenium) and antibiotic resistance elements (ampicillin-resistant bacteria, tetracycline-resistant bacteria, ARB total abundance and sulII) (p < 0.05). These results underscore the importance of monitoring the role of WWTP in spreading antibiotic resistance, in line with the One Health approach. Additionally, our findings suggest the need of interventions to reduce human health risks associated with the reuse of wastewater for agricultural purposes.

Unveiling the critical role of overlooked consumer protist-bacteria interactions in antibiotic resistance gene dissemination in urban sewage systems

Antibiotic resistance genes (ARGs) are emerging contaminants of significant concern due to their role in facilitating the spread of antibiotic resistance, especially high-risk ARGs, which are characterized by high human accessibility, gene mobility, pathogenicity, and clinical availability. Studies have shown that cross-domain interactions, such as those between consumer protists (consumers) and bacteria, can influence bacterial diversity, distribution, and function through top-down control. The consumers-bacteria interactions may also affect the occurrence and distribution of ARGs, yet this has been scarcely explored in field investigations. We conducted a city-scale investigation of ARGs, protists, and bacterial communities across each unit of the urban sewage system (USS), including 49 sewage pumping stations (SW), as well as influent (IF), activated sludge (AS), and effluent (EF) from seven wastewater treatment plants. Interestingly, consumers-bacteria interactions, as indicated by indices of bipartite relevance networks (i.e., connectedness and cohesion), increased from SW and IF to AS and EF. Structural equation modelling (SEM) revealed that consumers-bacteria interactions had a greater influence on the abundance of total ARGs and high-risk ARGs than seasonal or environmental factors. Notably, the total effects of consumers-bacteria interactions in SEM were significant (P < 0.05) and comparable in both IF and EF, even with the decrease in ARG abundance from IF to EF. This suggests a potential risk of ARG spread to the environment, facilitated by consumer protists in the EF. Additionally, the relevance network also demonstrated an increasing trend in the relationships between consumer protists and potential hosts of high-risk ARGs from raw sewage (SW and IF) to AS and EF. Overall, this study emphasizes the importance of integrating multitrophic microbial interactions to better understand and mitigate the dissemination of ARGs in sewage systems.

Metagenomics-resolved genomics provide novel ecological insights into resistome community coalescence of wastewater in river environment

The discharge of wastewater into rivers can lead to resistome coalescence, thereby enhancing the spread risk of antibiotic resistance genes (ARGs) through mixing of exogenous wastewater resistome communities with indigenous riverine communities. At present, the understanding on the role of resistome community coalescence in the dissemination of ARGs is still very limited, and little is known about the process and its ecological implications. To bridge the gap, this study has conducted field-based surveys and microcosm experiments to deeply dissect the coalescence of resistome community in wastewater within river environment, utilizing genome-centric metagenomic analysis approach. The field investigation suggests resistome coalescence enhances the abundance and diversity of ARGs in the receiving river. Furthermore, the microcosm experiments reveal the effect of mixing ratio on resistome coalescence in the water-sediment system and decipher the temporal attenuation dynamics of the coalesced resistome in the environment. The results show the higher proportion of wastewater has a greater impact on ARGs in the water, whereas the effect of mixing ratio is lesser in the sediments. Temporally, the source-specific ARGs originating from wastewater exhibit decreasing trends over the experimental duration, and relatively, the attenuation in the water is more pronounced than that in the sediments. Interestingly, natural light not only facilitates the attenuation of ARGs in the water but may also induce their deposition at the water-sediment interface. Variance partitioning analyses suggest the microbiome, mobilome, and abiotic factors collectively shape the coalescence of the resistome communities in the environment. The study provides empirical evidence on resistome coalescence in river systems, which is instrumental in gaining a better understanding of the spread mechanism of ARGs in the environment.

Septic tanks as a pathway for emerging contaminants to the aquatic environment-Need for alternative rural wastewater treatment?

Septic tanks (STs) as a decentralised approach to community wastewater treatment were investigated as a pathway for emerging contaminants (ECs) entering the aquatic environment. A broad range of ECs were examined in five community STs (population equivalents 217-475) and receiving rivers in Scotland over 12 months. All 68 studied ECs were detected at least once in ST influent or effluent at a broad concentration range from ng L-1 - μg L-1 which can surpass freshwater predicted no-effect concentrations. Pharmaceuticals with acute use, such as antibiotics and antifungals, had high monthly variability and concentrations can exceed those previously found in centralised wastewater treatment works. Differences between the STs demonstrate the impact of localised prescription and population behaviour on EC concentrations. The similarities in concentrations between influent and effluent, suggest limited or no removal of ECs in STs. Hence, dilution of the discharges is required to mitigate environmental risk. Although the contribution of ECs sorbed to suspended solids to the total EC concentration was generally small (<10%), higher contributions (>30%) were observed for fluoroquinolone antibiotics (ofloxacin and ciprofloxacin), antidepressants (fluoxetine), and antifungals (clotrimazole). A wide range of ECs were also detected in rivers upstream and downstream of the ST discharge points, and concentrations increased by up to 95% downstream. In general, risk quotients (RQs) in the rivers were low, indicating small risk for the environment. However, higher RQs (>1) were found for ibuprofen, diclofenac and ciprofloxacin in a few samples. Therefore, reducing their concentration by improving ST performance or through sustainable medicines use may be needed at low dilution locations to mitigate any risk.

A Surveillance Study of Culturable and Antimicrobial-Resistant Bacteria in Two Urban WWTPs in Northern Spain

BACKGROUND/OBJECTIVES

Wastewater treatment plants (WWTPs) are hotspots for the spread of antimicrobial resistance into the environment. This study aimed to estimate the proportion of clinically relevant antimicrobial-resistant bacteria in two Spanish urban WWTPs, located in the region of La Rioja (Spain); Methods: Ninety-four samples (48 water/46 sludge) were collected and streaked on ten different selective media, in order to recover the culturable bacterial diversity with relevant resistance phenotypes: Extended-Spectrum β-Lactamase-producing Escherichia coli/Klebsiella pneumoniae (ESBL-Ec/Kp), Carbapenem-resistant Enterobacteriaceae (CR-E), Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin-resistant Enterococcus faecium/faecalis (VR-E. faecium/faecalis). Isolates were identified by MALDI-TOF and were tested for antimicrobial susceptibility using the disk diffusion method. The confirmation of ESBL production was performed by the double-disk test; Results: A total of 914 isolates were recovered (31 genera and 90 species). Isolates with clinically relevant resistance phenotypes such as ESBL-Ec/Kp and CR-E were recovered in the effluent (0.4 × 100-4.8 × 101 CFU/mL) and organic amendment samples (1.0-101-6.0 × 102 CFU/mL), which are discharged to surface waters/agricultural fields. We reported the presence of VR-E. faecium in non-treated sludge and in the digested sludge samples (1.3 × 101-1 × 103 CFU/mL). MRSA was also recovered, but only in low abundance in the effluent (0.2 × 101 CFU/mL); Conclusions: This study highlights the need for improved wastewater technologies and stricter regulations on the use of amendment sludge in agriculture. In addition, regular monitoring and surveillance of WWTPs are critical for early detection and the mitigation of risks associated with the spread of antimicrobial resistance.

Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks

Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.

Dynamics of antibiotic resistance genes during manure composting: Reduction in herbivores manure and accumulation in carnivores

The elevated levels of antibiotic resistance genes (ARGs) in livestock manure represent a significant threat to both the environment and human health. Composting has been recognized as an effective strategy to mitigate the abundance of ARGs in manure. However, notable rebounds in ARGs abundance have been observed during this process. This study explored the changes in ARGs abundance and the underlying influencing factors during the composting of carnivore (chicken and pig) and herbivore (sheep and cow) manures, along with mushroom residues. The findings revealed that the total relative abundance of ARGs increased by 6.96 and 10.94 folds in chicken and pig manure composts, respectively, whereas it decreased by a remarkable 91.72% and 98.37% in sheep and cow manure composts. Nitrogen content emerged as the primary physicochemical factors governing the abundance of ARGs in chicken and pig manure composts. Conversely, carbon content played a pivotal role in determining ARGs abundance in chicken and pig manure composts. Furthermore, the presence of dominant hosts, such as Corynebacterium, Bacillus, and Clostridium, along with emerging bacteria like Thermobifida, Saccharomonospora, and Actinomadura, contributed significantly to the enrichment of total ARGs, including tetG, tetO, tetX, and sul2, in chicken and pig manure composts. The coexistence of these genes with mobile genetic elements and a plethora of host bacteria, coupled with their high abundance, renders them particularly high-risk ARGs. On the other hand, the observed decrease in the abundance of total ARGs in sheep and cow manure composts can be attributed to the decline in the population of host bacteria, specifically Atopostipes, Psychrobacter, and Corynebacterium. Collectively, these results provide crucial insights into the management of ARGs risks and offer essential theoretical support for enhancing the safe utilization of organic fertilizer in agriculture.

The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment

Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.

Extended-spectrum β-lactamase-producing bacteria and their resistance determinants in different wastewaters and rivers in Nepal

Wastewaters serve as significant reservoirs of antibiotic resistant bacteria. Despite the evidence of antimicrobial resistance in wastewaters and river water in Kathmandu, direct linkage between them is not discussed yet. This study investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing bacteria and associated resistance genes in wastewaters and river water. Out of 246 bacteria from wastewaters, 57.72% were ESBL producers and 77.64% of them were multidrug resistant (MDR). ESBL producing E. coli was dominant in municipal and hospital wastewaters (HWW) as well as in river water while K. pneumoniae was common in pharmaceutical wastewater. The blaSHV and blaTEM genes were prevalent and commonly co-occurred with aac(6')-Ib-cr in K. pneumoniae isolated pharmaceutical wastewater. blaCTX-M carrying E. coli from hospital co-harbored aac(6')-Ib-cr while that from municipal influent and river water co-harbored qnrS. Whole genome sequencing data revealed the presence of diverse ARGs in bacterial isolates against multiple antibiotics. In average, an E. coli and a K. pneumoniae isolate contained 55.75 ± 0.96 and 40.2 ± 5.36 ARGs, respectively. Multi-locus sequence typing showed the presence of globally high-risk clones with wider host range such as E. coli ST10, and K. pneumoniae ST15 and ST307 in HWW and river indicating frequent dissemination of antimicrobial resistance in wastewater of Kathmandu. Whole genome sequence data aligned with phenotypic antibiograms and resistance genes detected by PCR in selected isolates. The presence of significant plasmid replicons (IncF, IncY) and mobile genetic elements (IS903, IS26) indicate high frequency of spreading antibiotic resistance. These findings indicate burden and dissemination of antimicrobial resistance in the environment and highlight the need for effective strategies to mitigate the antibiotic resistance.

Change characteristics, bacteria host, and spread risks of bioaerosol ARGs/MGEs from different stages in sewage and sludge treatment process

The spread of antibiotic resistance genes (ARGs) in the atmospheric environment has seriously threatened human health. Wastewater treatment plants (WWTPs) are an important source of aerosol ARGs. A large WWTP, including sewage treatment process (SWP) and sludge treatment process (SDP), was selected in North China for sampling in this study. The content of ARGs, mobile genetic elements (MGEs), and bacterial genera in sewage/sludge and aerosols from different process stages was detected. The possible correlation between ARGs/ MGEs and bacteria was analyzed. The risk of antibiotic-resistant bacteria was evaluated and the diffusion of ARGs/MGEs was simulated. The results showed that the concentration of ARGs/MGEs varied as the process progressed, and which in the aeration tank was relatively high. The ARGs/MGEs content in SWP aerosol (8.35-163.27 copies/m3) was higher than that in SDP (5.52-16.36 copies/m3). The main ARGs/MGEs detected in SWP aerosol were tnpA-05, tnpA-04, and ermF, while the main ARGs/MGEs detected in SDP aerosol were sul1, ermF, and blaPAO. ARGs were positively correlated with most bacteria and Escherichia coli with ARGs carries higher cytotoxicity. ARGs/MGEs mainly diffused towards the southeast, which may cause harm to urban residents with the diffusion of aerosols. This study provides clues and theoretical basis for preventing the hazards of ARGs from WWTP sources.

The occurrence of heavy metals and antimicrobials in sewage sludge and their predicted risk to soil - Is there anything to fear?

The study assessed the occurrence of legally-monitored heavy metals and unmonitored antimicrobials in sludge from small, medium, large and very large municipal wastewater treatment plants (WWTPs), and the predicted environmental risk and risk of resistance selection associated with sludge administration to soil. The temporal variations of the studied compounds in sludge and associated risks to soil were determined by sampling over a year. Although the highest concentrations of heavy metals were noted in sludge from the largest WWTP, i.e. from 1.50 mg/kg (mean 1.61 mg/kg) for Cd to 2188 mg/kg (mean 1332 mg/kg) for Zn, the obtained values only reached a few percent of the legal limits. The same WWTP also demonstrated lower concentrations of antimicrobials compared to the smaller ones. The highest concentrations of antimicrobials, ranging from 24.04 μg/kg for trimethoprim to 900.24 μg/kg for tetracycline, were found in the small and medium WWTPs. However, due to lack of regulations at the national and EU levels, the results cannot be compared with legal limits. Principal Component Analysis (PCA), cluster and heatmap analysis separated samples according to WWTP size. Small WWTP demonstrated correlation with antimicrobials (tetracycline, trimethoprim, clindamycin, ciprofloxacin and ofloxacin), while the large and very large WWTP revealed correlations with heavy metals (Cu and Cr). The obtained environmental risk quotients confirmed that the heavy metals did not present a threat, measured either as individual risk quotients (RQenv), cumulative risk (RQcumulative) or risk of mixture of heavy metals (RQmix-metals). In the case of antimicrobials, only tetracycline demonstrated moderate RQenv, RQcumulative and RQmix-antimicrobials in the small WWTP sludge, with values of 0.1 to 1. Our findings highlight the importance of monitoring sewage sludge before soil application, especially from small WWTPs, to reduce the potential environmental impact of antimicrobials. They also confirm our previous data regarding the environmental risk associated with various toxic compounds, including emerging contaminants, in the sludge from small WWTPs.

Synergistic Control of Trimethoprim and the Antimicrobial Resistome in Electrogenic Microbial Communities

Synergistic control of the risks posed by emerging antimicrobials and antibiotic resistance genes (ARGs) is crucial for ensuring ecological safety. Although electrogenic respiration can enhance the biodegradation of several antimicrobials and reduce ARGs accumulation, the association mechanisms of antimicrobial biodegradation (trimethoprim, TMP) with the fate of the antimicrobial resistome remain unclear. Here, the biotransformation pathway of TMP, microbial associations, and functional gene profiles (e.g., degradation, antimicrobial resistance, and electron transfer) were analyzed. The results showed that the microbial electrogenic respiration significantly enhanced the biodegradation of TMP, especially with a cosubstrate sodium acetate supply. Electroactive bacteria enriched in the electrode biofilm positively correlated with potential TMP degraders dominated in the planktonic communities. These cross-niche microbial associations may contribute to the accelerated catabolism of TMP and extracellular electron transfer. Importantly, the evolution and dissemination of overall ARGs and mobile genetic elements (MGEs) were significantly weakened due to the enhanced cometabolic biodegradation of TMP. This study provides a promising strategy for the synergistic control of the water ecological risks of antimicrobials and their resistome, while also highlighting new insights into the association of antimicrobial biodegradation with the evolution of the resistome in an electrically integrated biological process.

Do Microorganisms in Bathing Water in Guadeloupe (French West Indies) Have Resistance Genes?

Waterborne faecal contamination is a major public health concern. The main objectives of this study were to investigate faecal contamination and Escherichia coli (E. coli) antibiotic resistance in recreational fresh water from Guadeloupe and to characterise the microbiome and resistome composition in biofilms from submerged rocks. Significant faecal contamination was observed at 14 freshwater sites. E. coli predominated (62%), followed by Enterobacter cloacae (11%) and Acinetobacter spp. (11%). Of 152 E. coli isolated, none produced extended-spectrum beta-lactamases (ESBLs), but 7% showed resistance to streptomycin and 4% to tetracycline. Biofilm resistome analysis revealed clinically significant antibiotic-resistance genes (ARGs), including those coding for resistance to sulfonamides (sul1), carbapenems (blaKPC), and third-generation cephalosporins (blaCTX-M). Mobile genetic elements (MGEs) (intI1, intI2, intI3) linked to resistance to aminoglycosides, beta-lactams, tetracycline, as well as heavy metal resistance determinants (copA, cusF, czcA, merA) conferring resistance to copper, silver, cadmium, and mercury were also detected. Diverse bacterial phyla were found in biofilm samples, of which Proteobacteria, Bacteroidetes, Planctonomycetes, and Cyanobacteria were predominant. Despite the frequent presence of E. coli exceeding regulatory standards, the low levels of antibiotic-resistant bacteria in freshwater and of ARGs and MGEs in associated biofilms suggest limited antibiotic resistance in Guadeloupean recreational waters.

High throughput qPCR unveils shared antibiotic resistance genes in tropical wastewater and river water

The global challenge posed by rising antimicrobial resistance, and the adoption of a One Health approach, has led to the prioritisation of surveillance for antibiotic resistance genes (ARGs) in various environments. Herein lies an information gap, particularly in the context of Thailand, where there is scarce data on ARG prevalence across diverse environmental matrices and throughout different seasons. This study aimed to fill this void, analysing ARG prevalence by high-throughput qPCR in influent (n = 12) and effluent wastewater (n = 12) and river water (n = 12). The study reveals a substantial and largely uniform presence of ARGs across all water sample types (87 % similarity). Intriguingly, no ARGs were exclusive to specific water types, indicating an extensive circulation of resistance determinants across the aquatic environment. The genes intI1, tnpA, and intI3, part of the integrons and mobile genetic elements group, were detected in high relative abundance in both wastewater and river water samples, suggesting widespread pollution of rivers with wastewater. Additional high-prevalence ARGs across all water types included qepA, aadA2, merA, sul1, qacF/H, sul2, aadB, and ereA. More alarmingly, several ARGs (e.g., blaVIM, intI3, mcr-1, mexB, qepA, vanA, and vanB) showed higher relative abundance in effluent and river water than in influents, which suggests malfunctioning or inadequate wastewater treatment works and implicates this as a possible mechanism for environmental contamination. Nine genes (i.e., blaCTX-M, blaVIM, emrD, ermX, intI1, mphA, qepA, vanA, and vanB) were recovered in greater relative abundance during the dry season in river water samples as compared to the wet season, suggesting there are seasonal impacts on the efficacy of wastewater treatment practices and pollution patterns into receiving waters. This study highlights the urgency for more effective measures to reduce antibiotic resistance dissemination in water systems.

Comparison of concentration and extraction workflows for qPCR quantification of intI1 and vanA in untreated wastewater

Quantitative polymerase chain reaction (qPCR) measurement of antibiotic resistance genes (ARGs) in untreated municipal wastewater may prove useful in combating the antimicrobial resistance crisis. However, harmonizing and optimizing qPCR-based workflows is essential to facilitate comparisons across studies, and includes achieving highly-effective ARG capture through efficient concentration and extraction procedures. In the current study, combinations of sample volume, membrane types and DNA extraction kits within filtration and centrifugation-based workflows were used to quantify 16S ribosomal RNA (16S rRNA), class 1 integron-integrase gene (intI1) and an ARG encoding resistance to vancomycin (vanA) in untreated wastewater sampled from three wastewater treatment plants (WWTPs). Highly abundant 16S rRNA and intI1 were detected in 100 % of samples from all three WWTPs using both 2 and 20 mL sample volumes, while lower prevalence vanA was only detected when using the 20 mL volume. When filtering 2 mL of wastewater, workflows with 0.20-/0.40-μm polycarbonate (PC) membranes generally yielded greater concentrations of the three targets than workflows with 0.22-/0.45-μm mixed cellulose ester (MCE) membranes. The improved performance was diminished when the sample volume was increased to 20 mL. Consistently greater concentrations of 16S rRNA, intI1 and vanA were yielded by filtration-based workflows using PC membranes combined with a DNeasy PowerWater (DPW) Kit, regardless of the sample volume used, and centrifugation-based workflows with DNeasy Blood & Tissue Kit for 2-mL wastewater extractions. Within the filtration-based workflows, the DPW kit yielded more detection and quantifiable results for less abundant vanA than the DNeasy PowerSoil Pro Kit and FastDNA™ SPIN Kit for Soil. These findings indicate that the performance of qPCR-based workflows for surveillance of ARGs in wastewater varies across targets, sample volumes, concentration methods and extraction kits. Workflows must be carefully considered and validated considering the target ARGs to be monitored.

The influence of combined treatment of municipal wastewater and landfill leachate on the spread of antibiotic resistance in the environment - A preliminary case study

Environmentally-friendly management of landfill leachate (LL) poses a challenge, and LL is usually co-treated with municipal wastewater in wastewater treatment plants (WWTPs). The extent to which the co-treatment of LL and municipal wastewater influences the spread of antibiotic resistance (AR) in the environment has not been examined to date. Two WWTPs with similar wastewater composition and technology were studied. Landfill leachate was co-treated with wastewater in one of the studied WWTPs. Landfill leachate, untreated and treated wastewater from both WWTPs, and river water sampled upstream and downstream from the wastewater discharge point were analyzed. Physicochemical parameters, microbial diversity, and antibiotic resistance genes (ARGs) abundance were investigated to determine the impact of LL co-treatment on chemical and microbiological contamination in the environment. Landfill leachate increased pollutant concentrations in untreated wastewater and river water. Cotreatment of LL and wastewater could affect the abundance and diversity of microbial communities and the interactions between microbial species. Co-treatment also decreased the stability of microbial co-occurrence networks in the examined samples. The mexF gene was identified as a potential marker of environmental pollution with LL. This is the first study to explore the impact of LL on the occurrence of AR determinants in wastewater and rivers receiving effluents.

Antibiotic resistance indicator genes in biofilm and planktonic microbial communities after wastewater discharge

The spread of bacteria with antibiotic resistance genes (ARGs) in aquatic ecosystems is of growing concern as this can pose a risk of transmission to humans and animals. While the impact of wastewater treatment plant (WWTP) effluent on ARG abundance in surface waters has been studied extensively, less is known about the fate of ARGs in biofilms. The proximity and dense growth of microorganisms in combination with the accumulation of higher antibiotic concentrations in biofilms might render biofilms a reservoir for ARGs. Seasonal parameters such as water temperature, precipitation, and antibiotic concentrations should be considered as well, as they may further influence the fate of ARGs in aquatic ecosystems. Here we investigated the effect of WWTP effluent on the abundance of the sulfonamide resistance genes sul1 and sul2, and the integrase gene intI1 in biofilm and surface water compartments of a river in Germany with a gradient of anthropogenic impact using quantitative PCR. Furthermore, we analyzed the bacterial community structure in both compartments via 16S rRNA gene amplicon sequencing, following the river downstream. Additionally, conventional water parameters and sulfonamide concentrations were measured, and seasonal aspects were considered by comparing the fate of ARGs and bacterial community diversity in the surface water compartment between the summer and winter season. Our results show that biofilm compartments near the WWTP had a higher relative abundance of ARGs (up to 4.7%) than surface waters (<2.8%). Sulfonamide resistance genes were more persistent further downstream (>10 km) of the WWTP in the hot and dry summer season than in winter. This finding is likely a consequence of the higher proportion of wastewater and thus wastewater-derived microorganisms in the river during summer periods. We observed distinct bacterial communities and ARG abundance between the biofilm and surface water compartment, but even greater variations when considering seasonal and spatiotemporal parameters. This underscores the need to consider seasonal aspects when studying the fate of ARGs in aquatic ecosystems.

Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments

There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.

The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream

Introduction

Currently there are sparse regulations regarding the discharge of antibiotics from wastewater treatment plants (WWTP) into river systems, making surface waters a latent reservoir for antibiotics and antibiotic resistance genes (ARGs). To better understand factors that influence the fate of ARGs in the environment and to foster surveillance of antibiotic resistance spreading in such habitats, several indicator genes have been proposed, including the integrase gene intI1 and the sulfonamide resistance genes sul1 and sul2.

Methods

Here we used quantitative PCR and long-read nanopore sequencing to monitor the abundance of these indicator genes and ARGs present as class 1 integron gene cassettes in a river system from pristine source to WWTP-impacted water. ARG abundance was compared with the dynamics of the microbial communities determined via 16S rRNA gene amplicon sequencing, conventional water parameters and the concentration of sulfamethoxazole (SMX), sulfamethazine (SMZ) and sulfadiazine (SDZ).

Results

Our results show that WWTP effluent was the principal source of all three sulfonamides with highest concentrations for SMX (median 8.6 ng/l), and of the indicator genes sul1, sul2 and intI1 with median relative abundance to 16S rRNA gene of 0.55, 0.77 and 0.65%, respectively. Downstream from the WWTP, water quality improved constantly, including lower sulfonamide concentrations, decreasing abundances of sul1 and sul2 and lower numbers and diversity of ARGs in the class 1 integron. The riverine microbial community partially recovered after receiving WWTP effluent, which was consolidated by a microbiome recovery model. Surprisingly, the relative abundance of intI1 increased 3-fold over 13 km of the river stretch, suggesting an internal gene multiplication.

Discussion

We found no evidence that low amounts of sulfonamides in the aquatic environment stimulate the maintenance or even spread of corresponding ARGs. Nevertheless, class 1 integrons carrying various ARGs were still present 13 km downstream from the WWTP. Therefore, limiting the release of ARG-harboring microorganisms may be more crucial for restricting the environmental spread of antimicrobial resistance than attenuating ng/L concentrations of antibiotics.

Leave No Trace? Ecological and anthropogenic determinants of antibiotic resistant bacteria in a recreational alpine environment

Antibiotic resistant bacteria (ARB) have been detected in remote environments, but the degree to which their presence is due to anthropogenic contamination remains unclear. Here, anthropogenic and ecological determinants of ARB were characterized in remote and highly visited areas of Rocky Mountain National Park in the United States. Soil and water samples were collected from 29 sites once a month for three months and measured for bacteria resistant to seven antibiotics with flow cytometry. A novel index of the likelihood of human presence (HPI) was generated for estimating human impact on ARB abundance. The HPI accounted for 44% of variation in ARB abundance in water samples (p < 0.0001) and 51% of variation in soil samples (p < 0.00001). Human presence index was illustrated as a reliable predictor of ARB abundance despite a tendency to underpredict at higher levels of human impact. Ecological determinants such as temperature, elevation, slope, and aspect were also found to be significantly associated with ARB abundance. These findings suggest that human presence drives the abundance of ARB in Rocky Mountain National Park, but ecological variables play a significant role in their presence and dispersal.

Seasonal dissemination of antibiotic resistome from livestock farms to surrounding soil and air: Bacterial hosts and risks for human exposure

Feces in livestock farms is a reservoir of antibiotic resistance genes (ARGs), which can disseminate into surrounding soil and air, bringing risks to human health. In this study, seasonal dissemination of ARGs in a livestock farm and implications for human exposure was explored. The experimental results showed that ARGs abundance basically ranked as feces > soil > air, and significant seasonal dependence was observed. The total ARGs in pig feces was relatively higher in autumn (10^9.7 copies g^-1) and winter (10^10.0 copies g^-1), and lower in summer (10^5.0 copies g^-1). Similarly, the lowest total ARGs in soil and air were also observed in summer. There were correlations among ARGs, integron intI1, and bacterial community. Total organic carbon was an important factor affecting ARGs distribution in the feces, and pH and moisture content significantly affected soil ARGs. The daily intakes of integron intI1 and ARGs from air were 10°^.5 copies h^-1 and 10^2.3 copies h^-1 for human exposure, respectively. Pseudomonas was a potential pathogenic host of bla_TEM-1 in feces, Pseudomonas and Acinetobacter were potential pathogenic hosts of multiple ARGs in soil, while ARGs in air did not migrate into pathogens.

Antibiotic resistant genes in the environment-exploring surveillance methods and sustainable remediation strategies of antibiotics and ARGs

Antibiotic Resistant Genes (ARGs) are an emerging environmental health threat due to the potential change in the human microbiome and selection for the emergence of antibiotic resistant bacteria. The rise of antibiotic resistant bacteria has caused a global health burden. The WHO (world health organization) predicts a rise in deaths due to antibiotic resistant infections. Since bacteria can acquire ARGs through horizontal transmission, it is important to assess the dissemination of antibioticresistant genes from anthropogenic sources. There are several sources of antibiotics, antibiotic resistant bacteria and genes in the environment. These include wastewater treatment plants, landfill leachate, agricultural, animal industrial sources and estuaries. The use of antibiotics is a worldwide practice that has resulted in the evolution of resistance to antibiotics. Our review provides a more comprehensive look into multiple sources of ARG's and antibiotics rather than one. Moreover, we focus on effective surveillance methods of ARGs and antibiotics and sustainable abiotic and biotic remediation strategies for removal and reduction of antibiotics and ARGs from both terrestrial and aquatic environments. Further, we consider the impact on public health as this problem cannot be addressed without a global transdisciplinary effort.

Antibiotic resistance genes in Chishui River, a tributary of the Yangtze River, China: Occurrence, seasonal variation and its relationships with antibiotics, heavy metals and microbial communities

The large-scale use and release of antibiotics may create selective pressure on antibiotic resistance genes (ARGs), causing potential harm to human health. River ecosystems have long been considered repositories of antibiotics and ARGs. Therefore, the distribution characteristics and seasonal variation in antibiotics and ARGs in the surface water of the main stream and tributaries of the Chishui River were studied. The concentrations of antibiotics in the dry season and rainy season were 54.18-425.74 ng/L and 66.57-256.40 ng/L, respectively, gradually decreasing along the river direction. The results of antibiotics in the dry season and rainy season showed that livestock and poultry breeding were the main sources in the surface water of the Chishui River basin. Risk assessments indicated high risk levels of OFL in both seasons. In addition, analysis of ARGs and microbial community diversity showed that sul1 and sul3 were the main ARGs in the two seasons. The highest abundance of ARGs was 7.70 × 10⁷ copies/L, and intl1 was significantly positively correlated with all resistance genes (p< 0.01), indicating that it can significantly promote the transmission of ARGs. Proteobacteria were the dominant microorganisms in surface water, with a higher average abundance in the dry season (60.64 %) than in the rainy season (39.53 %). Finally, correlation analyses were performed between ARGs and antibiotics, microbial communities and heavy metals. The results showed that there was a significant positive correlation between ARGs and most microorganisms and heavy metals (p< 0.01), indicating that occurrence and transmission in the environment are influenced by various environmental factors and cross-selection. In conclusion, the persistent residue and transmission of ARGs and their transfer to pathogens are a great threat to human health and deserve further study and attention.

Isolation and Characterization of Lytic Pseudomonas aeruginosa Bacteriophages Isolated from Sewage Samples from Tunisia

Bacteriophages could be a useful adjunct to antibiotics for the treatment of multidrug-resistant Pseudomonas aeruginosa infections. In this study, lytic P. aeruginosa myoviruses PsCh, PsIn, Ps25, and Ps12on-D were isolated from Tunisian sewage samples. Phage Ps12on-D displayed an adsorption time of ~10 min, a short latency period (~10 min), and a large burst size (~115 PFU per infected cell) under standard growth conditions. All phages were active at broad temperature (4 °C to 50 °C) and pH (3.0 to 11.0) ranges and were able to lyse a wide variety of P. aeruginosa strains isolated from clinical and environmental samples worldwide. Illumina sequencing revealed double-stranded DNA genomes ranging from 87,887 and 92,710 bp with high sequence identity to Pseudomonas phage PAK_P1. All four phages based on sequence analysis were assigned to the Pakpunavirus genus. The presented characterization and preclinical assessment are part of an effort to establish phage therapy treatment as an alternative strategy for the management of multidrug-resistant P. aeruginosa infections in Tunisia.

Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment-A Review

Over the past few decades, due to the excessive consumption of drugs in human and veterinary medicine, the antimicrobial resistance (AR) of microorganisms has risen considerably across the world, and this trend is predicted to intensify. Many worrying research results indicate the occurrence of pools of AR, both directly related to human activity and environmental factors. The increase of AR in the natural environment is mainly associated with the anthropogenic activity. The dissemination of AR is significantly stimulated by the operation of municipal facilities, such as wastewater treatment plants (WWTPs) or landfills, as well as biogas plants, agriculture and farming practices, including animal production and land application of manure. These activities entail a risk to public health by spreading bacteria resistant to antimicrobial products (ARB) and antibiotic resistance genes (ARGs). Furthermore, subinhibitory concentrations of antimicrobial substances additionally predispose microbial consortia and resistomes to changes in particular environments that are permeated by these micropollutants. The current state of knowledge on the fate of ARGs, their dissemination and the complexity of the AR phenomenon in relation to anthropogenic activity is inadequate. This review summarizes the state-of-the-art knowledge on AR in the environment, in particular focusing on AR spread in an anthropogenically altered environment and related environmental consequences.

The responses of marine anammox bacteria-based microbiome to multi-antibiotic stress in mariculture wastewater treatment

Saline mariculture wastewater containing multi-antibiotics poses a challenge to anaerobic ammonia oxidation (anammox) process. Herein, the halophilic marine anammox bacteria (MAB)-based microbiome was used for treating mariculture wastewater (35‰ salinity) under multi-antibiotics (enrofloxacin + oxytetracycline + sulfamethoxazole, EOS) stress. And the main focus of this study lies in the response of MAB-based microbiome against multi-antibiotics stress. It is found that MAB-based microbiome shows stable community structure and contributes high nitrogen removal efficiency (>90%) even under high stress of EOS (up to 4 mg·L^-1). The relative abundance of main functional genus Candidatus Scalindua, responsible for anammox, had little change while controlling the influent EOS concentration within 4 mg·L^-1, whereas, significantly decreased to 2.23% at EOS concentration of as high as 24 mg·L^-1. As an alternative, antibiotic resistance bacteria (ARB) species Rheinheimera dominated the microbial community of MAB-based biological reactor under extremely high EOS stress (e.g. 24 mg·L^-1 in influent). The response mechanism of MAB-based microbiome consists of extracellular and intracellular defenses with dependence of EOS concentration. For example, while EOS within 4 mg·L^-1 in this study, most of the antibiotics were retained by extracellular polymeric substances (EPS) via adsorption; If increasing the EOS concentration to 8 and even 24 mg·L^-1, part of antibiotics could intrude into the cells and cause the intracellular accumulation of antibiotic resistance genes (ARGs) (total abundance up to 2.44 × 10^-1 copies/16S rRNA) for EOS response. These new understandings will facilitate the practical implementation of MAB-based bioprocess for saline nitrogen- and antibiotics-laden wastewater treatment.

Metagenomic insights into resistome coalescence in an urban sewage treatment plant-river system

The effluents of sewage treatment plants (eSTP) are one of the critical contributors of antibiotic resistiome in rivers. Recently, community coalescence has been focused as the entire microbiome interchanges with one another. While works have reported the prevalence of antibiotic resistance genes (ARGs) in eSTP and their effects on river resistome, little research has investigated the extent of resistome coalescence in the environment. In the study, we have addressed the issue and focused on the resistome coalescence of eSTP in an urban river with a typical effluent/river coalescence model, by utilizing high-throughput sequencing (HTS)-based metagenomic assembly analysis. In all, a total of 609 ARGs were found in the eSTP-river system, conferring resistance to 30 antibiotic classes and including some emerging ARGs such as mcr-type, tetX and carbapenemase genes. Statistical analyses including linear discriminant analysis effect size (LEfSe) showed the coalescence of STP effluents increased the diversity and abundance of river resistome, indicating its low resistance to disturb the invasion of resistome community in eSTP. After coalescence in the river, the imprints of STP-derived ARGs presented a temporary increase and gradually decreased trend along the flow path. Further, an innovative fast expectation-maximization microbial source tracking (FEAST) method was used to quantitatively apportion the coalescence event, and demonstrated the contribution of eSTP on river resistome and its attenuation dynamics in the downstream. Notably, correlation-based network analysis and contig-based co-occurrence analysis showed the coalesced resistome in the downstream river co-occurred with human bacterial pathogens, mobile genetic elements and virulence factor genes, indicating potential resistome dissemination risk in the environment. This study provides more profound understanding of resistome coalescence between engineered and natural contexts, which is helpful for optimizing strategies to prevent and control resistome risk in aquatic environment.

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.

Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens

The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.

Multiple Antibiotic Resistance in Escherichia coli Isolates from Fecal and Water Sources in Laguna Lake, Philippines

Due to the misuse and overuse of antibiotics, antibiotic residues accumulate in natural environments, leading to the development of antibiotic-resistant bacteria (ARBs). The presence of ARBs in bodies of water poses health hazards to the surrounding community. This study focused on Laguna Lake, the largest lake in the Philippines, which serves as a water source for agriculture and domestic purposes. We aimed to detect the presence of antibiotic-resistant Escherichia coli from the lake waters and potential reservoirs of resistance as well as determine the multiple antibiotic resistance (MAR) indices of the isolates. E. coli (n = 450) was isolated from fecal-associated samples (chicken, cow, pig, human, sewage) and water samples (sites in Laguna Lake and selected river tributaries). The isolates were subjected to an antibiotic resistance assay using VITEK 2®. Among the 16 antibiotics tested, the isolates exhibited varying resistance to 14, but complete susceptibility to amikacin and tigecycline was observed. Isolates were most frequently resistant to ampicillin (196/450, 43.6%). Among fecal-associated samples, chicken isolates exhibited the highest MAR index (0.174), whereas samples from Pila River exhibited the highest MAR index (0.152) among water samples. The results of this study demonstrate the presence of multidrug-resistant E. coli in samples collected around Laguna Lake and reveal fecal and sewage sources as potential reservoirs of ARBs in the water body. With this information, the public is urged to use antibiotics responsibly to help mitigate the spread of antibiotic resistance.

Occurrence of antibiotic resistance genes and multidrug-resistant bacteria during wastewater treatment processes

Wastewater treatment plants (WWTPs) constantly receive a wide variety of contaminants, including pharmaceuticals, and are potential reservoirs of antibiotic resistance genes (ARGs). This favors the development of multidrug-resistant bacteria (MRB) through horizontal gene transfer. Samples from five different WWTP processes were collected in September 2020 and January 2021 to monitor ARG resistomes and culturable MRB in the presence of eight different antibiotics. Nanopore-based ARG abundance and bacterial community analyses suggested that ARG accumulation favors the generation of MRB. Activated and mixed sludges tended to have lower bacterial diversity and ARG abundance because of selective forces that favored the growth of specific microorganisms during aeration processes. Escherichia strains enriched in WWTPs (up to 71%) were dominant in all the samples, whereas Cloacamonas species were highly abundant only in anaerobically digested sludge samples (60%-79%). Two ARG types [sulfonamide resistance genes (sul1) and aminoglycoside resistance genes (aadA1, aadA13, and aadA2)] were prevalent in all the processes. The total counts of culturable MRB, such as Niabella, Enterococcus, Bacillus, and Chryseobacterium species, gradually increased during aerobic WWTP processes. Genomic analyses of all MRB isolated from the samples revealed that the resistome of Enterococcus species harbored the highest number of ARGs (7-18 ARGs), commonly encoding ant(6)-la, lnu(B), erm(B), and tet(S/M). On the other hand, Niablella strains possibly had intrinsic resistant phenotypes without ARGs. All MRB possessed ARGs originating from the same mobile genetic elements, suggesting that WWTPs are hotspots for the migration of ARGs and emergence of MRB.

River Biofilms Microbiome and Resistome Responses to Wastewater Treatment Plant Effluents Containing Antibiotics

Continuous exposure to low concentrations of antibiotics (sub-minimal inhibitory concentration: sub-MIC) is thought to lead to the development of antimicrobial resistance (AMR) in the environmental microbiota. However, the relationship between antibiotic exposure and resistance selection in environmental bacterial communities is still poorly understood and unproven. Therefore, we measured the concentration of twenty antibiotics, resistome quality, and analyzed the taxonomic composition of microorganisms in river biofilms collected upstream (UPS) and downstream (DWS) (at the point of discharge) from the wastewater treatment plant (WWTP) of Poitiers (France). The results of statistical analysis showed that the antibiotic content, resistome, and microbiome composition in biofilms collected UPS were statistically different from that collected DWS. According to Procrustes analysis, microbial community composition and antibiotics content may be determinants of antibiotic resistance genes (ARGs) composition in samples collected DWS. However, network analysis showed that the occurrence and concentration of antibiotics measured in biofilms did not correlate with the occurrence and abundance of antibiotic resistance genes and mobile genetic elements. In addition, network analysis suggested patterns of co-occurrence between several ARGs and three classes of bacteria/algae: Bacteroidetes incertae sedis, Cyanobacteria/Chloroplast, and Nitrospira, in biofilm collected UPS. The absence of a direct effect of antibiotics on the selection of resistance genes in the collected samples suggests that the emergence of antibiotic resistance is probably not only due to the presence of antibiotics but is a more complex process involving the cumulative effect of the interaction between the bacterial communities (biotic) and the abiotic matrix. Nevertheless, this study confirms that WWTP is an important reservoir of various ARGs, and additional efforts and legislation with clearly defined concentration limits for antibiotics and resistance determinants in WWTP effluents are needed to prevent their spread and persistence in the environment.

Resistant Genes and Multidrug-Resistant Bacteria in Wastewater: A Study of Their Transfer to the Water Reservoir in the Czech Republic

Wastewater is considered the most serious source of the spread of antibiotic resistance in the environment. This work, therefore, focuses on the fate and spread of antibiotic resistance genes (ARGs) in wastewater and the monitoring of multidrug-resistant strains. ARGs were monitored in the nitrification and sedimentation tanks of the wastewater treatment plant (WWTP) and in the dam into which this WWTP flows, at various times. The highest relative abundance was found for the blaTEM > tetW > blaNDM-1 > vanA resistance genes, respectively. An increased concentration of tetracycline (up to 96.00 ng/L) and ampicillin (up to 19.00 ng/L) was found in water samples compared to other antibiotics detected. The increased incidence of seven ARGs and four antibiotics was observed in the November and December sampling times. Isolated ampicillin-resistant strains showed a high degree of resistance to ampicillin (61.2% of the total isolates had a minimum inhibitory concentration (MIC) ≥ 20 mg/mL). In 87.8% of isolates, out of the total number, the occurrence of two or more ARGs was confirmed. These multidrug-resistant strains were most often identified as Aeromonas sp. This strain could represent a significant role in the spread of multidrug resistance through wastewater in the environment.

The enhancement of valley water retentiveness in climate change conditions

River system retentiveness must be enhanced to increase multidimensional environmental sustainability and thus ameliorate the effects of climate change and the occurrence of extreme hydrological events. The aim of the article is to demonstrate how ecohydrological Nature-Based Solutions can be combined with conventional infrastructure to improve WBSRCE benefits (Water, Biodiversity, ecosystem Services, Resilience, Culture, Education) by taking a holistic approach to multifunctional reservoir design. The paper proposes a new form of lateral reservoir, which is built without disturbing the meandering river and is supplied with good quality water through a monitoring and regulatory system; its design is based on thorough analysis of hydrological pulses and suspended matter and nutrients fluxes. The regulatory system also includes an innovative Sequential Sedimentation and Biofiltration System. Lateral reservoirs increase water retentiveness in the river valley by lifting ground water level and restoring surrounding wetlands, thus enhancing biodiversity, ecosystem services for society and the resilience of the river system to climate change. An integrative understanding of the interplay between hydrology and biocenosis can be used to enhance river system sustainability potential (WBSR) and harmonise societal needs with biosphere sustainability through culture and education (CE).

Occurrence of antibiotics and antibiotic resistance genes in WWTP effluent-receiving water bodies and reclaimed wastewater treatment plants

There is a growing concern on the fate and the consequent ecological or health risks of antibiotics and antibiotic resistance genes (ARGs) in natural or artificial water environment. The effluent of wastewater treatment plants (WWTPs) has been reported to be an important source of antibiotics and ARGs in the environment. WWTP effluent could be discharged into surface water bodies or recycled, either of which could lead to different exposure risks. The impact of WWTP effluents on the levels of antibiotics and ARGs in effluent-receiving water bodies and the removal efficiency of antibiotics and ARGs in reclaimed wastewater treatment plants (RWTPs) were seldom simultaneously investigated. Thus, in this study, we investigated the occurrence of antibiotics and ARGs in four WWTP effluents, and their downstream effluent-receiving water bodies and RWTPs in seasons of low-water-level. The total concentrations of ofloxacin, norfloxacin, ciprofloxacin, roxithromycin, azithromycin, erythromycin, tetracycline, oxytetracycline, chlortetracycline, and sulfamethoxazole in the secondary effluents were 1441.6-4917.6 ng L^-1. Ofloxacin had the highest concentration. The absolute and relative abundances of total ARGs (qnrD, qnrS, ermA, ermB, tetA, tetQ, sul1, and sul2) in the secondary effluents were 10³-10⁴ copies mL^-1 and 10^-4-10^-2 ARG/16S rRNA. Sul1 and sul2 were the major species with the highest detection frequencies and levels. In most cases, WWTP effluents were not the major contributors to the levels and species of antibiotics and ARGs in the surface water bodies. Four RWTPs removed 43.5-98.9% of antibiotics and - 0.19-2.91 log of ARGs. Antibiotics and ARGs increased in chlorination, ozonation and filtration units. Antibiotics had significantly positive correlations with ARGs, biological oxygen demands, total phosphorus, total nitrogen, and ammonia nitrogen in the four effluent-receiving water bodies. In RWTPs, the total concentrations of antibiotics showed a significant positive correlation with the total abundance of ARGs.

Persisting antibiotic resistance gene pollution and its association with human sewage sources in tropical marine beach waters

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are pollutants of worldwide concern that threaten human health and ecosystems. Anthropogenic activities and wastewater could be ARB and ARG pollution sources; however, research on ARG abundance and microbial source tracking (MST) of contamination in tropical marine waters is limited. This study examined spatiotemporal variations of six ARGs (bla_NDM, bla_TEM, bla_VIM, mcr-1, sul1, and tetQ) against the widely used antibiotic groups and a class 1 integron-integrase gene (intI1) at two Thai tropical recreational beaches (n = 41). Correlations between ARGs and sewage-specific MST markers (i.e., crAssphage and human polyomaviruses [HPyVs]) and fecal indicator bacteria (i.e., total coliforms, fecal coliforms, and enterococci) were also investigated. Bla_TEM, intI1, sul1, and tetQ were ubiquitous at both beaches (85.4-100% detection rate); intI1 was the most abundant (3-6 orders in log₁₀ copies/100 mL), followed by bla_TEM (2-4 orders), sul1 (2-3 orders), and tetQ (2-4 orders). Bla_NDM was found in 7.3% (up to 4 orders), and no mcr-1 was detected. Interestingly, bla_VIM was prevalent at one beach (2-5 orders; n = 17), but found in only one sample at the other (4 orders). Temporal, but not spatial, differences were noticed; bla_TEM was at higher levels in the wet season. IntI1 correlated with sul1 and tetQ (Spearman's rho = 0.47-0.97), suggesting potential horizontal gene transfer. CrAssphage, but not HPyVs, correlated with intI1, sul1, and tetQ (Spearman's rho = 0.50-0.74). Higher numbers of ARGs tended to co-occur in samples with higher crAssphage concentrations, implying sewage contribution to the marine water, with a persisting ARG background. This study provides insight into the ARG pollution status of tropical coastal waters and suggests crAssphage as a proxy for ARG pollution, which could facilitate effective management policies to minimize ARG dissemination in marine environments.

Reductive soil disinfestation attenuates antibiotic resistance genes in greenhouse vegetable soils

Reductive soil disinfestation (RSD) is an emerging technique that ameliorates soil degradation, but its effects against antibiotic resistance genes (ARGs) were unclear. Here, we examined soil properties, ARG types and numbers, and ARG profiles, and bacterial community compositions following 4 soil treatments: control; straw addition (SA); water flooding (WF); and RSD, both straw addition and water flooding. The results showed that the numbers of ARG types and subtypes decreased by 10.8% and 21.1%, respectively, after RSD, and the numbers of ARGs decreased by 18.6%. The attenuated multidrug, beta-lactam, macrolide, and phenicol resistance genes in the RSD soil corresponded to a decreased relative abundance of ARG subtypes (i.e., adeF, mdtM, TypeB_NfxB, mecA, nalC, OXA-60, and cmlA4). Taxa in phyla Proteobacteria, Actinobacteria, and Deinococcus-Thermus were the main hosts for dominant ARG subtypes and were inhibited by RSD. The selected bacterial genera and soil properties explained 83.4% of the variance in ARG composition, suggesting that the improved soil properties and the reduced potential ARG hosts produced by the interactions of straw addition and water flooding are likely responsible for ARG attenuation by RSD. Therefore, RSD has the potential to mitigate ARG pollution in soils.

Metagenomic Analysis Reveals the Fate of Antibiotic Resistance Genes in a Full-Scale Wastewater Treatment Plant in Egypt

Wastewater treatment plants (WWTPs) are recognized as hotspots for the dissemination of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in the environment. Our study utilized a high-throughput sequencing-based metagenomic analysis approach to compare the ARG abundance profiles of the raw sewage, treated effluent and activated sludge samples from a full-scale WWTP in Egypt. In addition, the difference in microbial community composition due to the treatment process was assessed. As a result, 578 ARG subtypes (resistance genes) belonging to 18 ARG types (antibiotic resistance classes) were identified. ARGs encoding for resistance against multidrug, aminoglycoside, bacitracin, beta-lactam, sulfonamide, and tetracycline antibiotics were the most abundant types. The total removal efficiency percentage of ARGs in the WWTP was found to be 98% however, the ARG persistence results indicated that around 68% of the ARGs in the influent could be found in the treated effluent. This finding suggests that the treated wastewater poses a potential risk for the ARG dissemination in bacterial communities of the receiving water bodies via horizontal gene transfer (HGT). The community composition at phylum level showed that Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant phyla in all datasets. Although the relative abundance of several pathogenic bacteria in the influent declined to less than 1% in the effluent, the taxonomic assignments at species level for the effluent and sludge metagenomes demonstrated that clinically important pathogens such as Escherichia coli, Klebsiella pneumonia, and Aeromonas caviae were present. Overall, the results of this study would hopefully enhance our knowledge about the abundance profiles of ARGs and their fate in different wastewater treatment compartments that have never been examined before.

Comparison of the elimination effectiveness of tetracycline and AmpC β-lactamase resistance genes in a municipal wastewater treatment plant using four parallel processes

Municipal wastewater treatment plants (mWWTPs), considered reservoirs of antibiotic resistance genes (ARGs), are selected to compare the contributions of technology and process to ARG removal. Fifteen ARGs (tetA, tetB, tetC, tetE, tetG, tetL, tetM, tetO, tetQ, tetS, tetX, MOX, CIT, EBC, and FOX) and two integron genes (intI1, intI2) were tracked and detected in wastewater samples from a large-scale mWWTP with four parallel processes, including three biological technologies of AAO (anaerobic-anoxic-oxic), AB (adsorption-biodegradation), and UNITANK, two different disinfection technologies, and two primary sedimentation steps. The results showed that ARGs were widely detected, among which tetA and tetM had the highest detection rate at 100%. AAO was the most effective process in removing ARGs, followed by the AB and UNITANK processes, where the separation step was critical: 37.5% AmpC β-lactamase genes were reduced by the secondary clarifier. UV disinfection was more efficient than chlorination disinfection by 47.0% in ARG removal. Both disinfection and primary sedimentation processes could effectively remove integrons, and the swirling flow grit chamber was a more effective primary settling facility in total ARG removal than the aerated grit chamber. The tet genes and AmpC β-lactamase genes were significantly correlated with the water quality indexes of BOD5, CODCr, SS, TP, TOC, pH and NH4+-N (p < 0.05). In addition, the correlation between efflux pump genes and AmpC β-lactamase genes was strongly significant (r2 = 0.717, p < 0.01). This study provides a more powerful guide for selecting and designing treatment processes in mWWTPs with additional consideration of ARG removal.

Metagenomic Survey Reveals More Diverse and Abundant Antibiotic Resistance Genes in Municipal Wastewater Than Hospital Wastewater

Alongside antibiotic resistance, co-selection of antibiotics, biocides, and metal resistance is a growing concern. While hospital wastewater is considered a hotspot for antibiotic-resistant bacteria (ARB) and genes (ARGs), the scenario in India, one of the biggest consumers of antibiotics, remains poorly described. In this study, we used metagenomic sequencing to characterize ARGs and biocide/metal resistance genes (BMRGs) in four wastewater treatment plants (WWTPs) in Jaipur City of India. We observed a significantly lower richness and abundance of ARGs in the influent of a WWTP exclusively receiving hospital wastewater when compared to other three WWTPs involving municipal wastewater treatment. Several tetracycline and macrolide-lincosamide-streptogramin resistance genes were enriched in influents of these three municipal wastewater-related treatment plants, whereas hospital wastewater had a higher abundance of genes conferring resistance to disinfectant-related compounds such as synergize and wex-cide-128, reflecting the patterns of antibiotic/disinfectant use. Of note, in the wastewater system with more chemicals, there was a strong correlation between the numbers of ARGs and BMRGs potentially harbored by common hosts. Our study highlights significant influxes of ARGs from non-hospital sources in Jaipur City, and thus more attention should be paid on the emergence of ARGs in general communities.

Assessing visitor use impact on antibiotic resistant bacteria and antibiotic resistance genes in soil and water environments of Rocky Mountain National Park

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been detected in soil and water in close proximity to anthropogenic sources, but the extent to which human impact plays into ARB and ARGs entering the environment is not well described. This study aimed to determine the impact of visitor use on ARB and ARGs in a national park environment. Soil (n = 240) and water (n = 210) samples were collected across a gradient of human activity in Rocky Mountain National Park and analyzed for bacteria resistant to doxycycline, levofloxacin, and vancomycin. Amount of physical effort required to access a sampling site was used as a metric for the likelihood of human presence. A subset of samples was analyzed for the presence and abundance of six ARGs using quantitative polymerase chain reaction. Linear regression analysis demonstrated that anthropogenic factors including hiking effort and proximity to a toilet significantly contributed to the variance of the abundance of ARB for multiple antibiotics in soil and water. Additionally, ecological factors such as water movement, soil texture, and season may play a role in the detection of ARB and ARGs. Predictive analysis suggests that both human presence and human activities, such as waste elimination, significantly contributed to the abundance of ARB in soil and water. The results of this work evidence that the ecology of antibiotic resistance in remote environments is more complex than anthropogenic impact alone, necessitating further environmental characterization of ARB and ARGs.

Occurrence of antibiotics and antibiotic resistance genes and their correlations in river-type drinking water source, China

The occurrence and distribution of antibiotics and antibiotic resistance genes (ARGs) in natural water has attracted worldwide attention. Antibiotic and ARG pollution in the surface water of drinking water sources might directly/indirectly affect human health. In this study, the distribution of 38 antibiotics, 10 ARGs, 2 integrons, and 16S r DNA in river-type water sources in a large city of China were monitored in winter, which was a period with high level of antibiotic pollution. The results showed that 20 antibiotics were detected with different detection frequencies. The antibiotic pollution in December 2019 was relatively high, with the total concentrations of antibiotics ranging from 281.95 to 472.42 ng/L, followed by that in January 2020 (191.70-337.29 ng/L) and November 2019 (161.25-309.72 ng/L). Sulfacetamide was dominant in November 2019 (23.52-219.00 ng/L) and in January 2020 (113.18-209 ng/L), while norfloxacin in December 2019 (146.72-290.20 ng/L). All the target antibiotics posed low or medium risk for aquatic organisms, and posed low health risk for mankind. Sul1 and erm36 were the predominant ARGs, and intI1 was the predominant integron in drinking water sources. Only tetA showed positive correlations with its corresponding antibiotic (tetracycline). The rest of ARGs showed no correlations with antibiotics or positive / negative correlations with their non-corresponding antibiotics. Overall, the antibiotics and ARG pollution in these water sources was relatively low. These findings provided some reference data for the distribution of antibiotics and ARGs in river-type drinking water sources of large cities in China.

On-site chlorination responsible for effective disinfection of wastewater from hospital

Both hospital effluent and a model sewage treatment plant (STP) wastewater prepared by mixing STP influent and STP secondary effluent at a volume ratio of 1:9 were directly treated with chlorine for investigation of their effects on disinfection of antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB). The overall results indicate that the chlorine disinfection effectively inactivated the majority of AMRB and AMSB, expect for MRSA and Staphylococcus aureus in both wastewaters. No significant differences could further be observed in the taxonomic diversity of micro-organisms after the treatment. The degrees of disinfection given by the direct chlorination were comparable to those attained by combination of conventional activated sludge process and additional chlorine treatment at the STP. The results of this study evoked a recommendation to operate local chlorination treatment directly for the wastewater from medicinal facilities prior to its flow into the STP as sewage. Although additional disinfection treatment at the STP seems necessary to remove the recalcitrant MRSA and Staphylococcus aureus, the present study desirably contributes to a great reduction of the loads of STP and urgent prevention of spreading of infectious diseases in the present state.

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.

Response of anammox granules to the simultaneous exposure to macrolide and aminoglycoside antibiotics: Linking performance to mechanism

Antibiotic pollution is becoming increasingly severe due to its extensive use. The potential application of the anaerobic ammonium oxidation (anammox) process in the treatment of wastewater containing antibiotics has attracted much attention. As common antibiotics, spiramycin (SPM) and streptomycin (STM) are widely used to treat human and animal diseases. However, their combined effects on the anammox process remain unknown. Therefore, this study systematically evaluated the response of the anammox process to both antibiotics. The half maximal inhibitory concentrations of SPM and STM were determined. The continuous-flow anammox system could adapt to SPM and STM at low concentrations, while antibiotics at high concentrations exhibited inhibitory effects. When the concentrations reached 5 mg L^-1 SPM and 50 mg L^-1 STM, the nitrogen removal efficiency dramatically decreased and then rapidly recovered within 8 days. Correspondingly, the abundances of dominant bacteria and genes also changed with antibiotic concentrations. In general, the anammox process showed a stable performance and a high resistance to SPM and STM, suggesting that acclimatization by elevating the concentrations was beneficial for the anammox process to obtain resistance to different antibiotics with high concentrations. This study provides guidance for the stable operation of anammox-based biological treatment of antibiotics containing wastewater.

Fate of antibiotic resistance genes during temperature-changed psychrophilic anaerobic digestion of municipal sludge

The effects of anaerobic digestion (AD) on the abundance of antibiotic resistance genes (ARGs) are highly related to operational temperature. However, the removal performance of ARGs in psychrophilic AD and changed temperatures simulating variable seasonal temperatures is poorly understood. Herein, we investigated the fate of ARGs, correlated bacterial communities and physicochemical properties of AD operation at psychrophilic (15 ℃), mesophilic (35 ℃), and temperature changed conditions (15 to 35 ℃ and 35 to 15 ℃). The results indicated that ammonia release was positively correlated with temperature. The mesophilic AD facilitated phosphorous intake and ARGs proliferation and selection with oxytetracycline (OTC), while psychrophilic AD was conducive to the removal and control of ARGs if no OTC existed. The diversity and composition of AD bacterial communities were influenced more by temperature than OTC. The dominant genera like Candidatus_Microthrix and Acinetobacter had dramatical abundance discrepancies at different temperatures and were obviously positively correlated with ARGs (tet39, tetC and mexD), mobile genetic elements (MGEs) intI, insert sequences (IS) and plasmid. The physicochemical properties of AD influenced the bacterial richness, which in turn significantly correlated with the ARGs abundances. Therefore, ARGs removal could be potentially optimized by eliminating bacterial hosts with deteriorated living conditions and decreased nutrients. This study clarified the response of antibiotic resistome to different temperature variation and highlighted the potential strategies for improved ARGs removal in AD.

Statistical Analysis of Graph-Theoretic Indices to Study EEG-TMS Connectivity in Patients With Depression

Aim

The objective of this work was to demonstrate the usefulness of a novel statistical method to study the impact of transcranial magnetic stimulation (TMS) on brain connectivity in patients with depression using different stimulation protocols, i.e., 1 Hz repetitive TMS over the right dorsolateral prefrontal cortex (DLPFC) (protocol G1), 10 Hz repetitive TMS over the left DLPFC (G2), and intermittent theta burst stimulation (iTBS) consisting of three 50 Hz burst bundle repeated at 5 Hz frequency (G3).

Methods

Electroencephalography (EEG) connectivity analysis was performed using Directed Transfer Function (DTF) and a set of 21 indices based on graph theory. The statistical analysis of graph-theoretic indices consisted of a combination of the k-NN rule, the leave-one-out method, and a statistical test using a 2 × 2 contingency table.

Results

Our new statistical approach allowed for selection of the best set of graph-based indices derived from DTF, and for differentiation between conditions (i.e., before and after TMS) and between TMS protocols. The effects of TMS was found to differ based on frequency band.

Conclusion

A set of four brain asymmetry measures were particularly useful to study protocol- and frequency-dependent effects of TMS on brain connectivity.

Significance

The new approach would allow for better evaluation of the therapeutic effects of TMS and choice of the most appropriate stimulation protocol.