Neighbor urban wastewater treatment plants display distinct profiles of bacterial community and antibiotic resistance genes

A microbiome-biochar composite synergistically eliminates the environmental risks of antibiotic mixtures and their toxic byproducts

This study developed a continuous reactor system employing a hybrid hydrogel composite synthesized using a complex sludge microbiome and an adsorbent (HSA). This HSA-based system effectively eliminated the environmental risks associated with a mixture of the antibiotics ciprofloxacin and sulfamethoxazole, which exhibited higher toxicity in combination than individually at environmentally relevant levels. Analytical chemistry experiments revealed the in-situ generation of various byproducts (BPs) within the bioreactor system, with two of these BPs recording toxicity levels that surpassed those of their parent compound. The HSA approach successfully prevented the functional microbiome from being washed out of the reactor, while HSA efficiently removed antibiotic residues in their original and BP forms through synergistic adsorptive and biotransformation mechanisms, ultimately reducing the overall ecotoxicity. The use of HSA thus demonstrates promise not only as a mean to reduce the threat posed by toxic antibiotic residues to aquatic ecosystems but also as a practical solution to operational challenges, such as biomass loss/washout, that are frequently encountered in various environmental bioprocesses.

Dynamic migration and risk of cephalosporin antibiotic resistance genes: Move from pharmaceutical plants through wastewater treatment plants to coastal tidal flats sediments

The migration and dissemination of antibiotics and their corresponding antibiotic resistance genes (ARGs) from pharmaceutical plants through wastewater treatment to the environment introduce exogenous ARGs, increasing the risk of antibiotic resistance. Cephalosporin antibiotics (Ceps) are among the most widely used antibiotics with the largest market scale today, and the issue of resistance is becoming increasingly severe. In this study, a cephalosporin pharmaceutical plant was selected and metagenomic analysis was employed to investigate the dissemination patterns of cephalosporin antibiotics (Ceps) and their ARGs (CepARGs) from the pharmaceutical plant through the wastewater treatment plant to tidal flats sediments. The findings revealed a significant reduction in the total concentration of Ceps by 90.32 % from the pharmaceutical plant's Pioneer Bio Reactor (PBR) to the effluent of the wastewater treatment plant, and a notable surge of 172.13 % in the relative abundance of CepARGs. It was observed that CepARGs originating from the PBR could migrate along the dissemination chain, contributing to 60 % of the CepARGs composition in tidal flats sediments. Microorganisms play a crucial role in the migration of CepARGs, with efflux-mediated CepARGs, as an intrinsic resistance mechanism, exhibiting a higher prospensity for migration due to their presence in multiple hosts. While Class I risk CepARGs are present at the pharmaceutical and wastewater plant stages, Class I ina-CepARGs are completely removed during wastewater treatment and do not migrate to the environment. This study reveals the dynamic migration characteristics and potential risk changes regarding Ceps and CepARGs in real dissemination chains, providing new theoretical evidence for the mitigation, control, and risk prevention of CepARGs.

Integron-associated genes are reliable indicators of antibiotic resistance in wastewater despite treatment- and seasonality-driven fluctuations

The present study aims to characterize the bacterial community, resistome and integron abundance of a municipal wastewater treatment plant (WWTP) over the course of 12 months and evaluate the year-long performance of integron-related genes as potential indicators of antibiotic resistance mechanisms in influents and effluents. For that, total DNA was extracted and subjected to 16S rRNA-targeted metabarcoding, high-throughput (HT) qPCR (48 targets) and standard qPCR (5 targets). Targets included integrase genes, antibiotic resistance genes (ARGs) and putative pathogenic groups. A total of 16 physicochemical parameters determined in the wastewater samples were also considered. Results revealed that the WWTP treatment significantly impacted the bacterial community, as well as the content in ARGs and integrase genes. Indeed, there was a relative enrichment from influent to effluent of 13 pathogenic groups (e.g., Legionella and Mycobacterium) and genes conferring resistance to sulphonamides, aminoglycosides and disinfectants. Effluent samples (n = 25) also presented seasonal differences, with an increase of the total ARGs' concentration in summer, and differences between winter and summer on relative abundance of sulphonamide and disinfectant resistance mechanisms. From the eight putative integron-related genes selected, all were positively correlated with the total ARGs' content in wastewater and the relative abundance of resistance to most of the specific antibiotic classes. The genes intI1, blaGES and qacE∆1 were the most strongly correlated with the total concentration of ARGs. Genes blaGES and blaVIM, were better correlated to resistance to beta-lactams, aminoglycosides and tetracyclines. This study supports the use of integron-related genes as powerful indicators of antibiotic resistance in wastewater, being robust despite the variability caused by wastewater treatment and seasonality.

The influence of the phylum Planctomycetota in the environmental resistome

Antimicrobial resistance is one of the leading causes of death worldwide and research on this topic has been on the spotlight for a long time. More recently and in agreement with the One Health Approach, the focus has moved towards the environmental resistome. Members of the phylum Planctomycetota are ubiquitously present in the environment including in hotspots for antimicrobial resistance selection and dissemination. Furthermore, phenotypic broad-range resistance has been observed in diverse members of this phylum. Here we review the evidence available on antimicrobial resistance in the underexploited Planctomycetota and highlight key aspects for future studies.

Occurrence, environmental impact and fate of pharmaceuticals in groundwater and surface water: a critical review

In many nations and locations, groundwater serves as the population's primary drinking water supply. However, pharmaceuticals found in groundwater and surface waters may affect aquatic ecosystems and public health. As a result, their existence in natural raw waters are now more widely acknowledged as a concern. This review summarises the evidence of research on pharmaceuticals' occurrence, impact and fate, considering results from different water bodies. Also, various analytical techniques were reviewed to compare different pharmaceuticals' detection frequencies in water bodies. These include liquid chromatography-mass spectrometry (LC-MS), high-performance liquid chromatography (HPLC), ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), and gas chromatography-mass spectrometry (GC-MS). However, owing to LC-MS's high sensitivity and specification, it is the most reported instrument used for analysis. The PRISMA reviewing methodology was adopted based on relevant literature in order to focus on aim of the review. Among other pharmaceuticals reviewed, sulfamethoxazole was found to be the most frequently detected drug in wastewater (up to 100% detection frequency). The most reported pharmaceutical group in this review is antibiotics, with sulfamethoxazole having the highest concentration among the analysed pharmaceuticals in groundwater and freshwater (up to 5600 ng/L). Despite extensive study and analysis on the occurrence and fate of pharmaceuticals in the environment, appropriate wastewater management and disposal of pharmaceuticals in the water environment are not still monitored regularly. Therefore, there is a need for mainstream studies tailored to the surveillance of pharmaceuticals in water bodies to limit environmental risks to human and aquatic habitats in both mid and low-income nations.

Fecal antibiotic resistance genes were transferred through the distribution of soil-lettuce-snail food chain

Massive antibiotic resistance genes (ARG) were detected in the soil modified by manure, which may affect human life safety through the food chain. However, the transmission of ARGs through the soil-plant-animal food chain is still unclear. Therefore, this study used high-throughput quantitative PCR technology to explore the effects of pig manure application on ARGs and bacterial communities in soil, lettuce phyllosphere, and snail excrement. The results showed that a total of 384 ARGs and 48 MEGs were detected in all samples after 75 days of incubation. The diversity of ARGs and MGEs in soil components increased significantly by 87.04% and 40% with the addition of pig manure. The absolute abundance of ARGs in the phyllosphere of lettuce was significantly higher than that of the control group, with a growth rate of 212.5%. Six common ARGs were detected between the three components of the fertilization group, indicating that there was internal transmission of fecal ARGs between the trophic levels of the food chain. Firmicutes and Proteobacteria were identified as the dominant host bacteria in the food chain system, which were more likely to be used as carriers of ARGs to promote the spread of resistance in the food chain. The results were used to assess the potential ecological risks of livestock and poultry manure. It provides theoretical basis and scientific support for the formulation of ARG prevention and control policies.

Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics

Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.

Does carbon cloth really improve thermophilic anaerobic digestion performance on a larger scale? focusing on statistical analysis and microbial community dynamics

Currently, the phenomenon of direct interspecies electron transfer (DIET) is of great interest in the technology of anaerobic digestion (AD) due to potential performance benefits. However, the conditions for the occurrence of DIET and its limits on improving AD under conditions close to real have not been studied enough. This research is concentrated on the effect of conductive carbon cloth (R3), in comparison with a dielectric fiberglass cloth (R2) and control (R1), on the AD performance in large (90 L) thermophilic reactors, fed with a mixture of simulated organic fraction of municipal solid waste and sewage sludge. While organic loading rate (OLR) was gradually increased from 2.4 to 8.66 kg VS/(m³ day), a statistically significant (p < 0.05) difference in biogas production was observed between R1 and both R2 and R3. However, at a maximum OLR of 12.12 kg VS/(m³ day) in R3, an increase in biogas production (p < 0.05) was observed both compared to R1 (by 8.97%) and R2 (by 4.24%). The content of volatile fatty acids in R3 as a whole was the lowest, especially at the maximum OLR. Biofilm on carbon cloth was rich in syntrophic microorganisms of the genera Tepidanaerobacter, as well as Defluviitoga, capable of DIET in mixed cultures with Methanothrix, which was the most abundant methanogen in biofilm. Suspended Bifidobacterium, Fervidobacterium and Anaerobaculum were negatively affected, while Defluviitoga, Methanothermobacter and Methanosarcina, on the contrary, were positively affected by the increase in OLR and showed, respectively, a negative and positive correlation (p < 0.05) with the main AD performance parameters.

Elemental composition and microbial community differences between wastewater treatment plant effluent and local natural surface water: A Zhengzhou city study

Wastewater treatment plant (WWTP) effluent is discharged into rivers as supplemental water, which may result in ecological risk. This study compares the element composition and microbial community of WWTP effluent and natural surface water (NSW) and reveals the potential ecological risk of WWTP effluent discharge. Twenty recently upgraded WWTPs and three relatively large reservoirs in Zhengzhou city, China, were selected. The contents of N, P, S, K, Ca, Mg, B, Si, Na, Fe, Mn, Co, Ni and Sn were significantly higher in WWTP effluent than in NSW, while those of Mo, V, Pb and Cd were significantly lower. There was no significant difference between WWTP effluent and NSW in terms of the element imbalance index (IMI) (representing the extent of imbalance of element proportions) relative to the class IV surface water quality standard (the control standard for most Chinese rivers). The macronutrient IMI relative to the Hoagland formula was significantly lower in WWTP effluent than in NSW, and WWTP effluent discharge could significantly lower this index in NSW; this may be an important cause of primary productivity explosion. The microbial diversity was significantly higher in WWTP effluent than in NSW. The predicted relative abundances of mobile genetic elements and oxidative-stress-tolerant phenotypes were significantly higher in WWTP effluent than in NSW, whereas the abundance of gram-negative phenotypes was significantly lower, and that of potential pathogenic phenotypes was slightly lower. The effluent from upgraded WWTPs exhibited a low risk of pathogen diffusion but a high risk of antibiotic resistance gene diffusion. The element composition and microbial community should be considered when evaluating the ecological risk of WWTP effluent discharge.

Microalgae simultaneously promote antibiotic removal and antibiotic resistance genes/bacteria attenuation in algal-bacterial granular sludge system

This study investigated the effects of microalgae growth on antibiotic removal and the attenuation of antibiotic resistance genes (ARGs)/ARGs host bacteria in algal-bacterial granular sludge (ABGS) system. In the presence of tetracycline (TC) and sulfadiazine (SDZ) mixture (2-4 mg/L), microalgae could grow on bacterial granular sludge (BGS) to form ABGS, with a chlorophyll-a content of 7.68-8.13 mg/g-VSS being achieved. The removal efficiencies of TC and SDZ by ABGS were as high as 79.0 % and 94.0 %, which were 4.3-5.0 % higher than those by BGS. Metagenomic analysis indicated that the relative abundances of TC/SDZ- related ARGs and mobile genetic elements (MGEs) in BGS were 56.1 % and 22.1 % higher than those in ABGS. A total of 26 ARGs were detected from the granules, and they were identified to associate with 46 host bacteria. 13 out of 26 ARGs and 13 out of 46 hosts were shared ARGs and hosts, respectively. The total relative abundance of host bacteria in BGS was 30.8 % higher than that in ABGS. Scenedesmus and Chlorella were the dominant microalgae that may reduce the diversity of ARGs hosts. Overall, ABGS is a promising biotechnology for antibiotic-containing wastewater treatment.

Enhanced removal of antibiotics and decreased antibiotic resistance genes in the photo-sequencing batch reactor during the aquaculture wastewater treatment

The performance of photo-sequencing batch reactor (PSBR) in removing multiple antibiotics and nutrients from aquaculture wastewater as well as the antibiotic resistance genes (ARGs) proliferation were firstly investigated during the long-term experiments. The operational conditions (i.e. light intensity, light time, aeration and solid retention time) were optimised to realise the simultaneous removal of antibiotics and nutrients. It was found that, compared with traditional SBR, PSBR has similar nutrient removal rate and a 30% higher antibiotics removal rate due to the corporation of microalgae (Chlorella) and bacteria, and the absolute abundance of ARGs decreased by 78% in PSBR. Further investigation showed that PSBR had certain advantages in removing quinolones and the corresponding removal rate could reach up to 90%. In terms of the mechanisms, the possible metabolic pathway of antibiotic was analysed and the intermediate metabolites were different from that of the reported studies. The microbial communities were also affected by microalgae and the relative abundance of certain bacteria (such as members of the families Rhodocyclaceae and Burkholderiaceae), which were positively correlated with some ARGs, decreased in PSBR. This study provides an alternative and effective method to aquaculture wastewater treatment, which present high nutrients and antibiotics removal efficiencies and low ARGs transmission.

The balance between treatment efficiency and receptor quality determines wastewater impacts on the dissemination of antibiotic resistance

This study investigated the balance between treatment efficiency and impact caused by urban wastewater treatment plants (UWTPs) on the dissemination of antibiotic resistance. Four full-scale UWTPs (PT1-PT4) and the receiving river were sampled over four campaigns. The 16 S rRNA gene, two mobile genetic elements (MGEs), eight antibiotic resistance genes (ARGs), and culturable bacteria were monitored over different treatment stages and in hospital effluent. The bacterial and antibiotic resistance load was not significantly different in the inflow of the four UWTPs (p > 0.01). Biological treatment promoted ARGs reduction values up to 2.5 log-units/mL, while UV (PT1, PT2) or sand filtration/ozonation (PT3) led to removal values < 0.6 log-units/mL. The final effluent of PT3, with the highest removal rates and significantly lower ARGs abundance, was not significantly different from the receiving water body. Emerging ARGs (e.g., bla_VIM, bla_OXA-48, and bla_KPC) were sporadically detected in the river, although more frequent downstream. Hospital effluent might contribute for the occurrence of some, but not all these ARGs in the river. A major conclusion was that the impact of the UWTPs on the river was not only determined by treatment efficiency and final effluent quality, but also by the background contamination of the river and/or dilution rate.

Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods

Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.

Characteristics changes on Applications of Antibiotics and Current Approaches to Enhance Productivity with Soil Microbiome

The contamination of environmental sully with antibiotics is regarded as a major problem today and predictable to attain more recognition in near future. However, human intervention resulting in antibiotic consumption is being enhancing all around the world. Our review of literature revealed the role of microbiome in sully and how antibiotic resistant genes raised. The structure of antibiotics basically influenced by natural components such as biotic and abiotic push which shifts based on different soils. Therefore, management of microbiome in soil and their expression studies were distinctively revealed. The assessment of antibiotic resistance genes with help of next generation sequencing provided a clear comprehension on genome and transcriptome of the bacterial genes. Thus, interaction of microbiome with soil can also be well understood. The current findings in our study will guide every researcher to follow logical protocol in analyzing microbiota composition is covered as well and also to understand its metagenomic and sequenced with next-generation sequencer which helps to comprehend the diverse micro-flora present in soil and its operation. Finally, later progresses in bioinformatics computer program, flow of work, and applications for analyzing metagenomic information are put in a nutshell.

Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle

Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.

Diversity of Multidrug-Resistant Bacteria in an Urbanized River: A Case Study of the Potential Risks from Combined Sewage Overflows

Wastewater contamination and urbanization contribute to the spread of antibiotic resistance in aquatic environments. This is a particular concern in areas receiving chronic pollution of untreated waste via combined sewer overflow (CSO) events. The goal of this study was to expand knowledge of CSO impacts, with a specific focus on multidrug resistance. We sampled a CSO-impacted segment of the James River (Virginia, USA) during both clear weather and an active overflow event and compared it to an unimpacted upstream site. Bacteria resistant to ampicillin, streptomycin, and tetracycline were isolated from all samples. Ampicillin resistance was particularly abundant, especially during the CSO event, so these isolates were studied further using disk susceptibility tests to assess multidrug resistance. During a CSO overflow event, 82% of these isolates were resistant to five or more antibiotics, and 44% were resistant to seven or more. The latter statistic contrasts starkly with the upstream reference site, where only 4% of isolates displayed resistance to more than seven antibiotics. DNA sequencing (16S rRNA gene) revealed that ~35% of our isolates were opportunistic pathogens, comprised primarily of the genera Stenotrophomonas, Pseudomonas, and Chryseobacterium. Together, these results demonstrate that CSOs can be a significant source of viable clinically-relevant bacteria to the natural environment and that multidrug resistance is an important understudied component of the environmental spread of antibiotic resistance.

Azole antifungal resistance in fungal isolates from wastewater treatment plant effluents

Wastewater treatment plants (WWTPs) can be significant sources of antifungal resistant fungi, which can disseminate further in the environment by getting into rivers together with effluents discharged from WWTPs and pose a risk for human health. In this study, the presence of azole resistance was determined in fungal isolates from treated effluents of two WWTPs using the standard microdilution method from Clinical and Laboratory Standards Institute (CLSI). A total of 41 fungal isolates representing 23 fungal species and 16 fungal genera were obtained. Fungal genera related to the known human and/or plant pathogens such as Aspergillus, Fusarium, and Candida were detected. Among the observed species, the susceptibility of Aspergillus fumigatus and Fusarium oxysporum was tested against fluconazole (FCZ), ketoconazole (KTZ), itraconazole (ITZ), and voriconazole (VCZ). The isolate A. fumigatus was susceptible to KTZ, ITZ, and VCZ, while it showed resistance against FCZ. On the contrast, the isolate F. oxysporum showed resistance to KTZ, ITZ, and VCZ. Comparatively, VCZ showed highest activity against both A. fumigatus and F. oxysporum. Analysis of the gene Cyp51A for the A. fumigatus isolate showed no evidence of drug resistance that could be related to point mutations and/or tandem repeats in the gene. To the best of our knowledge, this is the first susceptibility test study on A. fumigatus and F. oxysporum isolates from the WWTPs of South Africa. In conclusion, this study indicated an urgent need for thorough investigation with larger group of fungal isolates from different regions of South Africa to broadly understand the role of WWTPs in the dissemination of azole antifungal drug resistance.

Variation in microbial populations and antibiotic resistance genes in mariculture sediments in the present of the seaweed Ulva fasciata and under selective pressure of oxytetracycline

The widely distributed seaweed Ulva fasciata has nutrient absorption abilities and can be used in the bioremediation of polluted maricultural environments. This study explored microbial community and antibiotic resistance gene (ARG) variation in mariculture sediments in response to different trace levels (10, 100, and 500 μg L^-1) of oxytetracycline (OTC) and the presence of Ulva fasciata. The increase in OTC level promoted nutrient (NO₃_-N and PO₄^3--P) removal mainly due to Ulva fasciata adsorption. The abundances of the Euryarchaeota and Planctomycetes phyla in sediments were positively related to the increase in OTC stress, while a negative correlation occurred for the Proteobacteria phylum via metagenomic analysis. Compared with the control system, the increase rates of total ARGs were 3.90%, 7.36% and 13.42% at the OTC levels of 10, 100 and 500 μg L^-1, respectively. OTC stress mainly favoured the collateral enrichment of non-corresponding polypeptide and MLS ARGs, mainly due to the enrichment of the phyla Planctomycetes and Euryarchaeota by the synergistic effect of OTC and nutrients. The results of quantitative PCR with tetracycline resistance genes (TRGs) (tetO, tetT, tetPB, tetW and otrA) and a horizontal transfer gene (intl1) demonstrated that all of genes had much higher gene numbers in sediments after 3 months of OTC stress than in those without OTC stress, which was strongly related to the variation in the phyla Bacteroidetes, Gemmatimonadetes and Acidobacteria. The significant correlation between intl1 and the target TRGs is indicative of the important role of the horizontal transfer of integron-resistant genes in the spread of TRGs.

Pharmaceutical pollution of water resources in Nakivubo wetlands and Lake Victoria, Kampala, Uganda

This study investigated the occurrence and removal in wastewater and water bodies in Nakivubo wetland area and Inner Murchison Bay, Lake Victoria, of common prescription and non-prescription pharmaceutically-active substances (PhACs) sold in Kampala city, Uganda. A questionnaire was sent to 20 pharmacies in Kampala, to identify the most commonly sold PhACs in the city. During two sampling campaigns, samples were collected from Bugolobi wastewater treatment plant (WWTP) influent and effluent and surface water samples from Nakivubo channel, Nakivubo wetland and Inner Murchison Bay. The concentrations of 28 PhACs, organic matter, solids and nutrients in water samples were analysed. Ciprofloxacin (antibiotic), cetirizine (anti-allergy), metformin (anti-diabetes), metronidazole (antibiotic) and omeprazole (gastric therapy) were reported by pharmacies to be the PhACs most commonly sold in the study area. Chemical analysis of water samples revealed that trimethoprim (antibiotic) and sulfamethoxazole (antibiotic) were the dominant PhACs in water from all sites except Lake Victoria. Other PhACs such as atenolol (anti-hypertensive), carbamazepine (anti-epileptic) and diclofenac (anti-inflammatory) were also found at all study sites except Lake Victoria. ∑PhACs in effluent from Bugolobi WWTP (13000-37,600 ng L^-1) was higher than in the corresponding influent (4000-28,000 ng L^-1), indicating poor removal of PhACs within the WWTP. ∑PhACs decreased by a factor of 2-6 between Bugolobi WWTP effluent and Nakivubo channel (5700 ng L^-1), due to dilution and sorption to channel sediment, and by a factor of 1-3 between the Nakivubo channel and Nakivubo wetland (3900-5400 ng L^-1), due to sorption to sediment and uptake by plants in the wetland. No detectable levels of PhACs were found in water from Lake Victoria. Overall, this investigation demonstrated that PhACs in wastewater enter Nakivubo water system. Thus, Bugolobi WWTP needs to be upgraded to improve PhACs removal from wastewater. Considering the high occurrence of antibiotics in the water system in Kampala, development and spread of antimicrobial resistance within the area should also be investigated.

Metagenomic analysis of β-lactamase and carbapenemase genes in the wastewater resistome

The emergence and spread of resistance to antibiotics among bacteria is the most serious global threat to public health in recent and coming decades. In this study, we characterized qualitatively and quantitatively β-lactamase and carbapenemase genes in the wastewater resistome of Central Wastewater Treatment Plant in Koziegłowy, Poland. The research concerns determination of the frequency of genes conferring resistance to β-lactam and carbapenem antibiotics in the genomes of culturable bacteria, as well as in the wastewater metagenome at three stages of treatment: raw sewage, aeration tank, and final effluent. In the final effluent we found bacteria with genes that pose the greatest threat to public health, including genes of extended spectrum β-lactamases - bla_CTX-M, carbapenemases - bla_NDM, bla_VIM, bla_GES, bla_OXA-48, and showed that during the wastewater treatment their frequency increased. Moreover, the wastewater treatment process leads to significant increase in the relative abundance of bla_TEM and bla_GES genes and tend to increase the relative abundance of bla_CTX-M, bla_SHV and bla_OXA-48 genes in the effluent metagenome. The biodiversity of bacterial populations increased during the wastewater treatment and there was a correlation between the change in the composition of bacterial populations and the variation of relative abundance of β-lactamase and carbapenemase genes. PCR-based quantitative metagenomic analysis combined with analyses based on culture methods provided significant information on the routes of ARBs and ARGs spread through WWTP. The limited effectiveness of wastewater treatment processes in the elimination of antibiotic-resistant bacteria and resistance genes impose the need to develop an effective strategy and implement additional methods of wastewater disinfection, in order to limit the increase and the spread of antibiotic resistance in the environment.

Fate of environmental pollutants

This annual review covers the literature published in 2018 on topics related to the occurrence and fate of environmental pollutants in wastewater. Due to the vast amount of literature published on this topic, we have discussed only a portion of the quality research publications, due to the limitation of space. The abstract search was carried out using Web of Science, and the abstracts were selected based on their relevance. In a few cases, full-text articles were referred to understand new findings better. This review is divided into the following sections: antibiotic-resistant bacteria (ARBs) and antibiotic-resistant genes (ARGs), disinfection by-products (DBPs), drugs of abuse (DoAs), estrogens, heavy metals, microplastics, per- and polyfluoroalkyl compounds (PFAS), pesticides, and pharmaceuticals and personal care products (PPCPs), with the addition of two new classes of pollutants to previous years (DoAs and PFAS).

Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance

Antibiotic-resistant organisms (AROs) are a major concern to public health worldwide. While antibiotics have been naturally produced by environmental bacteria for millions of years, modern widespread use of antibiotics has enriched resistance mechanisms in human-impacted bacterial environments. Antibiotic resistance genes (ARGs) continue to emerge and spread rapidly. To combat the global threat of antibiotic resistance, researchers must develop methods to rapidly characterize AROs and ARGs, monitor their spread across space and time, and identify novel ARGs and resistance pathways. We review how high-throughput sequencing-based methods can be combined with classic culture-based assays to characterize, monitor, and track AROs and ARGs. Then, we evaluate genomic and metagenomic methods for identifying ARGs and biosynthetic pathways for novel antibiotics from genomic data sets. Together, these genomic analyses can improve surveillance and prediction of emerging resistance threats and accelerate the development of new antibiotic therapies to combat resistance.