Dynamic assessment of the floc morphology, bacterial diversity, and integron content of an activated sludge reactor processing hospital effluent

Evidence of Bacterial Community Coalescence between Freshwater and Discharged tpm-Harboring Bacterial Taxa from Hospital and Domestic Wastewater Treatment Plants among Epilithic Biofilms

The ability of WWTP outflow bacteria at colonizing rock surfaces and contributing to the formation of river epilithic biofilms was investigated. Bacterial community structures of biofilms (b-) developing on rocks exposed to treated wastewaters (TWW) of a hospital (HTWW) and a domestic (DTWW) clarifier, and to surface waters of the stream located at 10 m, 500 m, and 8 km from the WWTP outlet, were compared. Biofilm bacterial contents were analyzed by cultural approaches and a tpm-based DNA metabarcoding analytical scheme. Co-occurrence distribution pattern analyses between bacterial datasets and eighteen monitored pharmaceuticals were performed. Higher concentrations of iohexol, ranitidine, levofloxacin, and roxithromycin were observed in the b-HTWW while atenolol, diclofenac, propranolol, and trimethoprim were higher in the b-DTWW. MPN growth assays showed recurrent occurrences of Pseudomonas aeruginosa and Aeromonas caviae among these biofilms. An enrichment of multi-resistant P. aeruginosa cells was observed in the hospital sewer line. P. aeruginosa MPN values were negatively correlated to roxithromycin concentrations. The tpm DNA metabarcoding analyses confirmed these trends and allowed an additional tracking of more than 90 species from 24 genera. Among the recorded 3082 tpm ASV (amplicon sequence variants), 41% were allocated to the Pseudomonas. Significant differences through ANOSIM and DESeq2 statistical tests were observed between ASV recovered from b-HTWW, b-DTWW, and epilithic river biofilms. More than 500 ASV were found restricted to a single sewer line such as those allocated to Aeromonas popoffii and Stenotrophomonas humi being strictly found in the b-HTWW file. Several significant correlations between tpm ASV counts per species and pharmaceutical concentrations in biofilms were recorded such as those of Lamprocystis purpurea being positively correlated with trimethoprim concentrations. A tpm source tracking analysis showed the b-DTWW and b-HTWW tpm ASV to have contributed, respectively, at up to 35% and 2.5% of the epilithic river biofilm tpm-taxa recovered downstream from the WWTP outlet. Higher contributions of TWW taxa among epilithic biofilms were recorded closer to the WWTP outlet. These analyses demonstrated a coalescence of WWTP sewer communities with river freshwater taxa among epilithic biofilms developing downstream of a WWTP outlet.

Dairy manure as a potential source of crop nutrients and environmental contaminants

Although animal manure is applied to agricultural fields for its nutrient value, it may also contain potential contaminants. To determine the variability in such contaminants as well as in valuable nutrients, nine uncomposted manure samples from Idaho dairies collected during 2.5 years were analyzed for macro- and micro-nutrients, hormones, phytoestrogens, antibiotics, veterinary drugs, antibiotic resistance genes, and genetic elements involved in the spread of antibiotic resistance. Total N ranged from 6.8 to 30.7 (C:N of 10 to 21), P from 2.4 to 9.0, and K from 10.2 to 47.7 g/kg manure. Zn (103 - 348 mg/kg) was more abundant than Cu (56 - 127 mg/kg) in all samples. Phytoestrogens were the most prevalent contaminants detected, with concentrations fluctuating over time, reflecting animal diets. This is the first study to document the presence of flunixin, a non-steroidal anti-inflammatory drug, in solid stacked manure from regular dairy operations. Monensin was the most frequently detected antibiotic. Progesterones and sulfonamides were regularly detected. We also investigated the relative abundance of several types of plasmids involved in the spread of antibiotic resistance in clinical settings. Plasmids belonging to the IncI, IncP, and IncQ1 incompatibility groups were found in almost all manure samples. IncQ1 plasmids, class 1 integrons, and sulfonamide resistance genes were the most widespread and abundant genetic element surveyed, emphasizing their potential role in the spread of antibiotic resistance. The benefits associated with amending agricultural soils with dairy manure must be carefully weighed against the potential negative consequences of any manure contaminants.

Performance and Microbial Community of Different Biofilm Membrane Bioreactors Treating Antibiotic-Containing Synthetic Mariculture Wastewater

The performance of pollutant removals, tetracycline (TC) and norfloxacin (NOR) removals, membrane fouling mitigation and the microbial community of three Anoxic/Oxic membrane bioreactors (AO-MBRs), including a moving bed biofilm MBR (MBRa), a fixed biofilm MBR (MBRb) and an AO-MBR (MBRc) for control, were compared in treating antibiotic-containing synthetic mariculture wastewater. The results showed that MBRb had the best effect on antibiotic removal and membrane fouling mitigation compared to the other two bioreactors. The maximum removal rate of TC reached 91.65% and the maximum removal rate of NOR reached 45.46% in MBRb. The addition of antibiotics had little effect on the removal of chemical oxygen demand (COD) and ammonia nitrogen (NH₄⁺-N)—both maintained more than 90% removal rate during the entire operation. High-throughput sequencing demonstrated that TC and NOR resulted in a significant decrease in the microbial diversity and the microbial richness MBRs. Flavobacteriia, Firmicutes and Azoarcus, regarded as drug-resistant bacteria, might play a crucial part in the removal of antibiotics. In addition, the dynamics of microbial community had a great change, which included the accumulation of resistant microorganisms and the gradual reduction or disappearance of other microorganisms under antibiotic pressure. The research provides an insight into the antibiotic-containing mariculture wastewater treatment and has certain reference value.

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?

A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.

Limited influence of hospital wastewater on the microbiome and resistome of wastewater in a community sewerage system

Effluents from wastewater treatment plants (WWTPs) have been proposed to act as point sources of antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) in the environment. Hospital sewage may contribute to the spread of ARB and ARGs as it contains the feces and urine of hospitalized patients, who are more frequently colonized with multi-drug resistant bacteria than the general population. However, whether hospital sewage noticeably contributes to the quantity and diversity of ARGs in the general sewerage system has not yet been determined.Here, we employed culture-independent techniques, namely 16S rRNA gene sequencing and nanolitre-scale quantitative PCRs, to assess the role of hospital effluent as a point source of ARGs in the sewerage system, through comparing microbiota composition and levels of ARGs in hospital sewage with WWTP influent with and without hospital sewage.Compared to other sites, hospital sewage was richest in human-associated bacteria and contained the highest relative levels of ARGs. Yet, the relative abundance of ARGs was comparable in the influent of WWTPs with and without hospital sewage, suggesting that hospitals do not contribute importantly to the quantity and diversity of ARGs in the investigated sewerage system.

The importance of lag time extension in determining bacterial resistance to antibiotics

It is widely appreciated that widespread antibiotic resistance has significantly reduced the utility of today's antibiotics. Many antibiotics now fail to cure infectious diseases, although they are classified as effective bactericidal agents based on antibiotic susceptibility tests. Here, via kinetic growth assays, we evaluated the effects of 12 commonly used antibiotics on the lag phase of a range of pure environmental isolates and of sludge bacterial communities with a high diversity. We show that an extended lag phase offers bacteria survival advantages and promotes regrowth upon the removal of antibiotics. By utilizing both lag phase extension and IC50, the killing efficiency of an antibiotic on a strain or a community can be easily revealed. Interestingly, for several strains of relevance to endemic nosocomial infections (e.g. Acinetobacter sp. and Pseudomonas aeruginosa) and the diverse sludge communities, tetracycline and quinolone antibiotics are most likely to be resisted via extended lag phase. This discovery is significant from a clinical point view since underestimation of bacteria resistance can lead to the recurrence of diseases.

Dynamic changes of bacterial community in activated sludge with pressurized aeration in a sequencing batch reactor

This study aimed to investigate the organic removal efficiency and microbial population dynamics in activated sludge with pressurized aeration. The activated sludge was fed with synthetic wastewater composed of simple carbon source to avoid the effect of complex components on microbial communities. The pressurized acclimation process was conducted in a bench-scale sequencing batch reactor (SBR) under 0.3 MPa gage pressure. Another SBR was running in atmospheric environment as a control reactor, with the same operation parameters except for the pressure. Bacterial diversity was investigated by Illumina sequencing technology. The results showed that the total organic carbon removal efficiency of the pressurized reactor was significantly higher, while the mixed liquor suspended solids concentrations were much lower than those of the control reactor. Moderate pressure of 0.3 MPa had little effect on Alpha-diversity of bacterial communities due to the similar running conditions, e.g., feed water, solids retention time (SRT) and the cyclic change of dissolved oxygen (DO) concentrations. Although the relative percentage of the bacterial community changed among samples, there was no major change of predominant bacterial populations between the pressurized group and the control group. Pressurized aeration would have a far-reaching impact on microbial community in activated sludge when treating wastewaters being unfavorable to the dissolution of oxygen.

Impact of wastewater treatment plant discharge on the contamination of river biofilms by pharmaceuticals and antibiotic resistance

Wastewater treatment plants (WWTPs) are one of the main sources of pharmaceutical residue in surface water. Epilithic biofilms were collected downstream from 12 WWTPs of various types and capacities to study the impacts of their discharge through the changes in biofilm composition (compared to a corresponding upstream biofilm) in terms of pharmaceutical concentrations and bacterial community modifications (microbial diversity and resistance integrons). The biofilm is a promising indicator to evaluate the impacts of WWTPs on the surrounding aquatic environment. Indeed, the use of biofilms reveals contamination hot spots. All of the downstream biofilms present significant concentrations (up to 965ng/g) of five to 11 pharmaceuticals (among the 12 analysed). Moreover, the exposition to the discharge point increases the presence of resistance integrons (three to 31 fold for Class 1) and modifies the diversity of the bacterial communities (for example cyanobacteria). The present study confirms that the discharge from WWTPs has an impact on the aquatic environment.

Abundance of antibiotic resistance genes in five municipal wastewater treatment plants in the Monastir Governorate, Tunisia

Antimicrobial resistance is a growing and significant threat to global public health, requiring better understanding of the sources and mechanisms involved in its emergence and spread. We investigated the abundance of antibiotic resistance genes (ARGs) before and after treatment in five wastewater treatment plants (WWTPs) located in different areas of the Monastir Governorate (Tunisia). Three of these WWTPs (Frina, Sahline and Zaouiet) use a conventional activated sludge process as secondary treatment, whereas the WWTP located in Beni Hassen applies an ultraviolet disinfection step after the activated sludge process and the WWTP located in Moknine treats wastewater using naturally aerated lagoons as a secondary treatment process. The abundance of six ARGs (bla_CTX-M, bla_TEM, qnrA, qnrS, sul I and ermB) and the class 1 integron-integrase gene (intI1) were determined by quantitative PCR. All ARGs and the intI1 gene were detected in the wastewater samples, except the bla_CTX-M gene, which was not detected in both influent and effluent samples from Sahline and Beni Hassen WWTPs, and the qnrS gene, which was not detected neither in the WWTP influent in Moknine nor in the WWTP effluent in Beni Hassen. Although the relative concentration of ARGs was generally found to be similar between samples collected before and after the wastewater treatment, the abundance of bla_CTX-M, bla_TEM, and qnrS genes was higher in the effluent of the Frina WWTP which, unlike other WWTPs, not only receives domestic or industrial sewage but also untreated hospital waste. To the best of our knowledge, this study quantified for the first time the abundance of ARGs in different Tunisian WWTPs, and the results agree with previous studies suggesting that conventional wastewater treatment does not efficiently reduce ARGs. Therefore, these findings could be useful to improve the design or operation of WWTPs.

Microbial-based evaluation of foaming events in full-scale wastewater treatment plants by microscopy survey and quantitative image analysis

Activated sludge systems are prone to be affected by foaming occurrences causing the sludge to rise in the reactor and affecting the wastewater treatment plant (WWTP) performance. Nonetheless, there is currently a knowledge gap hindering the development of foaming events prediction tools that may be fulfilled by the quantitative monitoring of AS systems biota and sludge characteristics. As such, the present study focuses on the assessment of foaming events in full-scale WWTPs, by quantitative protozoa, metazoa, filamentous bacteria, and sludge characteristics analysis, further used to enlighten the inner relationships between these parameters. In the current study, a conventional activated sludge system (CAS) and an oxidation ditch (OD) were surveyed throughout a period of 2 and 3 months, respectively, regarding their biota and sludge characteristics. The biota community was monitored by microscopic observation, and a new filamentous bacteria index was developed to quantify their occurrence. Sludge characteristics (aggregated and filamentous biomass contents and aggregate size) were determined by quantitative image analysis (QIA). The obtained data was then processed by principal components analysis (PCA), cross-correlation analysis, and decision trees to assess the foaming occurrences, and enlighten the inner relationships. It was found that such events were best assessed by the combined use of the relative abundance of testate amoeba and nocardioform filamentous index, presenting a 92.9 % success rate for overall foaming events, and 87.5 and 100 %, respectively, for persistent and mild events.

Popular pharmaceutical residues in hospital wastewater: quantification and qualification of degradation products by mass spectroscopy after treatment with membrane bioreactor

The occurrence of drugs in wastewater has been considered an imminent risk to the population, for the treatments used are usually ineffective. The presence of four popular drug residues (metformin, paracetamol, tetracycline, and enalapril) in hospital effluents, by using ultra-fast liquid chromatography tandem mass spectrometry (UFLC-MS/MS) with electrospray (ESI) ionization, and removal/degradation by membrane bioreactor (MBR) system are investigated in this study. For analysis method, all standard calibration curves showed satisfactory linearity (R (2) ≥ 0.993) within a relatively wide range. The recovery was between 70.4 and 105.0 %, and the relative standard deviation (RSD) values were within the ranges of 8.2 and 13.5 %. The effluent samples were collected at the end of the process treated in a bench-scale MBR treatment system and preconcentrated on solid-phase extraction (SPE) cartridges. Following that procedure, the chemical analysis demonstrated that the MBR system was effective in enalapril 94.3 ± 7.63 %, tetracycline 99.4 ± 0.02 %, and paracetamol 98.8 ± 0.86 % removal. However, the polar metformin was less effectively removed (35.4 ± 12.49 %). Moreover, the degradation products were investigated using high-resolution mass spectrometry (HRMS) by quadrupole-time of flight (Q-TOF), which has been indicated a tetracycline metabolite. In order to investigate the environmental impact, the wastewater potential risk was evaluated. The risk quotient (RQ) by measure environmental concentration (MEC) and its predicted no effect concentration (PNEC) ratio (RQ = MEC/PNEC) was between 0.003 (enalapril) to 0.815 (paracetamol). Finally, this work demonstrates that UFLC-MS/MS (ESI-Q) is a sensitive and selective method for drug analysis in wastewater and with ESI-Q-TOF has the accuracy required for determining the degradation products of these compounds. Also, it indicated that membrane bioreactor systems represent a new generation of processes that have proved to outperform conventional treatment showing better effluent quality. The removal capacity studied in this work demonstrates the efficiency of this process.

Survival of Antibiotic Resistant Bacteria and Horizontal Gene Transfer Control Antibiotic Resistance Gene Content in Anaerobic Digesters

Understanding fate of antibiotic resistant bacteria (ARB) vs. their antibiotic resistance genes (ARGs) during wastewater sludge treatment is critical in order to reduce the spread of antibiotic resistance through process optimization. Here, we spiked high concentrations of tetracycline-resistant bacteria, isolated from mesophilic (Iso M1-1-a Pseudomonas sp.) and thermophilic (Iso T10-a Bacillus sp.) anaerobic digested sludge, into batch digesters and monitored their fate by plate counts and quantitative polymerase chain reaction (QPCR) of their corresponding tetracycline ARGs. In batch studies, spiked ARB plate counts returned to baseline (thermophilic) or 1-log above baseline (mesophilic) while levels of the ARG present in the spiked isolate [tet(G)] remained high in mesophilic batch reactors. To compare results under semi-continuous flow conditions with natural influent variation, tet(O), tet(W), and sul1 ARGs, along with the intI1 integrase gene, were monitored over a 9-month period in the raw feed sludge and effluent sludge of lab-scale thermophilic and mesophilic anaerobic digesters. sul1 and intI1 in mesophilic and thermophilic digesters correlated positively (Spearman rho = 0.457-0.829, P < 0.05) with the raw feed sludge. There was no correlation in tet(O) or tet(W) ratios in raw sludge and mesophilic digested sludge or thermophilic digested sludge (Spearman rho = 0.130-0.486, P = 0.075-0.612). However, in the thermophilic digester, the tet(O) and tet(W) ratios remained consistently low over the entire monitoring period. We conclude that the influent sludge microbial composition can influence the ARG content of a digester, apparently as a result of differential survival or death of ARBs or horizontal gene transfer of genes between raw sludge ARBs and the digester microbial community. Notably, mesophilic digestion was more susceptible to ARG intrusion than thermophilic digestion, which may be attributed to a higher rate of ARB survival and/or horizontal gene transfer between raw sludge bacteria and the digester microbial community.

Hospital effluents management: Chemical, physical, microbiological risks and legislation in different countries

Hospital wastewater (HWW) can contain hazardous substances, such as pharmaceutical residues, chemical hazardous substances, pathogens and radioisotopes. Due to these substances, hospital wastewater can represent a chemical, biological and physical risk for public and environmental health. In particular, several studies demonstrate that the main effects of these substances can't be neutralised by wastewater treatment plants (WWTPs). These substances can be found in a wide range of concentrations due to the size of a hospital, the bed density, number of inpatients and outpatients, the number and the type of wards, the number and types of services, the country and the season. Some hazardous substances produced in hospital facilities have a regulatory status and are treated like waste and are disposed of accordingly (i.e., dental amalgam and medications). Legislation is quite homogeneous for these substances in all industrial countries. Problems that have emerged in the last decade concern substances and microorganisms that don't have a regulatory status, such as antibiotic residues, drugs and specific pathogens. At a global level, guidelines exist for treatment methods for these effluents, but legislation in all major industrial countries don't contain limitations on these parameters. Therefore, a monitoring system is necessary for these effluents as well as for substances and pathogens, as these elements can represent a risk to the environment and public health.

Validated predictive modelling of the environmental resistome

Multi-drug-resistant bacteria pose a significant threat to public health. The role of the environment in the overall rise in antibiotic-resistant infections and risk to humans is largely unknown. This study aimed to evaluate drivers of antibiotic-resistance levels across the River Thames catchment, model key biotic, spatial and chemical variables and produce predictive models for future risk assessment. Sediment samples from 13 sites across the River Thames basin were taken at four time points across 2011 and 2012. Samples were analysed for class 1 integron prevalence and enumeration of third-generation cephalosporin-resistant bacteria. Class 1 integron prevalence was validated as a molecular marker of antibiotic resistance; levels of resistance showed significant geospatial and temporal variation. The main explanatory variables of resistance levels at each sample site were the number, proximity, size and type of surrounding wastewater-treatment plants. Model 1 revealed treatment plants accounted for 49.5% of the variance in resistance levels. Other contributing factors were extent of different surrounding land cover types (for example, Neutral Grassland), temporal patterns and prior rainfall; when modelling all variables the resulting model (Model 2) could explain 82.9% of variations in resistance levels in the whole catchment. Chemical analyses correlated with key indicators of treatment plant effluent and a model (Model 3) was generated based on water quality parameters (contaminant and macro- and micro-nutrient levels). Model 2 was beta tested on independent sites and explained over 78% of the variation in integron prevalence showing a significant predictive ability. We believe all models in this study are highly useful tools for informing and prioritising mitigation strategies to reduce the environmental resistome.

Integrons: past, present, and future

Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.

Quantitative and qualitative impact of hospital effluent on dissemination of the integron pool

There is increasing evidence that human activity, and especially the resulting effluent, has a major role in the dissemination of bacterial antibiotic-resistance determinants in the environment. Hospitals are the major antibiotic consumers and thus facilitate the spread of antibiotic resistance. Questions are increasingly being raised about the management of hospital effluents, but their involvement in antibiotic-resistance dissemination has never been assessed. Integrons are a paradigm of genetic transfer between the environmental resistome and both commensal and pathogenic bacteria. In order to assess the impact of hospital activities on antibiotic-resistance dissemination in the environment, we monitored integrons and their gene cassettes in hospital effluents, and their release in the environment. We found that bacterial communities present in a hospital effluent contained a high proportion of integrons. In terms of both their gene cassette diversity and gene cassette arrays, the urban effluent and municipal wastewater treatment plant (WWTP) influent were most similar, whereas the hospital effluent and recirculation sludge exhibited very specific patterns. We found that anthropogenic activities led to the release of abundant integrons and antibiotic-resistance gene cassettes, but we observed no specific impact of hospital activities on the receiving environment. Furthermore, although the WWTP did not reduce the normalized integron copy number, it reduced the diversity of gene cassette arrays contained in the raw wastewater, underlining the effect of the biological treatment on the anthropogenic integron pool arriving at the WWTP.