Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR.

The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R2 > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.

Combining High-Resolution Mass Spectrometry and Chemiluminescence Analysis to Characterize the Composition and Fate of Total N-Nitrosamines in Wastewater Treatment Plants.

Monitoring the prevalence and persistence of N-nitrosamines and their precursors in wastewater treatment plants (WWTPs) and effluent-receiving aquatic compartments is a priority for utilities practicing wastewater recycling or exploiting wastewater-impacted source waters. In this work, we developed an analytical framework that combines liquid chromatography-high-resolution mass spectrometry (LC-HRMS) with acidic triiodide-chemiluminescence analysis to characterize the composition and fate of total N-nitrosamines (TONO) and their precursors along the treatment trains of eight WWTPs in New York. Through the parallel application of LC-HRMS and chemiluminescence methods, the TONO scores for 41 N-nitrosamines containing structurally diverse substituents on their amine nitrogen were derived based on their solid-phase extraction recoveries and conversion efficiencies to nitric oxide. Correcting the compositional analysis of TONO using the TONO scores of target N-nitrosamines refined the assessment of the reduction or accumulation of TONO and their precursors across treatment steps in WWTPs. Nontargeted analysis prioritized seven additional N-nitrosamines for confirmation by reference standards, including three previously uncharacterized species: N-nitroso-tert-butylphenylamine, N-nitroso-2-pyrrolidinmethanol, and N-nitrosodesloratadine, although they only served as minor components of TONO. Overall, our study establishes an adaptable methodological framework for advancing the quantitative and qualitative analysis of specific and unknown components of TONO across water treatment and reuse scenarios.

Soluble carbon source recovery using preconditioning coagulants for applicable short-term fermentation of waste activated sludge in WWTPs.

A huge production of waste activated sludge (WAS) has been a burden for wastewater treatment plants (WWTPs) with high disposal cost and little benefit back to wastewater purification. The short-chain fatty acids (SCFAs) produced by a short-term acidogenic fermentation of WAS before methane production have been proven to be a high-quality carbon source available for microbial denitrification process. The dual purpose of full recovery of fermentation liquid products and facilitating disposal of residual solid waste necessitate an efficient solid-liquid separation process of short-term fermentation liquid. The transformation and loss of various soluble carbon sources between solid and liquid are very important issues for carbon recovery efficiency when combining short-term fermentation and sludge dewatering in WWTPs. Here we testified the three conventional preconditioning coagulants, Polyferric Sulfate (PFS), Poly Aluminum Chloride (PAC) and Polyacrylamide (PAM), to improve the efficiency of subsequent solid-liquid separation. The results show that conversion yield of SCFAs in the liquid phase of sludge after short-term fermentation was 195 mg COD/g VSS, when using the coagulants PFS, PAC, and PAM for recovery, the recovery ratio was 79.5%, 82.0%, and 85.9%, respectively, while the dewaterability could be improved after preconditioning short-term fermentation sludge. The complexation of Al3+/Fe3+ in metal coagulants with carboxyl groups of SCFA demonstrated by Density Functional Theory calculation led to small part of soluble carbons co-migration to the solid phase, mainly a loss of high molecular weight organic compounds (carbohydrate, proteins, humic acids), while the application of PAM had little impact on carbon recovery. Economic calculations further showed PAM preconditioning short-term fermentation liquid of WAS could achieve higher recovery benefits.

Regulatory of salinity on assembly of activated sludge microbial communities and nitrogen transformation potential in industrial plants of the lower Yangtze River basin.

This study aims to thoroughly investigate the impact mode of salinity carried by industrial wastewater on the anaerobic-anoxic-oxic (A2O) sludge in wastewater treatment plants (WWTPs). Through comprehensive investigation of the A2O stage activated sludge (AS) from 19 industrial WWTPs in the downstream area of the Yangtze River, China, A total of 38 samples of anaerobic sludge and oxic sludge were collected and analyzed. We found that salinity stress significantly inhibits the growth of the AS community, particularly evident in the anaerobic sludge community. Furthermore, the high-saline environment induces changes in the structure and functional patterns of the AS community, leading to intensive interactions and resource exchanges among microorganisms. Halophilic microorganisms may play a crucial role in this process, significantly impacting the overall community structure, especially in the oxic sludge community. Additionally, salinity stress not only suppresses the nitrogen transformation potential of the AS but also leads to the accumulation of nitrite, thereby increasing the emission potential of both NO and N2O, exacerbating the greenhouse effect of the A2O process in industrial WWTPs. The findings of this study provide necessary theoretical support for maintaining the long-term stable operation of the A2O sludge system in industrial WWTPs, reducing carbon footprint, and improving nitrogen removal efficiency.

Tracking SARS-CoV-2 and its variants in wastewater in Tunisia.

Wastewater-based genomic surveillance can improve community prevalence estimates and identify emerging variants of pathogens. Wastewater influents and treated effluents from six wastewater treatment plants (WWTPs) in Tunisia were analyzed between December 2021 and July 2022. Wastewater samples were analyzed with reverse transcription solid digital PCR (RT-sdPCR) and whole-genome sequencing to determine the amount of SARS-CoV-2 RNA and assign SARS-CoV-2 lineages. The virus variants detected in wastewater samples were compared with COVID-19 prevalence data. The quantitative results in wastewater influents revealed that viral RNA concentrations at the treatment plants corroborate with locally reported clinical cases and show an increase before the increment of clinically diagnosed new COVID-19 cases between April and July 2022. Delta and Omicron variants were identified in the Tunisian wastewater. Interestingly, the presence of variant BA.5 was detected in samples prior to its inclusion as a variant of concern (VOC) by the Tunisian National Health Authorities. SARS-CoV-2 was detected in wastewater effluents, indicating that the wastewater treatment techniques used in the majority of Tunisian WWTPs are inefficient in removing the virus traces. This study reports the first identification of SARS-CoV-2 VOCs in Tunisian wastewater samples.

Machine learning reveals the selection pressure exerted by nonantibiotic pharmaceuticals at environmentally relevant concentrations on antibiotic resistance genotypes.

The emergence and increasing prevalence of antibiotic resistance pose a global public risk for human health, and nonantimicrobial pharmaceuticals play an important role in this process. Herein, five nonantimicrobial pharmaceuticals, including acetaminophen (ACT), clofibric acid (CA), carbamazepine (CBZ), caffeine (CF) and nicotine (NCT), tetracycline-resistant strains, five ARGs (sul1, sul2, tetG, tetM and tetW) and one integrase gene (intI1), were detected in 101 wastewater samples during two typical sewage treatment processes including anaerobic-oxic (A/O) and biological aerated filter (BAF) in Harbin, China. The impact of nonantibiotic pharmaceuticals at environmentally relevant concentrations on both the resistance genotypes and resistance phenotypes were explored. The results showed that a significant impact of nonantibiotic pharmaceuticals at environmentally relevant concentrations on tetracycline resistance genes encoding ribosomal protection proteins (RPPs) was found, while no changes in antibiotic phenotypes, such as minimal inhibitory concentrations (MICs), were observed. Machine learning was applied to further sort out the contribution of nonantibiotic pharmaceuticals at environmentally relevant concentrations to different ARG subtypes. The highest contribution and correlation were found at concentrations of 1400-1800 ng/L for NCT, 900-1500 ng/L for ACT and 7000-10,000 ng/L for CF for tetracycline resistance genes encoding RPPs, while no significant correlation was found between the target compounds and ARGs when their concentrations were lower than 500 ng/L for NCT, 100 ng/L for ACT and 1000 ng/L for CF, which were higher than the concentrations detected in effluent samples. Therefore, the removal of nonantibiotic pharmaceuticals in WWTPs can reduce their selection pressure for resistance genes in wastewater.

Analytical Methods for the Determination of Pharmaceuticals and Personal Care Products in Solid and Liquid Environmental Matrices: A Review.

Among the various compounds regarded as emerging contaminants (ECs), pharmaceuticals and personal care products (PPCPs) are of particular concern. Their continuous release into the environment has a negative global impact on human life. This review summarizes the sources, occurrence, persistence, consequences of exposure, and toxicity of PPCPs, and evaluates the various analytical methods used in the identification and quantification of PPCPs in a variety of solid and liquid environmental matrices. The current techniques of choice for the analysis of PPCPs are state-of-the-art liquid chromatography coupled to mass spectrometry (LC-MS) or tandem mass spectrometry (LC-MS2). However, the complexity of the environmental matrices and the trace levels of micropollutants necessitate the use of advanced sample treatments before these instrumental analyses. Solid-phase extraction (SPE) with different sorbents is now the predominant method used for the extraction of PPCPs from environmental samples. This review also addresses the ongoing analytical method challenges, including sample clean-up and matrix effects, focusing on the occurrence, sample preparation, and analytical methods presently available for the determination of environmental residues of PPCPs. Continuous development of innovative analytical methods is essential for overcoming existing limitations and ensuring the consistency and diversity of analytical methods used in investigations of environmental multi-class compounds.

Monitoring Pharmaceuticals and Personal Care Products in Healthcare Effluent Wastewater Samples and the Effectiveness of Drug Removal in Wastewater Treatment Plants Using the UHPLC-MS/MS Method.

A multi-residue UHPLC-MS/MS analytical method, previously developed for monitoring 52 pharmaceuticals in drinking water, was used to analyse these pharmaceuticals in wastewater originating from healthcare facilities in the Czech Republic. Furthermore, the methodology was expanded to include the evaluation of the effectiveness of drug removal in Czech wastewater treatment plants (WWTPs). Of the 18 wastewater samples analysed by the validated UHPLC-MS/MS, each sample contained at least one quantifiable analyte. This study reveals the prevalence of several different drugs; mean concentrations of 702 µg L-1 of iomeprol, 48.8 µg L-1 of iopromide, 29.9 µg L-1 of gabapentin, 42.0 µg L-1 of caffeine and 82.5 µg L-1 of paracetamol were present. An analysis of 20 samples from ten WWTPs revealed different removal efficiencies for different analytes. Paracetamol was present in the inflow samples of all ten WWTPs and its removal efficiency was 100%. Analytes such as caffeine, ketoprofen, naproxen or atenolol showed high removal efficiencies exceeding 80%. On the other hand, pharmaceuticals like furosemide, metoprolol, iomeprol, zolpidem and tramadol showed lower removal efficiencies. Four pharmaceuticals exhibited higher concentrations in WWTP effluents than in the influents, resulting in negative removal efficiencies: warfarin at -9.5%, indomethacin at -53%, trimethoprim at -54% and metronidazole at -110%. These comprehensive findings contribute valuable insights to the pharmaceutical landscape of wastewater from healthcare facilities and the varied removal efficiencies of Czech WWTPs, which together with the already published literature, gives a more complete picture of the burden on the aquatic environment.

An assessment and characterization of pharmaceuticals and personal care products (PPCPs) within the Great Lakes Basin: Mussel Watch Program (2013-2018).

Defining the environmental occurrence and distribution of chemicals of emerging concern (CECs), including pharmaceuticals and personal care products (PPCPs) in coastal aquatic systems, is often difficult and complex. In this study, 70 compounds representing several classes of pharmaceuticals, including antibiotics, anti-inflammatories, insect repellant, antibacterial, antidepressants, chemotherapy drugs, and X-ray contrast media compounds, were found in dreissenid mussel (zebra/quagga; Dreissena spp.) tissue samples. Overall concentration and detection frequencies varied significantly among sampling locations, site land-use categories, and sites sampled proximate and downstream of point source discharge. Verapamil, triclocarban, etoposide, citalopram, diphenhydramine, sertraline, amitriptyline, and DEET (N,N-diethyl-meta-toluamide) comprised the most ubiquitous PPCPs (> 50%) detected in dreissenid mussels. Among those compounds quantified in mussel tissue, sertraline, metformin, methylprednisolone, hydrocortisone, 1,7-dimethylxanthine, theophylline, zidovudine, prednisone, clonidine, 2-hydroxy-ibuprofen, iopamidol, and melphalan were detected at concentrations up to 475 ng/g (wet weight). Antihypertensives, antibiotics, and antidepressants accounted for the majority of the compounds quantified in mussel tissue. The results showed that PPCPs quantified in dreissenid mussels are occurring as complex mixtures, with 4 to 28 compounds detected at one or more sampling locations. The magnitude and composition of PPCPs detected were highest for sites not influenced by either WWTP or CSO discharge (i.e., non-WWTPs), strongly supporting non-point sources as important drivers and pathways for PPCPs detected in this study. As these compounds are detected at inshore and offshore locations, the findings of this study indicate that their persistence and potential risks are largely unknown, thus warranting further assessment and prioritization of these emerging contaminants in the Great Lakes Basin.

Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes.

Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.