Molecular analysis for screening human bacterial pathogens in municipal wastewater treatment and reuse

The factors controlling antibiotic resistance genes in different treatment processes of mainstream full-scale wastewater treatment plants

The alteration of antibiotic resistance genes (ARGs) in wastewater has been less studied in wastewater treatment plants (WWTPs), making it difficult to assess ARGs' spreading risk comprehensively. Therefore, this study investigated the distribution and reduction of ARGs in the main process (Anaerobic-Anoxic-Oxic with Membrane Bio-Reactor (A2/O + MBR), Oxidation Ditch with sedimentation (OD), and Cyclic Activated Sludge System (CASS) with sedimentation) and disinfection process (Ultra-violet and Chlorination) of full-scale WWTPs. The wastewater was sampled before and after the different main process and disinfection process; then, the diversity and abundance of ARGs and mobile genetic genes (MGEs, helping the horizontal transfer of ARGs) in wastewater of different treatment stages were determined by a real-time high-throughput quantitative PCR (HT-qPCR) system. It was found that similar influents would result in similar ARGs in wastewater samples, independent of the treatment processes used. The main process could effectively reduce the abundance of ARGs and MGEs by 1.80-2.12 and 1.46-2.18 logarithm units, respectively. The main factors affecting ARGs were mainly wastewater quality index, especially COD, and MGEs like transposase and insertion sequences which were significantly associated with 66 and 48 subtypes of ARGs, respectively. Moreover, disinfection was more effective than the main process in inactivating antibiotic resistance bacteria (ARB), and the removal rate of ARB by disinfection reached 43.53 %-100 %. However, there are still risks of ARB regeneration (up to 4.22 log units) in the effluent of WWTPs. In the future, nutrient removal and disinfection process improvement is necessary to benefit ARG and ARB removal.

Wastewater surveillance beyond COVID-19: a ranking system for communicable disease testing in the tri-county Detroit area, Michigan, USA

Introduction

Throughout the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has been utilized to monitor the disease in the United States through routine national, statewide, and regional monitoring projects. A significant canon of evidence was produced showing that wastewater surveillance is a credible and effective tool for disease monitoring. Hence, the application of wastewater surveillance can extend beyond monitoring SARS-CoV-2 to encompass a diverse range of emerging diseases. This article proposed a ranking system for prioritizing reportable communicable diseases (CDs) in the Tri-County Detroit Area (TCDA), Michigan, for future wastewater surveillance applications at the Great Lakes Water Authority's Water Reclamation Plant (GLWA's WRP).

Methods

The comprehensive CD wastewater surveillance ranking system (CDWSRank) was developed based on 6 binary and 6 quantitative parameters. The final ranking scores of CDs were computed by summing the multiplication products of weighting factors for each parameter, and then were sorted based on decreasing priority. Disease incidence data from 2014 to 2021 were collected for the TCDA. Disease incidence trends in the TCDA were endowed with higher weights, prioritizing the TCDA over the state of Michigan.

Results

Disparities in incidences of CDs were identified between the TCDA and state of Michigan, indicating epidemiological differences. Among 96 ranked CDs, some top ranked CDs did not present relatively high incidences but were prioritized, suggesting that such CDs require significant attention by wastewater surveillance practitioners, despite their relatively low incidences in the geographic area of interest. Appropriate wastewater sample concentration methods are summarized for the application of wastewater surveillance as per viral, bacterial, parasitic, and fungal pathogens.

Discussion

The CDWSRank system is one of the first of its kind to provide an empirical approach to prioritize CDs for wastewater surveillance, specifically in geographies served by centralized wastewater collection in the area of interest. The CDWSRank system provides a methodological tool and critical information that can help public health officials and policymakers allocate resources. It can be used to prioritize disease surveillance efforts and ensure that public health interventions are targeted at the most potentially urgent threats. The CDWSRank system can be easily adopted to geographical locations beyond the TCDA.

Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment

Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.

High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant

In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.

Implications for assessing sludge hygienization: Differential responses of the bacterial community, human pathogenic bacteria, and fecal indicator bacteria to sludge pretreatment-anaerobic digestion

Sewage sludge is the byproduct of wastewater treatment plants, which host enormous diversity of microbes including potential pathogens. However, there are still challenges in assessing hygienization during sludge stabilization due to the complex relationships between dominant microbes and human pathogenic bacteria (HPB), and the accuracy of fecal indicator bacteria (FIB) is also disputed. Here, the responses of the bacterial community, HPB, and FIB to sludge pretreatment-anaerobic digestion (AD) were comprehensively compared using culture-based and 16S rRNA gene molecular analysis methodologies. Bacterial and HPB communities differed in response to sludge pretreatment-AD. AD drove the variation of bacterial community, but led to the convergence of HPB communities in pretreated sludge, indicating the existence of ecological niches that favors HPB dissemination in digesters. The correlation analysis indicated that FIB was suitable for characterizing general pathogen removal instead of showing the real pattern of HPB (i.e., each HPB), implying the need for comprehensive assessment approaches. Moreover, AD-related parameters including pH, total solids destruction, and methane yield were found to play important role in assessing pathogen inactivation given their correlation. This work provides theoretical basis for the selection of appropriate sludge stabilization approaches and future supervision of biosolids biosafety, which finally benefits human health.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Seasonal and Technological Shifts of the WHO Priority Multi-Resistant Pathogens in Municipal Wastewater Treatment Plant and Its Receiving Surface Water: A Case Study

The present study was focused on the identification of multi-resistant bacteria from the WHO priority pathogens list in the samples taken from different stages of the full-scale municipal wastewater treatment plant and receiving water. Additionally, the seasonal variations of the selected multi-resistant pathogens were analyzed in the samples. In order to the aim of the study, the metagenomic DNA from the collected samples was isolated and sequenced. The samples were collected in three campaigns (spring, summer, autumn). Metagenomic DNA was isolated by the commercial kits, according to the manufacturer's instruction. Illumina sequencing system was employed, and the R program was used to metagenomic analysis. It was found that the wastewater samples and receiving water contained the multi-resistant bacteria from the WHO priority pathogens list. The seasonal and technological variations affected the distribution of the pathogens in the wastewater. No effect of the effluent on the pathogens in the receiving water was observed. The results indicated that antibiotic-resistant "priority pathogens" from the WHO list are there in the waste- and receiving water. Technological process and seasons effected their distribution in the environment. Metagenomic analysis can be used as sufficient tool in microbiological and human health risk assessment.

Role of Bacillus inoculation in rice straw composting and bacterial community stability after inoculation: Unite resistance or individual collapse

Bacillus is the classic inoculant in rice straw composting. However, there has been no in-depth study of the mechanism promoting the degradation of lignocellulose and the change of indigenous bacterial communities after Bacillus inoculation. Moreover, the stability of bacterial communities is a significant challenge in achieving the efficacy of inoculation. In this study, the ecological succession and yield-resource acquisition-stress tolerance (Y-A-S) framework were combined with Redundancy analysis (RDA) and changes in relative abundance, Bacillus was found to be a pioneer bacterium that adopts a resource acquisition-stress tolerance strategy. The structural equation model (SEM) revealed that in addition to exerting a degradation effect, Bacillus inoculation could also indirectly affect lignocellulose degradation by changing the bacterial community. Random forest model and network analysis indicated a change in bacterial communities after inoculation, and bacteria with more complex relationships and weaker decomposition ability were key to the stability of bacterial communities.

Use of Electrocoagulation for Treatment of Pharmaceutical Compounds in Water/Wastewater: A Review Exploring Opportunities and Challenges

Increasing dependency on pharmaceutical compounds including antibiotics, analgesics, antidepressants, and other drugs has threatened the environment as well as human health. Their occurrence, transformation, and fate in the environment are causing significant concerns. Several existing treatment technologies are there with their pros and cons for the treatment of pharmaceutical wastewater (PWW). Still, electrocoagulation is considered as the modern and decisive technology for treatment. In the EC process, utilizing electricity (AC/DC) and electrodes, contaminants become coagulated with the metal hydroxide and are separated by co-precipitation. The main mechanism is charge neutralization and adsorption of contaminants on the generated flocs. The range of parameters affects the EC process and is directly related to the removal efficiency and its overall operational cost. This process only could be scaled up on the industrial level if process parameters become optimized and energy consumption is reduced. Unfortunately, the removal mechanism of particular pharmaceuticals and complex physiochemical phenomena involved in this process are not fully understood. For this reason, further research and reviews are required to fill the knowledge gap. This review discusses the use of EC for removing pharmaceuticals and focuses on removal mechanism and process parameters, the cost assessment, and the challenges involved in mitigation.

A Quantitative Metagenomic Sequencing Approach for High-Throughput Gene Quantification and Demonstration with Antibiotic Resistance Genes

Comprehensive microbial risk assessment requires high-throughput quantification of diverse microbial risks in the environment. Current metagenomic next-generation sequencing approaches can achieve high-throughput detection of genes indicative of microbial risks but lack quantitative capabilities. This study developed and tested a quantitative metagenomic next-generation sequencing (qmNGS) approach. Numerous xenobiotic synthetic internal DNA standards were used to determine the sequencing yield (Y_seq) of the qmNGS approach, which can then be used to calculate absolute concentration of target genes in environmental samples based on metagenomic sequencing results. The qmNGS approach exhibited excellent linearity as indicated by a strong linear correlation (r² = 0.98) between spiked and detected concentrations of internal standards. High-throughput capability of the qmNGS approach was demonstrated with artificial Escherichia coli mixtures and cattle manure samples, for which 95 ± 3 and 208 ± 4 types of antibiotic resistance genes (ARGs) were detected and quantified simultaneously. The qmNGS approach was further compared with quantitative real-time PCR (qPCR) and demonstrated comparable levels of accuracy and less variation for the quantification of six target genes (16S, tetO, sulI, tetM, ermB, and qnrS). IMPORTANCE Monitoring and comprehensive assessment of microbial risks in the environment require high-throughput gene quantification. The quantitative metagenomic NGS (qmNGS) approach developed in this study incorporated numerous xenobiotic and synthetic DNA internal standard fragments into metagenomic NGS workflow, which are used to determine a new parameter called sequencing yield that relates sequence base reads to absolute concentration of target genes in the environmental samples. The qmNGS approach demonstrated excellent method linearity and comparable performance as the qPCR approach with high-throughput capability. This new qmNGS approach can achieve high-throughput and accurate gene quantification in environmental samples and has the potential to become a useful tool in monitoring and comprehensively assessing microbial risks in the environment.

Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples

Purpose

Ready-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market.

Methods

The study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3.

Results

Bacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1).

Conclusion

The results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

The behavior of antibiotic-resistance genes and their relationships with the bacterial community and heavy metals during sewage sludge composting

The main contributors to antibiotic resistance genes (ARGs) profiles during the composting process under the addition of biochar (BC) and peat (PT) were not fully explored. This study investigated the influence of BC and PT amendment on ARGs fate, the bacterial community and heavy metals in sewage sludge compost. Compared to control, BC and PT declined the total abundances of ARGs by 17.6% and 43.0% after composting. Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla across the composting process, among which, members of Firmicutes (mainly Bacillaceae) were the potential hosts for multiple ARGs. BC and PT addition declined the abundance of bacterial pathogens such as Bacteroides and Pseudomonas. Besides, the concentrations of copper (Cu), zinc (Zn) and lead (Pb) were less in BC and PT treatments than control on day 40, and these metals displayed significant positive correlations to sul1 and intI1. Furthermore, variation partitioning analysis (VPA) revealed that the bacterial community exhibited the most contribution to the ARG patterns, as much as 34.0%, followed by heavy metals (10.8%) and intI1 gene (1.5%). These results suggested that biochar and peat can reduce the risks of ARGs in sewage sludge mainly by sharping the bacterial composition.

Bacterial community evolution along full-scale municipal wastewater treatment processes

Sewage pollution is a major threat to public health because sewage is always accompanied by pathogens. Generally, wastewater treatment plants (WWTP) receive and treat sewage to control pathogenic risks and improve environmental health. This study investigated the changes in the bacterial community over the course of treatment by a WWTP. Illumina MiSeq high-throughput sequencing was performed to characterize the bacterial communities in the WWTP. This study found that potential pathogens in the WWTP, especially the genera Arcobacter and Acinetobacter, were greatly reduced. In addition, high chemical oxygen demand levels provided excessive growth substrates for the genera Hyphomicrobium and Rhodoplanes, the abundance of which could exceed autotrophic bacteria, increasing the ammonium removal. According to the network analysis, the bacterial assemblage was not randomly arranged in the WWTP, and various defined processes led to higher intra-phylum (such as Proteobacteria) coexistence than expected. Moreover, the metabolic functions of bacterial communities significantly improved in the WWTP compared with the influent. Together, the data in this study emphasize the need to understand the bacterial community of WWTPs better. When analyzing the risks of WWTP drainage systems to the environment and human health, these data should be considered.

Combination of flow cytometry and molecular analysis to monitor the effect of UVC/H2O2 vs UVC/H2O2/Cu-IDS processes on pathogens and antibiotic resistant genes in secondary wastewater effluents

The efficiency of a new Advanced Oxidation Process (AOP), namely the photo Fenton like process UV-C/H₂O₂/IDS-Cu, in removing determinants of antibiotic resistance and pathogenic bacteria was compared to a consolidated AOP (namely UV-C/H₂O₂) in a secondary treated municipal WasteWater (WW). A reductionist experimental laboratory-based approach was applied on real WW and the parameters were collected by an alternative integrated approach using (i) flow cytometry to enumerate bacteria and test for the fitness of the bacterial communities and (ii) molecular analyses to define the community composition (16S rRNA amplicon sequencing) and the abundances of Antibiotic Resistance Genes (ARGs) and of the class 1 integron (intI1 gene) (by quantitative PCR). The same approach was applied also to post-treatment regrowth tests (24 h) to define the potential persistence of the tested parameters. These experiments were performed in both, human pathogens favorable conditions (HPC, in rich medium and 37°C) and in environmental mimicking conditions (EMC, original WW and 20°C). UV-C/H₂O₂/IDS-Cu process resulted to be more effective than the UV-C/H₂O₂in inactivating bacterial cells in the EMC post-treatment regrowth experiments. Both AOPs were efficiently abating potential human pathogenic bacteria and ARGs in the HPC regrowth experiments, although this trend could not be detected in the measurements taken immediately after the disinfection. In comparison with the UV-C/H₂O₂, the UV-C/H₂O₂/IDS-Cu process did not apparently offer significant improvements in the abatement of the tested parameters in the WW effluent but, by evaluating the results of the regrowth experiments it was possible to extrapolate more complex trends, suggesting contrasting efficiencies visible only after a few hours. This study offers a detailed view on the abatement efficiency of microbiological/genetic parameters for the UV-C/H₂O₂/IDS-Cu process, calling for technical adjustments for this very promising technology. At the same time, our results clearly demonstrated the inadequacy of currently applied methodologies in the evaluation of specific parameters (e.g. determinants of antibiotic resistance and pathogenic bacteria) in WW.

Stochastic determination of the spatial variation of potentially pathogenic bacteria communities in a large subtropical river

Understanding the composition and assembly mechanism of waterborne pathogen is essential for preventing the pathogenic infection and protecting the human health. Here, based on 16S rRNA sequencing, we investigated the composition and spatial variation of potentially pathogenic bacteria from different sections of the Pearl River, the most important source of water for human in Southern China. The results showed that the potential pathogen communities consisted of 6 phyla and 64 genera, covering 11 categories of potential pathogens mainly involving animal parasites or symbionts (AniP), human pathogens all (HumPA), and intracellular parasites (IntCelP). Proteobacteria (75.87%) and Chlamydiae (20.56%) were dominant at the phylum level, and Acinetobacter (35.01%) and Roseomonas (8.24%) were dominant at the genus level. Multivariate analysis showed that the potential pathogenic bacterial community was significantly different among the four sections in the Pearl River. Both physicochemical factors (e.g., NO₃-N, and suspended solids) and land use (e.g., urban land and forest) significantly shaped the pathogen community structure. However, spatial effects contributed more to the variation of pathogen community based on variation partitioning and path analysis. Null model based normalized stochasticity ratio analysis further indicated that the stochastic process rather than deterministic process dominated the assembly mechanisms by controlling the spatial patterns of potential pathogens. In conclusion, high-throughput sequencing shows great potential for monitoring the potential pathogens, and provided more comprehensive information on the potentially pathogenic community. Our study highlighted the importance of considering the influences of dispersal-related processes in future risk assessments for the prevention and control of pathogenic bacteria.

Deep-amplicon sequencing (DAS) analysis to determine the presence of pathogenic Helicobacter species in wastewater reused for irrigation

Wastewater has become one of the most important and least expensive water for the agriculture sector, as well as an alternative to the overexploitation of water resources. However, inappropriate treatment before its reuse can result in a negative impact on the environment, such as the presence of pathogens. This poses an increased risk for environmental safety, which can subsequently lead to an increased risk for human health. Among all the emerging wastewater pathogens, bacteria of the genus Helicobacter are some of the most disturbing ones, since they are directly related to gastric illness and hepatobiliary and gastric cancer. Therefore, the aim of this study was to determine the presence of potentially pathogenic Helicobacter spp. in treated wastewater intended for irrigation. We used a next generation sequencing approach, based on Illumina sequencing in combination with culture and other molecular techniques (qPCR, FISH and DVC-FISH), to analyze 16 wastewater samples, with and without an enrichment step. By culture, one of the direct samples was positive for H. pylori. FISH and DVC-FISH techniques allowed for detecting viable Helicobacter spp., including H. pylori, in seven out of eight samples of wastewater from the tertiary effluents, while qPCR analysis yielded only three positive results. When wastewater microbiome was analyzed, Helicobacter genus was detected in 7 samples. The different molecular techniques used in the present study provided evidence, for the first time, of the presence of species belonging to the genus Helicobacter such as H. pylori, H. hepaticus, H. pullorum and H. suis in wastewater samples, even after disinfection treatment.

Characteristics of submicron aerosols produced during aeration in wastewater treatment

Submicron aerosols (SAs) emitted during wastewater treatment may harm the human circulation system, respiratory cells, and deep lungs. Despite this threat, SAs remain poorly understood. In this study, a laboratory simulation aerosol generator was manufactured, and the particle number size distributions, aerosol liquid water content (ALWC), and chemical and microbial composition of SAs from aeration were analyzed. Under stable aeration conditions, the unimodal SA size distribution ranged from 68 to 350 nm. The ALWC of peak size (170 nm) was 11-21 μg/m³. Na was the dominant major element in SAs with the concentration of 5.61 μg/m³. Total organic carbon accounted for 97% of the total carbon in the SAs. Arcobacter, Methanobrevibacter, and Fusarium were the dominant SA bacteria, archaea, and fungi, respectively, and a number of viruses were also detected. Thirty-two antibiotic resistant genes, and virulence factors of which 23% were offensive virulence factors, were detected in the SAs. The results predicted that 2% of the genes in SAs were directly related to human health. Thus, SAs may pose disproportionately high risks to human health.

Monitoring Opportunistic Pathogens in Domestic Wastewater from a Pilot-Scale Anaerobic Biofilm Reactor to Reuse in Agricultural Irrigation

Wastewater reuse for agricultural irrigation in many developing countries is an increasingly common practice. Regular monitoring of indicators can help to identify potential health risks; therefore, there is an urgent need to understand the presence and abundance of opportunistic pathogens in wastewater, as well as plant phyllosphere and rhizosphere. In this study, an anaerobic biofilm reactor (ABR) was developed to treat rural domestic wastewater; the performance of pollutants removal and pathogenic bacteria elimination were investigated. Additionally, we also assessed the physicochemical and microbiological profiles of soil and lettuces after wastewater irrigation. Aeromonas hydrophila, Arcobacter sp., Bacillus cereus, Bacteroides sp., Escherichia coli, Legionella sp., and Mycobacterium sp. were monitored in the irrigation water, as well as in the phyllosphere and rhizosphere of lettuces. Pathogens like B. cereus, Legionella sp. and Mycobacterium sp. were present in treated effluent with relatively high concentrations, and the levels of A. hydrophila, Arcobacter sp., and E. coli were higher in the phyllosphere. The physicochemical properties of soil and lettuce did not vary significantly. These data indicated that treated wastewater irrigation across a short time period may not alter the soil and crop properties, while the pathogens present in the wastewater may transfer to soil and plant, posing risks to human health.

Diversity and abundance of bacterial pathogens in urban rivers impacted by domestic sewage

In developing countries, many urban rivers are suffering from heavy contamination by untreated sewage, which implies great microbial risks. However, information regarding the bacterial pathogen diversity and distribution in urban rivers is highly limited. In this study, 41 water samples of fifteen rivers and eight samples from two sewage treatment plants in Changzhou City of Yangtze River Delta were sampled. Next-generation sequencing and a self-built reference pathogen database were used to investigate the diversity of enteric and environmental pathogens. The results indicated that the studied urban rivers were harboring diverse potential pathogen species, which primarily included enteric pathogens in Arcobacter and Bacteroides, and environmental pathogens in Acinetobacter, Aeromonas and Pseudomonas. Quantification of twelve pathogens/indicators of interest by qPCR showed that Escherichia coli, Enterococcus faecalis, Campylobacter jejuni, Arcobacter cryaerophilus, Acinetobacter johnsonii, Acinetobacter lwoffii and Aeromonas spp. were abundant, with median values ranging from 3.30 to 5.85 log₁₀ copies/100 mL, while Salmonella, Legionella pheumophila, Mycobacterium avium, Pseudomonas aeruginosa and Staphylococcus aureus were infrequently quantified. The pollution of nutrients and human intestinal microorganisms indicated by specific markers were found to be prevalent but with different levels in the rivers. The correlation analyses revealed that the diversity (p < 0.01) and concentrations (p < 0.05) of the enteric pathogens highly correlated to the human fecal marker abundances, which indicated that the enteric pathogens in the urban rivers were likely to have originated from domestic sewage. The environmental pathogens, which are different from the enteric ones, showed various distribution patterns, and some of them were more abundant in the rivers of rich nutrient. Our findings provide a comprehensive understanding of the bacterial pathogen distribution and influencing factors in urban rivers that are impacted by domestic sewage, thereby establishing the foundation for urban water management.

Detecting antibiotic resistance genes and human potential pathogenic Bacteria in fishmeal by culture-independent method

Fishmeal is a fundamental ingredient of feedstuffs and is used globally in aquaculture. However, there are few data on the antibiotic resistance genes (ARGs) and human pathogenic bacteria in fishmeal and little understanding of the potential risks of fishmeal application in mariculture systems. Here, we investigated the high-throughput profiles of ARGs and human potential pathogenic bacteria (HPPB) in representative fishmeals (n = 5) and the potential impact of fishmeal on mariculture sediments. ARGs were quantified with microbial DNA quantitative PCR arrays and HPPB were analyzed with Illumina sequencing of 16S rRNA genes. The impact of the fishmeal on the aquaculture sediments was assessed in a microcosm study. Twenty-four unique ARGs (3-14 per sample) and 25 HPPB species were detected in the fishmeal samples. The most prevalent ARGs were fluoroquinolone resistance genes. The overall abundance of HPPB was 5.0-25.5%, and the HPPB species were dominated by Vibrio parahaemolyticus, Clostridium novyi, and Escherichia coli. In the mariculture microcosm sediment, fishmeal significantly increased the normalized abundance of the class I integrase gene (25.4-fold), which plays an important role in the dissemination of ARGs. Dosing with fishmeal also contributed to increases in a resident sulfanilamide resistance gene (sulI gene) and the emergence of a macrolide resistance gene (ermB gene) in the sediment. These findings demonstrated that fishmeal itself is an underestimated reservoir and source of ARGs and HPPBs, and that the application of fishmeal facilitates the dissemination of ARGs in aquaculture sediments. Our results extend our knowledge of the ARGs and HPPB within fishmeal and may provide a feasible and effective approach to the detection of ARGs and HPPB in fishmeal during food safety inspection. Graphical abstract ᅟ.

A culture-dependent and metagenomic approach of household drinking water from the source to point of use in a developing country

Rural households in developing countries rely on communal water supplies and household water frequently becomes contaminated following its collection, transportation and during its storage. Using culture-dependent and -independent techniques, we examined the changes in microbial water quality between communal tap water and household water storage in a rural area of Cameroon, Africa. The culturable fecal indicator bacteria (FIB) were used to assess the potential health risks associated with different household water storage conditions (e.g., type of container and open vs. closed container) and interventions (e.g., water storage days, cleaned on the last day of use, and hygiene practices). Only the amount of days the water was stored significantly differed (p-value < 0.05), which showed that potential health risks increased when water was stored for more than 3 days. The higher abundance of molecular FIB in biofilm than household water suggested that omnipresent biofilm in household water could potential health risk. The high-throughput sequencing revealed that the most abundant phylum was Proteobacteria, followed by Actinobacteria and Bacteroidetes in both the water and the biofilm samples. Bacterial genera seen in biofilm bacteria, such as Pseudomonas, Acinetobacter and Comamonas. Acinetobacter, Chryseobacterium, Stenotrophomonas and Corynebacterium, were relatively more abundant in the biofilm than in the water. Potential bacterial pathogens including Acinetobacter baumannii, Citrobacter freundii, Stenotrophomonas maltophilia and Haemophilus influenza, were detected in household water and biofilm. The microbial quality might be affected by water-storage time and households repeatedly using the same water storage containers without proper sanitization, triggering microbial regrowth and biofilm formation on water containers. Higher bacterial diversity and potentially pathogenic bacteria found in the biofilm samples of a household water supply are unhealthy for the house's inhabitants. It is important to develop interventions aimed at preventing the formation of these dangerous biofilms in a communal water supply.

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination

State of art metagenomics were used to investigate the microbial population, antibiotic resistance genes and plasmids of medical interest in wastewater used for urban agriculture in Ouagadougou (Burkina Faso). Wastewater samples were collected from three canals near agricultural fields in three neighbourhoods. Assessment of microbial population diversity revealed different microbial patterns among the different samples. Sequencing reads from the wastewaters revealed different functional specializations of microbial communities, with the predominance of carbohydrates and proteins metabolism functions. Eleven pathogen-specific and 56 orthologous virulence factor genes were detected in the wastewater samples. These virulence factors are usually found in human pathogens that cause gastroenteritis and/or diarrhoea. A wide range of antibiotic resistance genes was identified; 81 are transmissible by mobile genetic elements. These included seven different extended spectrum β-lactamase genes encoding synthesis of four enzyme families, including two metallo-β-lactamases (bla_AIM-1 and bla_GES-21). Ten different incompatibility groups of Enterobacteriaceae plasmid replicons (ColE, FIB, FIC, FII, P, Q, R, U, Y, and A/C), and 30 plasmid replicon types from Gram-positive bacteria. All are implicated in the wide distribution of antibiotic resistance genes. We conclude that wastewater used for urban agriculture in the city represents a high risk for spreading bacteria and antimicrobial resistance among humans and animals.

Variation of bacterioplankton community along an urban river impacted by touristic city: With a focus on pathogen

Bacterioplankton communities play a critical role in ecological processes in river systems, and shifts of their composition may impact microbial levels and raise public health concerns. The aim of this study was to comprehensively analyze the essential factors influencing bacterioplankton community, along with pathogen, and to estimate the health risk caused by the pathogens downstream of the Liushahe River, which is located in the famous touristic city Xishuangbanna. Results showed that wastewater treatment plants (WWTPs) and a subtropical recreational park impacted the bacterioplankton community and pathogen population, and potential pathogen identification demonstrated that 76 of 145 reference genera were present in the river. Moreover, the bacterioplankton community and pathogen were differently impacted by environmental gradients, and SRP, NO₂ and pH were main factors influencing bacterioplankton community while pathogen population was highly correlated with temperature and turbidity. In addition, it is noted that the pathogen population was dominated by bacterioplankton community and this might because the capacity of resistance invasion pathogen was determined by of bacterioplankton community diversity. Therefore, bacterioplankton community diversity can be used to control and predict the amount of pathogens. Quantitative microbial risk assessment (QMRA) also revealed that the infection risks of Escherichia coli (E. coli), Mycobacterium avium (M. avium), and Pseudomonas aeruginosa (P. aeruginosa) during five recreational activities, especially water-based activities in the touristic city, were greater than that in natural areas and mostly exceeded the U.S. EPA risk limit for recreational activities. Our study offered the first insight into the potential relationship between the bacterioplankton community and bacterial pathogens within a touristic river.

Characterization and source analysis of indoor/outdoor culturable airborne bacteria in a municipal wastewater treatment plant

The potential health risks of airborne bacteria emission from a wastewater treatment process have been concerned. However, few studies have investigated the differences in community structure between indoor and outdoor bacteria. In this work, the characterization of airborne bacteria was studied in a municipal wastewater treatment plant in Beijing, China. Two indoor (i.e., fine screen room and sludge dewatering house) and two outdoor (i.e., aeration tank and control site) sampling sites were selected. An Andersen six-stage impactor was used for collecting culturable airborne bacteria in the air, and Illumina MiSeq sequencing was conducted to track the emission source of the culturable airborne bacteria. The results indicate that, compared with the outdoor aeration tank site, the concentrations of culturable airborne bacteria in the indoor fine screen room with poor ventilation were more than ten times higher and the particle size was about twice as large. The community structures of indoor and outdoor culturable airborne bacteria were obviously different. Enterobacteriaceae and opportunistic pathogens were detected in indoor culturable airborne bacteria, with wastewater and sludge dewatering machine identified as the primary sources. Conversely, Enterobacteriaceae and opportunistic pathogens were not detected in outdoor culturable airborne bacteria. Outdoor high wind speed might have resulted in rapid dilution and mixing of culturable airborne bacteria generated from the aeration tank with the ambient air. The results of the present research suggest that covering pollution sources, increasing ventilation rates, and using protective measures for personnel should be implemented to decrease the exposure risk to indoor culturable airborne bacteria.

Multiplex PCR coupled with direct amplicon sequencing for simultaneous detection of numerous waterborne pathogens

The current water quality monitoring and regulation approaches use fecal indicator bacteria (FIB) to indirectly assess health risks from fecal pathogens. Direct detection of waterborne pathogens is expected to provide more accurate and comprehensive risk assessment, which however has been hindered by the lack of methods for simultaneous detection of the numerous waterborne pathogens. This study aimed to develop a mPCR-NGS approach that uses the high sequencing depth of NGS and sequence-based detection to significantly increase the multiplex level of mPCR for direct pathogen detection in water. Individual PCR primers were designed for 16 target marker genes of nine different bacterial pathogens, and an optimal combination of primers with least primer complementarities was identified for the multiplex setting. Using an artificial tester sample, the mPCR system was optimized for annealing temperature and primer concentration, and bioinformatic procedures were developed to directly detect the target marker gene amplicons in NGS sequence reads, which showed simultaneous detection of 14 different target genes in one reaction. The effectiveness of the developed mPCR-NGS approach was subsequently demonstrated on DNA extracts from stream water samples and their counterparts that were spiked with various target pathogen DNA, and all target genes spiked into the environmental water samples were successfully detected. Several key issues for further improving the mPCR-NGS approach were also identified and discussed.

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater

This study aimed to investigate the bacterial communities and antibiotic resistance genes (ARGs) in 16 wastewater treatment plants (WWTPs) treating municipal, industrial and mixed wastewater. Wastewater types showed obvious effects on bacterial communities and functions. Nitrosomonas, Nitrospira, Hyphomicrobium and Accumulibacter were the main functional genera. Mycobacterium was the dominant potential pathogens. A total of 69 ARGs were obtained, and the dominant ARGs subtypes were similar in different WWTPs. Efflux pumps were the most common resistance mechanisms. Copper and zinc resistance genes were the main metal resistance genes (MRGs). Wastewater types affected the distributions of ARGs and MRGs, and they were more similar in industrial and mixed wastewater. The co-occurrence of ARGs existed within or across ARG types, and they were also positively linked to MRGs, some functional and pathogenic genera or environmental factors. This study furthers the understanding of interactions between bacterial communities, ARGs and MRGs in different WWTPs.

Soil types influence the fate of antibiotic-resistant bacteria and antibiotic resistance genes following the land application of sludge composts

Sewage sludge was generally considered a significant reservoir of antibiotic resistance genes (ARGs) and could enter agricultural systems as fertilizer after composting. Soil types and the discrepancy of sludge composts could have influenced the fate of antibiotic-resistant bacteria (ARB) following the land application of sludge composts, which deserved to be clarified. Thus, the fate of ARB and ARGs following the land application of three types of sludge composts (A, B, and C) to three different soils (red soil, loess, and black soil) was investigated. The results showed that tetX, which was enriched the most during composting, did not affect the soil resistome, whereas tetG did. Soil types influenced the dynamics of ARB and ARGs significantly, whereas no significant difference was observed among compost types. The advantage of reducing ARGs during the composting process in compost B did not extend to land application. Land application of composts influenced the microbial community significantly at the early stage, but the microbial community returned to the control pattern gradually. Changes in the microbial community contributed more to the dynamics of ARGs in red and black soil compared with other factors, including co-selection from heavy metals, horizontal gene transfer, biomass and environmental factors, whereas horizontal gene transfer, reflected by intI1 levels, contributed the most in loess.

Abundances and profiles of antibiotic resistance genes as well as co-occurrences with human bacterial pathogens in ship ballast tank sediments from a shipyard in Jiangsu Province, China

Ship ballasting operations may transfer harmful aquatic organisms across global ocean. This study aims to reveal the occurrences and abundances of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in ballast tank sediments. Nine samples were collected and respectively analyzed by real-time quantitative PCR and high-throughput sequencing technologies. Ten ARGs (aadA1, blaCTX-M, blaTEM, ermB, mefA, strB, sul1, sul2, tetM, and tetQ) and the Class-I integron gene (intI1) were highly prevalent (10⁵-10⁹ gene copies/g) in ballast tank sediments. The sul1 was the most abundant ARG with the concentration of 10⁸-10⁹ copies/g and intI1 was much more abundant than the ARGs in ballast tank sediments. The strong positive correlations between intI1 and ARGs (blaCTX-M, sul1, sul2 and tetM) indicated the potential spread of ARGs via horizontal gene transfer. In ballast tank sediments, 44 bacterial species were identified as HBPs and accounted for 0.13-21.46% of the total bacterial population although the three indicator pathogenic microbes (Vibrio cholerae, Escherichia coli, and Enterococci) proposed by the International Maritime Organization were not detected. Pseudomonas pseudoalcaligenes, Enterococcus hirae, Shigella sonnei and Bacillus anthracis were the dominant pathogens in ballast tank sediments. Zn and P in sediments had positive effects on the ARGs. Network analysis results indicated that sul1 and sul2 genes existed in several bacterial pathogens. Ballast tank sediments could be regarded as a carrier for the migration of ARGs. It is important to manage ballast tank sediments reasonably in order to prevent the dissemination of ARGs and bacterial pathogens.

Potential human pathogenic bacteria in five hot springs in Eritrea revealed by next generation sequencing

Human pathogens can survive and grow in hot springs. For water quality assessment, Escherichia coli or Enterococci are the main thermotolerant enteric bacteria commonly used to estimate the load of pathogenic bacteria in water. However, most of the environmental bacteria are unculturable thus culture methods may cause bias in detection of most pathogens. Illumina sequencing can provide a more comprehensive and accurate insight into environmental bacterial pathogens, which can be used to develop better risk assessment methods and promote public health awareness. In this study, high-throughput Illumina sequencing was used to identify bacterial pathogens from five hot springs; Maiwooi, Akwar, Garbanabra, Elegedi and Gelti, in Eritrea. Water samples were collected from the five hot springs. Total community DNA was extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4—V7) of the extracted DNA was amplified and library construction done according to Illumina sequencing protocol. The sequence reads (length >200 bp) from Illumina sequencing libraries ranged from 22,091 sequences in the wet sediment sample from Garbanabra to 155,789 sequences in the mat sample from Elegedi. Taxonomy was assigned to each OTU using BLASTn against a curated database derived from GreenGenes, RDPII, SILVA SSU Reference 119 and NCBI. The proportion of potential pathogens from the water samples was highest in Maiwooi (17.8%), followed by Gelti (16.7%), Akwar (13.6%) and Garbanabra (10.9%). Although the numbers of DNA sequence reads from Illumina sequencing were very high for the Elegedi (104,328), corresponding proportion of potential pathogens very low (3.6%). Most of the potential pathogenic bacterial sequences identified were from Proteobacteria and Firmicutes. Legionella and Clostridium were the most common detected genera with different species. Most of the potential pathogens were detected from the water samples. However, sequences belonging to Clostridium were observed more abundantly from the mat samples. This study employed high-throughput sequencing technologies to determine the presence of pathogenic bacteria in the five hot springs in Eritrea.

Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: Implications for water quality management

The risk of pathogen exposure in recreational water is a concern worldwide. Moreover, suspended particles, as ideal shelters for pathogens, in these waters also need attention. However, the risk caused by the pathogen-particle attachment is largely unknown. Accordingly, water samples in three recreational lakes in Beijing were collected and separated into free-floating (FL, 0.22-5μm) and particle-attached (PA, >5μm) fractions. Next-generation sequencing (NGS) was employed to determine the diversity of genera containing pathogens, and quantitative PCR (qPCR) was used to assess the presence of genes from Escherichia coli (uidA), Salmonella enterica (invA), Aeromonas spp. (aerA), Mycobacterium avium (16S) and Pseudomonas aeruginosa (oaa). The NGS results showed stable pathogen genera composition distinctions between the PA and FL fractions. Some genera, such as Aeromonas and Mycobacterium, exhibited higher abundances in the PA fractions. qPCR revealed that most of the gene concentrations were higher within particles than were FL fractions. Some gene levels showed correlations with the particle concentrations and lake nutrient levels. Further quantitative microbial risk assessment (QMRA) of selected strains (S. enterica and M. avium) indicated a higher health risk during secondary contact activities in lakes with more nutrients and particles. We concluded that suspended particles (mainly composed of algae) in urban recreational water might influence the pathogen distribution and could serve as reservoirs for pathogen contamination, with important management implications.

Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico

Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater affects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specific adaptations to drought and sodium content in specific land use systems. Predicted functionality profiles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles differed among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identified potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profiles provided extensive understanding of the short-term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands.

Inhibition of anaerobic digestion processes: Applications of molecular tools

Inhibition of anaerobic digestion (AD) due to perturbation caused by substrate composition and/or operating conditions can significantly reduce performance. Such perturbations could be limited by elucidating microbial community response to inhibitors and devising strategies to increase community resilience. To this end, advanced molecular methods are increasingly being applied to study the AD microbiome, a diverse community of microbial populations with complex interactions. This literature review of AD inhibition studies indicates that inhibitory concentrations are highly variable, likely stemming from differences in community structure or activity profile and previous exposure to inhibitors. More recent molecular methods such as 'omics' tools, substrate mapping, and real-time sequencing are helping to unravel the complexity of AD inhibition by elucidating physiological and ecological significance of key microbial populations. The AD community must strive towards developing predictive abilities to avoid system failure (e.g., real-time tracking of an indicator species) to improve resilience of AD systems.

Elucidating microbial community adaptation to anaerobic co-digestion of fats, oils, and grease and food waste

Despite growing interest in co-digestion and demonstrated process improvements (e.g., enhanced stability and biogas production), few studies have evaluated how co-digestion impacts the anaerobic digestion (AD) microbiome. Three sequential bench-scale respirometry experiments were conducted at thermophilic temperature (50 °C) with various combinations of primary sludge (PS); thickened waste activated sludge (TWAS); fats, oils, and grease (FOG); and food waste (FW). Two additional runs were then performed to evaluate microbial inhibition at higher organic fractions of FOG (30-60% volatile solids loading (VSL; v/v)). Co-digestion of PS, TWAS, FOG, and FW resulted in a 26% increase in methane production relative to digestion of PS and TWAS. A substantial lag time was observed in biogas production for vessels with FOG addition that decreased by more than half in later runs, likely due to adaptation of the microbial community. 30% FOG with 10% FW showed the highest increase in methane production, increasing 53% compared to digestion of PS and TWAS. FOG addition above 50% VSL was found to be inhibitory with and without FW addition and resulted in volatile fatty acid (VFA) accumulation. Methane production was linked with high relative activity and abundance of syntrophic fatty-acid oxidizers alongside hydrogenotrophic methanogens, signaling the importance of interspecies interactions in AD. Specifically, relative activity of Syntrophomonas was significantly correlated with methane production. Further, methane production increased over subsequent runs along with methyl coenzyme M reductase (mcrA) gene expression, a functional gene in methanogens, suggesting temporal adaptation of the microbial community to co-digestion substrate mixtures. The study demonstrated the benefits of co-digestion in terms of performance enhancement and enrichment of key active microbial populations.

Profiles and drivers of antibiotic resistance genes distribution in one-stage and two-stage sludge anaerobic digestion based on microwave-H2O2 pretreatment

Three anaerobic digestion (AD) processes of waste activated sludge (WAS) were established including the control (mono-WAS), one-stage AD and two-stage AD along with microwave-H₂O₂ pre-treatment (MW-H₂O₂) to investigate the profiles and drivers of antibiotic resistance genes (ARGs) distribution concerning co-selection from heavy metals, intI1 and microbial community through qPCR and high-throughput sequencing method. Results showed that MW-H₂O₂ could reduce the absolute gene copies of all ARGs while increased the relative abundance of most ARGs. After subsequent AD, both total ARGs quantities and relative abundance were enriched while two-stage AD showed some advantages over ARGs abundance reduction. Besides, AD was more effective on the potential pathogens reduction than MW-H₂O₂. AD could reduce the role of intI1 on the spread of ARGs, while mantel test and procrustes analysis indicated that the variation of ARGs abundance was closely associated with the discrepancy of bacterial community.

Chemical fingerprinting of saline water intrusion into sewage lines

High salinity in sewage sludge can affect not only the operation of wastewater treatment plants (WWTPs) but also the quality of treated water generated, thereby limiting its downstream reuse. Using data on geochemical parameters, both for the central WWTP in Abu Dhabi, UAE, and literature values for potential regional saline water sources (e.g., shallow groundwater and regional Arabian Gulf seawater), a variety of chemical fingerprinting diagnostic ratios were calculated and plotted in order to determine the source of salinity in the municipal sewage. Data were compared with data from a regional WWTP that was not impacted by salinity. Monitoring data demonstrated persistently elevated levels of salinity in the municipal wastewater arriving at the central WWTP from the city. Dilution/concentration analysis using a conductivity vs. chloride plot showed both potential sources, i.e. Arabian Gulf seawater and coastal hypersaline groundwater, as feasible sources of wastewater salinization. Further diagnostic analysis using a Panno Plot indicated that coastal groundwater was the only likely source of salinization of municipal sewage. Additional confirmation of the identity of the source and the extent of mixing using different lines of evidence like stable isotope ratios is recommended for future study.

Fishmeal Application Induces Antibiotic Resistance Gene Propagation in Mariculture Sediment

Antibiotic resistance genes (ARGs) are globally prevalent in mariculture sediment, and their presence is an issue of concern in the context of antibiotic use. Although large amounts of fishmeal have been released into the sediment, the role of fishmeal in ARG dissemination remains unclear. In this study, high-throughput ARG profiles in representative fishmeal products and the impact of fishmeal on the sediment resistome were investigated. A total of 132 unique ARGs and 4 mobile genetic elements (MGEs) were detected in five fishmeal products. ARG abundance and diversity in the mariculture microcosm sediment were significantly increased by the addition of fishmeal, and trends in ARG patterns correlated with the resident bacterial community in sediment (P < 0.05). After DNase treatment of fishmeal removed 84.3% of total ARGs, the remaining nutrients in fishmeal increased the relative abundance but not the diversity of ARGs in microcosm sediment. Our study has revealed for the first time that fishmeal itself is a major reservoir for ARGs, and the shift in the bacterial community induced by the nutrients in fishmeal is the main driver shaping the resistome in mariculture microcosm sediment. Our findings caution against the previously unperceived risk of ARG propagation in fishmeal-receiving ecosystems.

Evaluation of bacterial pathogen diversity, abundance and health risks in urban recreational water by amplicon next-generation sequencing and quantitative PCR

The microbial quality of urban recreational water is of great concern to public health. The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks. To assess the levels of bacterial pathogens and health risks in urban recreational water, we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year. The pathogen diversity revealed by 16S rRNA gene targeted next-generation sequencing (NGS) showed that 16 of 40 genera and 13 of 76 reference species were present. The most abundant species were Acinetobacter johnsonii, Mycobacterium avium and Aeromonas spp. Quantitative polymerase chain reaction (qPCR) of Escherichia coli (uidA), Aeromonas (aerA), M. avium (16S rRNA), Pseudomonas aeruginosa (oaa) and Salmonella (invA) showed that the aerA genes were the most abundant, occurring in all samples with concentrations of 10^4-6 genome copies/100mL, followed by oaa, invA and M. avium. In total, 34.8% of the samples harbored all genes, indicating the prevalence of these pathogens in this recreational waterbody. Based on the qPCR results, a quantitative microbial risk assessment (QMRA) showed that the annual infection risks of Salmonella, M. avium and P. aeruginosa in five activities were mostly greater than the U.S. EPA risk limit for recreational contacts, and children playing with water may be exposed to the greatest infection risk. Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and qPCR.

Health risks associated with the pharmaceuticals in wastewater

The overwhelming population growth in recent decades and water crisis along with limited and uneven geographical distribution of fresh water resources is a growing challenge for the economic and human development. Wastewater reclamation and use could be an alternative for intact water sources and a promising solution to water scarcity and unequal distribution. However, wastewater is a double-edged resource both as an accessible water source for food production and human usage and concurrently may carry uncharacterized content with unknown toxicological profile causing acute or long-term health risks. Pharmaceuticals, cosmeceuticals, nanomaterials and their chemical decomposition derivatives found in wastewater are not well known in many cases. Their unknown toxicity, teratogenicity and carcinogenicity profile associated with lack of monitoring and control measures impose a significant hazard risk on the public health. This paper reviews the evidence on the health risks associated with the wastewater use for irrigated food production and the imposed risk on the end consumers mainly from pharmaceutical industry and related research facilities. Then, we suggest an applied framework for planning and policy-making to mitigate the health risks and optimally employ reclaimed wastewater for human purposes.

Elucidation of major contributors involved in nitrogen removal and transcription level of nitrogen-cycling genes in activated sludge from WWTPs

We investigated nitrogen-cycle bacterial communities in activated sludge from 8 municipal wastewater treatment plants (WWTPs). Redundancy analyses (RDA) showed that temperature was the most significant driving force in shaping microbial community structure, followed by influent NH₄⁺ and total nitrogen (TN). The diversity of ammonia oxidizing and nitrite reducing bacteria were investigated by the construction of amoA, nirS and nirK gene clone libraries. Phylogenetic analysis indicated that Thauera and Mesorhizobium were the predominant nitrite reducing bacteria, and Nitrosomonas was the only detected ammonia oxidizing bacteria in all samples. Quantification of transcription level of nirS and nirK genes indicated that nirS-type nitrite reducing bacteria played the dominant roles in nitrite reduction process. Transcription level of nirS gene positively correlated with influent NH₄⁺ and TN significantly, whereas inversely linked with hydraulic retention time. Temperature had a strong positive correlation to transcription level of amoA gene. Overall, this study deepened our understanding of the major types of ammonia oxidizing and nitrite reducing bacteria in activated sludge of municipal WWTPs. The relationship between transcription level of nitrogen-cycle genes and operational or environmental variables of WWTPs revealed in this work could provide guidance for optimization of operating parameters and improving the performance of nitrogen removal.

Mycobacteria in Municipal Wastewater Treatment and Reuse: Microbial Diversity for Screening the Occurrence of Clinically and Environmentally Relevant Species in Arid Regions

With accumulating evidence of pulmonary infection via aerosolized nontuberculous mycobacteria (NTM), it is important to characterize their persistence in wastewater treatment, especially in arid regions where treated municipal wastewater is extensively reused. To achieve this goal, microbial diversity of the genus Mycobacterium was screened for clinically and environmentally relevant species using pyrosequencing. Analysis of the postdisinfected treated wastewater showed the presence of clinically relevant slow growers like M. kansasii, M. szulgai, M. gordonae, and M. asiaticum; however, in these samples, rapid growers like M. mageritense occurred at much higher relative abundance. M. asiaticum and M. mageritense have been isolated in pulmonary samples from NTM-infected patients in the region. Diversity analysis along the treatment train found environmentally relevant organisms like M. poriferae and M. insubricum to increase in relative abundance across the chlorine disinfection step. A comparison to qPCR results across the chlorine disinfection step saw no significant change in slow grower counts at CT disinfection values ≤90 mg·min/L; only an increase to 180 mg·min/L in late May brought slow growers to below detection levels. The study confirms the occurrence of clinically and environmentally relevant mycobacteria in treated municipal wastewater, suggesting the need for vigilant monitoring of treated wastewater quality and disinfection effectiveness prior to reuse.

Measuring biomarkers in wastewater as a new source of epidemiological information: Current state and future perspectives

The information obtained from the chemical analysis of specific human excretion products (biomarkers) in urban wastewater can be used to estimate the exposure or consumption of the population under investigation to a defined substance. A proper biomarker can provide relevant information about lifestyle habits, health and wellbeing, but its selection is not an easy task as it should fulfil several specific requirements in order to be successfully employed. This paper aims to summarize the current knowledge related to the most relevant biomarkers used so far. In addition, some potential wastewater biomarkers that could be used for future applications were evaluated. For this purpose, representative chemical classes have been chosen and grouped in four main categories: (i) those that provide estimates of lifestyle factors and substance use, (ii) those used to estimate the exposure to toxicants present in the environment and food, (iii) those that have the potential to provide information about public health and illness and (iv) those used to estimate the population size. To facilitate the evaluation of the eligibility of a compound as a biomarker, information, when available, on stability in urine and wastewater and pharmacokinetic data (i.e. metabolism and urinary excretion profile) has been reviewed. Finally, several needs and recommendations for future research are proposed.

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry

Rapid detection of target bacteria is crucial to provide a safe food supply and to prevent foodborne diseases. Herein, we present an optical biosensor for identification and quantification of Escherichia coli (E. coli, used as a model indicator bacteria species) in complex food industry process water. The biosensor is based on a nanostructured, oxidized porous silicon (PSi) thin film which is functionalized with specific antibodies against E. coli. The biosensors were exposed to water samples collected directly from process lines of fresh-cut produce and their reflectivity spectra were collected in real time. Process water were characterized by complex natural micro-flora (microbial load of >10⁷ cell/mL), in addition to soil particles and plant cell debris. We show that process water spiked with culture-grown E. coli, induces robust and predictable changes in the thin-film optical interference spectrum of the biosensor. The latter is ascribed to highly specific capture of the target cells onto the biosensor surface, as confirmed by real-time polymerase chain reaction (PCR). The biosensors were capable of selectively identifying and quantifying the target cells, while the target cell concentration is orders of magnitude lower than that of other bacterial species, without any pre-enrichment or prior processing steps.

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water

The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river.

Linking nitrification characteristic and microbial community structures in integrated fixed film activated sludge reactor by high-throughput sequencing

The primary goal of this study is to investigate ammonia removal, abundance of nitrifying bacteria and microbial community structures in a laboratory-scale integrated fixed film activated sludge (IFAS) reactor. The results of Illumina MiSeq sequencing based on 16S rRNA genes showed Proteobacteria and Bacteroidetes were the dominant phyla in both biofilm and suspended sludge samples in the IFAS reactor. The dominant ammonia-oxidizing bacteria (AOB) species was Nitrosomonas and the dominant nitrite-oxidizing bacteria species was Nitrospira. The contribution of biofilm to ammonia removal increased from 4.0 ± 0.9% to 37.0 ± 2% when the temperature decreased from 25 °C to 10 °C. The real-time polymerase chain reaction (PCR) result showed the abundance of AOB in suspended sludge was higher than that in biofilm at the same time. However, nitrification is more dependent on attached growth than on suspended growth in the IFAS reactor at 15 °C and 10 °C and the abundance of AOB in biofilm was also higher than that in suspended sludge. The more robust ammonia removal rate at low temperatures by biofilm contributed to the relatively stable ammonia removal, and biofilm attached on carriers in the IFAS reactor is advantageous for nitrification in low-temperature environment.