Article

Tracking human sewage microbiome in a municipal wastewater treatment plant

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Abstract

Human sewage pollution is a major threat to public health because sewage always comes with pathogens. Human sewage is usually received and treated by wastewater treatment plants (WWTPs) to control pathogenic risks and ameliorate environmental health. However, untreated sewage that flows into water environments may cause serious waterborne diseases, as reported in India and Bangladesh. To examine the fate of the human sewage microbiome in a local municipal WWTP of Hong Kong, we used massively parallel sequencing of 16S rRNA gene to systematically profile microbial communities in samples from three sections (i.e., influent, activated sludge, and effluent) obtained monthly throughout 1 year. The results indicated that: (1) influent sewage bacterial profile reflected the human microbiome; (2) human gut bacterial community was the dominant force shaping influent sewage bacterial profile; (3) most human sewage bacteria could be effectively removed by the WWTP; (4) a total of 75 genera were profiled as potentially pathogenic bacteria, most of which were still present in the effluent although at a very low level; (5) a grouped pattern of bacterial community was observed among the same section samples but a dispersed pattern was found among the different section samples; and (6) activated sludge was less affected by the influent sewage bacteria, but it showed a significant impact on the effluent bacteria. All of these findings provide novel insights toward a mechanistic understanding of the fate of human sewage microbiome in the WWTP.

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... Similarity of microbial communities detected in TW-D and TW-W samples can be explained by similar urban catchments and sanitary networks but most of all by treatment processes served by the tested WWTPs (enhanced simultaneous C/N/P removal; for details see Materials and methods). Although, it should be noted that similar microbial communities in treated wastewater were also shown by others (Cai et al., 2014;Do et al., 2019;García-Armisen et al., 2014;Tiirik et al., 2021;Xue et al., 2019). For instance, Do et al. (2019), who tested WWTPs effluents in Ireland, reported among predominant phyla: ...
... Similar phyla, but in different share were noted in the outflows of WWTP located in Belgium (García-Armisen et al., 2014): Proteobacteria (up to 74%), followed by Bacteroidetes (up to 37%) and Actinobacteria (up to 18%). In WWTP from Hong Kong (Cai et al., 2014) the following share of phyla were found: Proteobacteria (up to 60%), Saccharibacteria/TM7 (up to 25%), Bacteroidetes and Acidobacteria (up to 20%), followed by Firmicutes (up to 14%). The microbial community of treated wastewater has been rarely studied, especially in terms of seasonal variations in composition and diversity , therefore this issue is not fully recognized and understood. ...
... The microbial community of treated wastewater has been rarely studied, especially in terms of seasonal variations in composition and diversity , therefore this issue is not fully recognized and understood. However, worldwide similarities observed until now at high taxonomic levels may suggest that the microbiome composition of WWTP effluents is to some extent consistent among WWTPs (Adrados et al., 2014;Cai et al., 2014;Silva-Bedoya et al., 2016). Wastewater treatment is intensively adjusted by operators in winter as a response to the current effectiveness of microbiological processes, particularly those linked to nitrogen and phosphorus removal. ...
Article
Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.
... Using BLASTN [40], we filtered the search results using an e value of 1e -50 and a similarity threshold of ≥ 80 %, keeping only the best hit. Given the limitations of the sequencing method (read length of ~ 150 bp per fragment, limited sequencing depth, and sequencing of random fragments), we binned sequences at genus level, to avoid overestimation of microbial diversity in the data set [28,41,42]. Singletons were removed and putative contaminants, such as sequences derived from macroscopic animals, higher plants (Streptophyta), and chloroplasts, were excluded. ...
... It can be concluded that primer-based approaches have only limited use for monitoring eukaryotic parasites in wastewater. An array of studies revealed that potentially harmful (parasitic) bacteria were strongly reduced during the initial phases of wastewater treatment [42,62,63]. Our study also shows a pronounced decrease in parasitic taxa between the inflow (sewage) and denitrification bioreactor, but, moreover, shows that this decrease also applies to eukaryotic parasites, protists in particular. ...
... Our study also shows a pronounced decrease in parasitic taxa between the inflow (sewage) and denitrification bioreactor, but, moreover, shows that this decrease also applies to eukaryotic parasites, protists in particular. This decrease can partly be explained by the transition in chemical conditions of the environment, flocculation, and sedimentation [1][2][3]42]. However, our network analyses suggest that predation may also play a role, as we found parasites to co-occur with a number of other taxa within the microbial WWTP community, indicating that trophic interactions, as suggested by laboratory experiments, could be taking place [13,14,60,64]. ...
Article
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Background During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of gut parasites. While the latter function is essential to minimize public health risks, the range of parasites involved and how they are removed is still poorly understood. Results Using shotgun metagenomic (DNA) and metatranscriptomic (RNA) sequencing data from ten wastewater treatment plants in Switzerland, we were able to assess the entire wastewater microbiome, including the often neglected microeukaryotes (protists). In the latter group, we found a surprising richness and relative abundance of active parasites, particularly in the inflow. Using network analysis, we tracked these taxa across the various treatment compartments and linked their removal to trophic interactions. Conclusions Our results indicate that the combination of DNA and RNA data is essential for assessing the full spectrum of taxa present in wastewater. In particular, we shed light on an important but poorly understood function of wastewater treatment – parasite removal.
... The most commonly reported MTBC in wastewater are M. tuberculosis and M. bovis (See Table 1). These bacteria were commonly reported, using conventional culture-based, biochemical analysis and molecular-based techniques, in raw wastewater [61][62][63][64], treated wastewater [64][65][66], activated sludge [65], soil [67] and water [16,61,67]. This could be attributed to the high number of human infections caused by these pathogens [68]. ...
... The most commonly reported MTBC in wastewater are M. tuberculosis and M. bovis (See Table 1). These bacteria were commonly reported, using conventional culture-based, biochemical analysis and molecular-based techniques, in raw wastewater [61][62][63][64], treated wastewater [64][65][66], activated sludge [65], soil [67] and water [16,61,67]. This could be attributed to the high number of human infections caused by these pathogens [68]. ...
... i) Domestic wastewater: This could be primarily due to gastrointestinal infections with MTBC (See Section 3.1) which results in the shedding of MTBC cells in human excreta. The human sewage microbiome is referred to as the collective microbes in sewage from human domestic waste such as feaces, urine, sweat, washing, bathing, etc. [65]. This is mainly derived from the human body including the skin, respiratory tract, oral cavity, gastrointestinal tract, and urogenital tract which ends up in wastewater treatment plants [65,125]. ...
Article
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Background The Mycobacterium tuberculosis complex (MTBC) consists of causative agents of both human and animal tuberculosis and is responsible for over 10 million annual infections globally. Infections occur mainly through airborne transmission, however, there are possible indirect transmissions through a faecal-oral route which is poorly reported. This faecal-oral transmission could be through the occurrence of the microbe in environments such as wastewater. This manuscript, therefore, reviews the source and fate of MTBC in the wastewater environment, including the current methods in use and the possible risks of infections. Results The reviewed literature indicates that about 20% of patients with pulmonary TB may have extra-pulmonary manifestations such as GITB, resulting in shedding in feaces and urine. This could potentially be the reason for the detection of MTBC in wastewater. MTBC concentrations of up to 5.5 × 10⁵ (±3.9 × 10⁵) copies/L of untreated wastewater have been reported. Studies have indicated that wastewater may provide these bacteria with the required nutrients for their growth and could potentially result in environmental transmission. However, 98.6 (± 2.7) %, removal during wastewater treatment, through physical-chemical decantation (primary treatment) and biofiltration (secondary treatment) has been reported. Despite these reports, several studies observed the presence of MTBC in treated wastewater via both culture-dependent and molecular techniques. Conclusion The detection of viable MTBC cells in either treated or untreated wastewater, highlights the potential risks of infection for wastewater workers and communities close to these wastewater treatment plants. The generation of aerosols during wastewater treatment could be the main route of transmission. Additionally, direct exposure to the wastewater containing MTBC could potentially contribute to indirect transmissions which may lead to pulmonary or extra-pulmonary infections. This calls for the implementation of risk reduction measures aimed at protecting the exposed populations.
... Earlier studies have shown that most pathogenic bacteria are decreased in their relative abundance in the WWTP, while others (e.g., Mycobacterium spp. and Clostridium spp.) increase [16,17]. Although wastewater and surface waters are different environments from the human gut, several pathogenic bacteria are known to be water-borne pathogens (species that are able to spread via aquatic ecosystems) while others can be classified as water-based pathogens (species that are able to grow and thrive in water systems) [18][19][20][21][22]. ...
... This study aimed to investigate the contribution of clinical wastewater on the bacterial composition in wastewater and the environment. We used 16S rRNA to broadly screen the relative abundance and fate of bacterial target taxa that were selected based on pathogenic potential: (i) pathogens of clinical relevance and AMR features (ESKAPE pathogens and WHO priority pathogens) [2][3][4]; (ii) water-based pathogens that can grow and thrive in water systems [18][19][20][21][22]; (iii) antibiotic-associated diarrhea (AAD) bacteria [8][9][10] and; (iv) bacteria that increase after WWTP treatment [16,17]. ...
... A total of 24 bacterial genera or species were selected as "target taxa" to study their changes in relative abundance and fate along the studied wastewater pathway (Table 2), based on pathogenicity, antibiotic resistance potential and known or possible association with WWTP. The taxa selection included: (1) the ESKAPE pathogens that are of particular clinical relevance and prone to antibiotic resistance [2,3], (2) the WHO priority pathogens for AMR [4], (3) water-based pathogens [18][19][20][21][22], (4) bacteria which are AAD associated/increased after antibiotic (AB) treatment [8][9][10], and (5) bacteria previously found at increased concentrations after WWTP treatment [16,17]. Some genera include bacteria that match with more than one of the five selection criteria. ...
Article
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This study pertains to measure differences in bacterial communities along the wastewater pathway, from sewage sources through the environment. Our main focus was on taxa which include pathogenic genera, and genera harboring antibiotic resistance (henceforth referred to as “target taxa”). Our objective was to measure the relative abundance of these taxa in clinical wastewaters compared to non-clinical wastewaters, and to investigate what changes can be detected along the wastewater pathway. The study entailed a monthly sampling campaign along a wastewater pathway, and taxa identification through 16S rRNA amplicon sequencing. Results indicated that clinical and non-clinical wastewaters differed in their overall bacterial composition, but that target taxa were not enriched in clinical wastewater. This suggests that treatment of clinical wastewater before release into the wastewater system would only remove a minor part of the potential total pathogen load in wastewater treatment plants. Additional findings were that the relative abundance of most target taxa was decreased after wastewater treatment, yet all investigated taxa were detected in 68% of the treated effluent samples—meaning that these bacteria are continuously released into the receiving surface water. Temporal variation was only observed for specific taxa in surface water, but not in wastewater samples.
... Aquatic microbial consortia represent important vehicles for the dissemination of microorganisms and a transmission source for bacteria carrying a variety of antimicrobial resistance genes. Hospital effluents and urban wastewaters are hotspots for horizontal gene transfer by mobile genetic elements (i.e., transposons and integron-associated gene cassettes) that can contribute to the spread and maintenance of antibiotic resistance genes (ARGs) within bacterial communities [6,7]. ...
... Tetracycline resistance was encoded by the tetA gene in 9.09% of the isolates, tetB gene in 7.79% of the isolates, and tetC gene also in 7.79% of the isolates resistant to tetracycline. All Fig. 2 Degree of antimicrobial resistance by the number of antibiotics (1)(2)(3)(4)(5)(6)(7) in Pseudomonas spp. isolates from the urban water cycle. ...
Article
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Selection and dissemination of resistant bacteria and antibiotic resistance genes (ARGs) require a deeper understanding since antibiotics are permanently released to the environment. The objective of this paper was to evaluate the phenotypic resistance of 499 isolates of Pseudomonas spp. from urban water sources, and the prevalence of 20 ARGs within those isolates. Resistance to penicillins, cephalosporins, carbapenems, quinolones, macrolides, and tetracyclines was mainly observed in the hospital effluent, municipal wastewater and river water downstream the city. Resistant strains were frequently identified as P. aeruginosa and P. putida. P. aeruginosa isolates were mostly resistant to cefepime, ceftazidime, imipenem, and gentamycin, while P. putida strains were especially resistant to piperacillin-tazobactam. ARGs such as blaTEM-1, blaSHV-1, blaPER-1, blaAmpC, blaVIM-1, PstS, qnrA, qnrB, ermB, tetA, tetB and tetC have been detected. The blaAmpC gene was found in P. aeruginosa, while blaTEM-1 and blaPER-1 genes were found in P. putida. Class 1 integron integrase gene was found in 6.81% of the Pseudomonas isolates.
... 36 Identification of Pathogenic Genomes. The candidate pathogenic genomes were first taxonomically identified based on two published reference pathogen lists containing 140 potentially human pathogenic genera 37 and 538 human pathogenic species. 38 Then, 3642 experimentally verified virulence factors downloaded from the pathogenic bacteria virulence factor database (VFDB, last update: June 27, 2020) 39 were used to construct a searchable blast database. ...
... Compared with the reported metagenomic contigs or gene fragments, 59,60 MAGs provide a more complete genome context allowing for more robust host identification at higher resolution, down to the genus or species level. In total, 20 potentially pathogenic MAGs were identified based on the published reference pathogen lists 37,38 and verified the presence of virulence factors. Seventeen out of the 20 pathogenic MAGs were found to encode multi-antibiotic resistance, and the aforementioned 5 MAGs that encode the largest number of ARGs (10 or 11) all belonged to the pathogenic group. ...
... Pseudomonas is ubiquitous in the environment, and pathogenic species of Pseudomonas can cause infections in hospital patients and/or those with weakened immune systems, such as pneumonia and blood infections [34]. The abundance of Mycobacterium significantly increased from influent to effluent samples in Plant A. This taxon has also been found in effluent and activated sludge of a WWTP in Hong Kong via metagenomic analysis [35,36]. ...
... For the virulence genes ciaB and pldA, 2 µL of template DNA, 12.5 µL of a SYBR Premix Ex Taq II (Tli RNase Plus) (Takara Bio), 0.1 µL each of 1 µM of ciaB-F and ciaB-R primers (for the ciaB gene) [42] or pldA-F and pldA-R primers (for the pldA gene) [42], and 10.3 µL of ultrapure water were used. qPCR was performed with a Thermal Cycler Dice Real Time System Single TP850 (Takara Bio) under the following thermal conditions: for Arcobacter 16S rRNA gene, 98 °C for 2 min, followed by 35 ...
Article
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This study aimed to identify the bacterial community in two wastewater treatment plants (WWTPs) and to determine the occurrence and reduction of Arcobacter, along with virulence genes (ciaB and pldA). A total of 48 samples (24 influent and 24 effluent) were collected at two WWTPs in southern Arizona in the United States, monthly from August 2011 to July 2012. Bacterial DNA extract was utilized for 16S rRNA metagenomic sequencing. Quantification of Arcobacter 16S rRNA gene was conducted using a recently developed SYBR Green-based quantitative PCR assay. Among 847 genera identified, 113 (13%) were identified as potentially pathogenic bacteria. Arcobacter 16S rRNA gene was detected in all influent samples and ten (83%) and nine (75%) effluent samples at each plant, respectively. Log reduction ratios of Arcobacter 16S rRNA gene in Plant A and Plant B were 1.7 ± 0.9 (n = 10) and 2.3 ± 1.5 (n = 9), respectively. The ciaB gene was detected by quantitative PCR in eleven (92%) and twelve (100%) of 12 influent samples from Plant A and Plant B, respectively, while the pldA gene was detected in eight (67%) and six (50%) influent samples from Plant A and Plant B, respectively. The prevalence of potentially pathogenic bacteria in WWTP effluent indicated the need for disinfection before discharge into the environment.
... Few studies have focused on the composition of cyanobacterial blooms in WWTFs; however, cyanobacteria are often incidentally detected in metagenomic studies that indiscriminately target the 16S rRNA gene. The microbial community studies listed in Table 1 demonstrate that cyanobacteria are frequently present in the effluent of WWTPs (Cai et al., 2014;Do et al., 2019;Greay et al., 2019;Tang et al., 2016) representing a potential risk to public health and safety if the effluent is released into receiving waters without further treatment. Additionally, the presence of toxic cyanobacteria in the sediment or activated sludge of various treatment plants is of particular concern as it demonstrates a possible seeding source for planktic bloom formation under favorable conditions (Cai et al., 2014). ...
... The microbial community studies listed in Table 1 demonstrate that cyanobacteria are frequently present in the effluent of WWTPs (Cai et al., 2014;Do et al., 2019;Greay et al., 2019;Tang et al., 2016) representing a potential risk to public health and safety if the effluent is released into receiving waters without further treatment. Additionally, the presence of toxic cyanobacteria in the sediment or activated sludge of various treatment plants is of particular concern as it demonstrates a possible seeding source for planktic bloom formation under favorable conditions (Cai et al., 2014). ...
Article
Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of sentinel species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.
... WWTP3 (Garmerwolde, Groningen, 340'146 p.e.) treats 71 800 m 3 d −1 (64% households,14% industry, and 1% hospital (totalling 1920 beds) in two separate treatment lines. Approximately 50% of the influent is treated in a two-stage activated sludge adsorption-bioxidation (AB) process ( Böhnke, 1997 ). The other half of the wastewater is treated by an aerobic granular sludge process (Nereda®). ...
... The high concentration of ermB gene in the influent cannot be associated with a direct antibiotic selective pressure within sewage, as erythromycin residues were not detected in the influent. The high occurrence of ermB might result from its location in Lactobacillales, which are common in the gut microbiome and, therefore, predominant taxa in the influent ( Ali et al., 2019 ;Cai et al., 2014 ). The high occurrence of sul1 may be explained by its extended use in the past and its association with MGE, such as integron class 1. ...
Article
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The occurrence and removal patterns of 24 antimicrobial agents and antimicrobial resistant determinants namely 6 antibiotic resistance genes (ARGs) and 2 mobile genetic elements (MGEs), and the fecal indica- tor E. coli were investigated in three full-scale wastewater treatment plants. Their waterlines and biosolids lines (including secondary treatment based on both granular and activated sludge) were sampled monthly throughout one year. Samples were analyzed by means of LC-MS/MS, qPCR and cell enumeration, respec- tively. The influence of rainfall, temperature, and turbidity on the occurrence and removal of the afore- mentioned agents was assessed through statistical linear mixed models. Ten of the antimicrobial agents (macrolides, fluoroquinolones, tetracyclines, and sulfonamides) were commonly found in influent in con- centrations of 0.1-2 μg L −1 , and the predominant ARGs were ermB and sul1 (6.4 and 5.9 log 10 mL −1 re- spectively). Warmer temperatures slightly reduced gene concentrations in influent whilst increasing that of E. coli and produced an uneven effect on the antimicrobial concentrations across plants. Rainfall di- luted both E. coli (-0.25 logs, p < 0.001) and antimicrobials but not genes. The wastewater treatment reduced the absolute abundance of both genes (1.86 logs on average) and E. coli (2.31 logs on average). The antimicrobials agents were also partly removed, but 8 of them were still detectable after treatment, and 6 accumulated in the biosolids. ARGs were also found in biosolids with patterns resembling those of influent. No significant differences in the removal of antimicrobials, genes and E. coli were observed when comparing conventional activated sludge with aerobic granular sludge. Irrespective of the type of sludge treatment, the removal of genes was significantly reduced with increasing hydraulic loads caused by rainfall (-0.35 logs per �average daily flow p < 0.01), and slightly decreased with increasing turbidity (-0.02 logs per �1 nephelometric turbidy unit p < 0.05) .
... with drainage systems to transport runoff and stormwater, increasing the overall microbial diversity. Previous research on wastewater influent demonstrates that the bacterial communities in raw sewage can serve as indicators of the human population in the surrounding areas, providing a valuable resource to understand population-level traits and health (1)(2)(3). ...
... Outliers consisted of samples from Queens, Brooklyn, and Staten Island as well as the sample collected from Brooklyn/Queens/Manhattan (Fig. S3a). To more closely examine the protein domains for evidence of auxiliary metabolic genes (AMGs), we removed virus-and phage-associated protein families, resulting in 8,240 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 protein families. AMGs are found in bacteriophage genomes but are derived from bacterial cells. ...
Article
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Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.
... A better understanding of the microbial diversity in septic tank system can improve the stability of the anaerobic process (Bitton, 1999;Connelly et al., 2019). Yet understanding the workings of the process is hampered by the paucity of research papers in the literature (Marti et al., 2013;Ye and Zhang, 2013;Cai et al., 2014;Logares et al., 2015;Newton et al., 2015;Connelly et al., 2019;Numberger et al., 2019). The microbes responsible for the metabolic reactions in the system are the crucial factor in the anaerobic process (Bitton, 1999;Schaider et al., 2017). ...
... Thus, it is not surprising that the higher abundance of Arcobacter cryaerophilus in the Pinheiros River may indicate heavy fecal contamination. Nevertheless, our results replicate the findings of the recent metagenomic sequencing studies that revealed a higher prevalence of Arcobacter in sewage ecosystems and wastewater treatment plants [48][49][50] and provides further support to the suggestion that Arcobacter is primarily planktonic 51 . In one study, a metagenomic assembly of the near-complete genome of Arcobacter cryaerophilus from untreated sewage influent samples recovered 25 putative antibiotic resistance genes 52 . ...
Article
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The Pinheiros River in São Paulo, Brazil, crosses through the capital city and has its confluence with the River Tiete, which comprises several reservoirs along its course. Although Pinheiros River is considered one of the heaviest polluted rivers in Brazil, little is known about its bacterial composition, their metabolic functions or how these communities are affected by the physicochemical parameters of the river. In this study, we used the 16S rRNA gene Illumina MiSeq sequencing to profile the bacterial community from the water surface at 11 points along the course of the River. Taxonomical composition revealed an abundance of Proteobacteria phyla, followed by Firmicutes and Bacteroidetes, with a total of 233 classified bacterial families and 558 known bacterial genera. Among the 35 potentially pathogenic bacteria identified, Arcobacter was the most predominant genus. The disrupted physicochemical parameters detected in this study may possibly contribute to the composition and distribution of the bacterial community in the Pinheiros River. Predictive functional analysis suggests the River is abundant in motility genes, including bacterial chemotaxis and flagellar assembly. These results provide novel and detailed insights into the bacterial communities and putative function of the surface water in the Pinheiros River.
... Microorganisms are a key part of wastewater treatment, and 95% of those found in wastewater treatment are bacteria (Martins et al., 2004). Bacteria found in municipal wastewater are often also found in association with human skin, respiratory tract, oral cavity, gastrointestinal tract and urogenital tract (Cai et al., 2014). Studies by Shanks et al. (2013) and Newton et al. (2015) found that between 12% and 15% of municipal wastewater taxa were likely attributed to human faeces and the most common microbes in faeces matched the most common and abundant in the wastewater microbial community. ...
Article
Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterised. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge, and post‐treatment effluent were characterised. From 3,163 Exact Sequence Variants (ESVs), 860 were annotated to species‐level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially humans‐associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human‐associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease‐producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human‐associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species‐level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem. This article is protected by copyright. All rights reserved.
... They are also referred to as emerging foodborne pathogens for over four decades, which indicates that the pathogenic potential of the genus has not been fully established. Its occurrence in urban-associated environmental waters [4][5][6] is worrying and could be a source of gastroenteritis. Species of Aeromonas have been implicated in diarrheal illnesses in children, which is aided by exposure to recreational water activities [7]. ...
Article
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Sequences of 105 Aeromonas species plasmids were probed for acquired anti-microbial resistance (AMR) genes using a bioinformatics approach. The plasmids showed no positive linear correlation between size and GC content and up to 55 acquired AMR genes were found in 39 (37%) plasmids after in silico screening for resistance against 15 antibiotic drug classes. Overall, potential multiple antibiotic resistance (p-MAR) index ranged from 0.07 to 0.53. Up to 18 plasmids were predicted to mediate multiple drug resistance (MDR). Plasmids pS121-1a (A. salmonicida), pWCX23_1 (A. hydrophila) and pASP-a58 (A. veronii) harboured 18, 15 and 14 AMR genes respectively. The five most occurring drug classes for which AMR genes were detected were aminoglycosides (27%), followed by beta-lactams (17%), sulphonamides (13%), fluoroquinolones (13%), and phenicols (10%). The most prevalent genes were a sulphonamide resistant gene Sul1, the gene aac (6')-Ib-cr (aminoglycoside 6'-N-acetyl transferase type Ib-cr) resistant to aminoglycosides and the blaKPC-2 gene, which encodes carbapenemase-production. Plasmid acquisition of AMR genes was mainly inter-genus rather than intra-genus. Eighteen plasmids showed template or host genes acquired from Pseudomonas monteilii, Salmonella enterica or Escherichia coli. The most occurring antimicrobial resistance determinants (ARDs) were beta-lactamase, followed by aminoglycosides acetyl-transferases, and then efflux pumps. Screening of new isolates in vitro and in vivo is required to ascertain the level of phenotypic expression of colistin and other acquired AMR genes detected.
... They are also referred to as emerging foodborne pathogens for over four decades, which indicates that the pathogenic potential of the genus has not been fully established. Its occurrence in urban-associated environmental waters [4][5][6] is worrying and could be a source of gastroenteritis. Species of Aeromonas have been implicated in diarrheal illnesses in children, which is aided by exposure to recreational water activities [7]. ...
Article
Full-text available
Sequences of 105 Aeromonas species plasmids were probed for acquired anti-microbial resistance (AMR) genes using a bioinformatics approach. The plasmids showed no positive linear correlation between size and GC content and up to 55 acquired AMR genes were found in 39 (37%) plasmids after in silico screening for resistance against 15 antibiotic drug classes. Overall, potential multiple antibiotic resistance (p-MAR) index ranged from 0.07 to 0.53. Up to 18 plasmids were predicted to mediate multiple drug resistance (MDR). Plasmids pS121-1a (A. salmonicida), pWCX23_1 (A. hydrophila) and pASP-a58 (A. veronii) harboured 18, 15 and 14 AMR genes respectively. The five most occurring drug classes for which AMR genes were detected were aminoglycosides (27%), followed by beta-lactams (17%), sulphonamides (13%), fluoroquinolones (13%), and phenicols (10%). The most prevalent genes were a sulphonamide resistant gene Sul1, the gene aac (6')-Ib-cr (aminoglycoside 6'-N-acetyl transferase type Ib-cr) resistant to aminoglycosides and the blaKPC-2 gene, which encodes carbapenemase-production. Plasmid acquisition of AMR genes was mainly inter-genus rather than intra-genus. Eighteen plasmids showed template or host genes acquired from Pseudomonas monteilii, Salmonella enterica or Escherichia coli. The most occurring antimicrobial resistance determinants (ARDs) were beta-lactamase, followed by aminoglycosides acetyl-transferases, and then efflux pumps. Screening of new isolates in vitro and in vivo is required to ascertain the level of phenotypic expression of colistin and other acquired AMR genes detected.
... In the context of municipal WWTPs, the influent sewage reflected the human gut microbiomes in cities which may change with human population variation (Newton et al. 2015). However, most human bacteria could be effectively removed by the municipal WWTPs, and the AS was less affected by influent sewage bacteria (Cai et al. 2013). Thus, municipal AS could keep its characteristic microbiome. ...
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The diversity and assembly of activated sludge microbiomes play a key role in the performances of municipal wastewater treatment plants (WWTPs), which are the most widely applied biotechnological process systems. In this study, we investigated the microbiomes of municipal WWTPs in Bangkok, Wuhan, and Beijing that respectively represent tropical, subtropical, and temperate climate regions, and also explored how microbiomes assembled in these municipal WWTPs. Our results showed that the microbiomes from these municipal WWTPs were significantly different. The assembly of microbiomes in municipal WWTPs followed deterministic and stochastic processes governed by geographical location, temperature, and nutrients. We found that both taxonomic and phylogenetic α-diversities of tropical Bangkok municipal WWTPs were the highest and were rich in yet-to-be-identified microbial taxa. Nitrospirae and β-Proteobacteria were more abundant in tropical municipal WWTPs, but did not result in better removal efficiencies of ammonium and total nitrogen. Overall, these results suggest that tropical and temperate municipal WWTPs harbored diverse and unique microbial resources, and the municipal WWTP microbiomes were assembled with different processes. Implications of these findings for designing and running tropical municipal WWTPs were discussed. Key points • Six WWTPs of tropical Thailand and subtropical and temperate China were investigated. • Tropical Bangkok WWTPs had more diverse and yet-to-be-identified microbial taxa. • Microbiome assembly processes were associated with geographical location.
... Researchers have performed substantial work on the microbiological safety of wastewater final effluents. Anthropogenic microorganisms in wastewater are the main microbial pathogens in wastewater final effluents [10]. The wastewater treatment process plays an important role in the retention of microbial pathogens in wastewater, and the retention efficiency is related to dissolved oxygen and temperature [11]. ...
Article
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Numerous bacteria, especially pathogens, exist in wastewater final effluents, which can lead to possible human health and ecological security risks when effluents are reused or discharged. However, the diversity, composition, and spatiotemporal dynamics of bacteria in wastewater final effluents remain poorly understood. In this study, a comprehensive analysis of the microbial community and pathogens in wastewater final effluents was performed using high-throughput sequencing. The results revealed that wastewater final effluents in autumn exhibited the highest bacterial community richness and diversity, while those in winter exhibited the lowest. Bacteria in wastewater final effluents predominantly belonged to five phyla, in the order of Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Firmicutes. At the species level, there were 8~15 dominant species in the wastewater final effluent in each season, and Dokdonella immobilis, Rhizobium gallicum, Candidatus Flaviluna lacus, and Planctomyces limnophilus were the most dominant species in spring, summer, autumn, and winter, respectively. The seasonal variability in bacteria suggested that the microbial diversity and community in wastewater final effluents were mainly influenced by temperature, salinity, disinfection methods, and flocculants. Notably, pathogenic bacteria in wastewater effluents had both the highest relative abundance and species abundance in summer. Arcobacter spp., Legionella spp., and Mycobacterium spp. were the dominant pathogenic bacteria, and all pathogenic bacteria were mainly associated with dermatosis, enteropathies, septicemia, and pneumonia.
... Global dissemination of bacterial antibiotic resistance is associated with a high medical cost, increased hospitalization cases and mortality rates. It is estimated that in the United States at least 2 million people are infected with antibiotic-resistant bacteria annually, with over 23,000 deaths as a result [2]. Therefore, there is a demanding need to control the spread and reduce the risk of antibiotic resistant bacteria in various sectors, such as agri-foods. ...
Article
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Antibiotic resistance poses safety risk to public health. Limited studies have considered the spread of resistance due to bacteria used in food production. We conducted a study investigating the antibiotic resistance of lactic acid bacteria from fermented dairy products in Tianjin. A total of 9 strains (3 Lactobacillus bulgaricus and 6 Streptococcus thermophilus) were isolated from commercial yogurt and cheese. Antibiotic resistance to 4 antibiotics of all isolates was analyzed by disc diffusion method and the corresponding resistance genes were determined using PCR and sequencing. Eight of 9 isolates were identified to be resistant to at least one antibiotic and 6 isolates displayed multi-drug resistance. Occurrence rate of antibiotic resistant strains to vancomycin, neomycin, gentamycin and streptomycin were 11.1%, 77.8%, 66.7% and 44.4%, respectively. The presence of antibiotic resistance genes van, aph or aadA2 were identified in 6 resistant strains. Sequencing results of aph and aadA2 amplicon demonstrated 100% and 99% identity to the resistant genes in vector pEXKm4 and Lactococcus lactis subsp. cremoris, respectively. L. bulgaricus and S. thermophilus used in dairy products can harbour antibiotic resistance genes and disseminate the resistance through food. Screening for antibiotic resistance in fermented foods should be a routine inspection for food safety.
... Several studies investigating the wastewater microbiome have been published 23,24 , but they generally involve partial 16S rRNA gene sequencing, a technique which usually does not enable microbial characterization at the lowest taxonomic levels (e.g. species/strains). ...
Article
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Kampala, the capital city of Uganda, is rapidly expanding without adequate wastewater treatment facilities to accommodate the current estimated population of 1.68 million people. Hence, freshwater bodies and natural ecosystems around the city are heavily polluted with organic and inorganic contaminants. Yet, there is a paucity of data on pathogenic microorganisms, which potentially threatens health of local communities. We performed a qualitative microbial analysis using a whole metagenome sequencing approach encompassing over 150 gigabases of sequencing data to characterize the Nakivubo wastewater system, which includes a wastewater channel and surrounding wetlands. We found that microbial diversity is heterogeneous throughout the system and that three community state types could be differentiated. We showed the presence of various waterborne agents of gastrointestinal infections in humans, which were associated with leakage occurring around two locations along the wastewater channel. Our data indicate that the microbial decontamination capacity of the local wastewater treatment facility was insufficient at the time of sampling, and that several areas of the wetlands were contaminated with human pathogens, indicating that parts of the wetlands are potentially unsafe for urban agriculture.
... In fact, our results suggest that a large portion of the IF indicator OTUs within Bacteroidetes and Firmicutes were possibly originating from human guts (Fig. 7). However, it is also notable that a large fraction of the indicator OTUs cannot be assigned to a certain environment due to (i) the limitation of the custom SILVA119 database used here considering a huge increase in the microbial biodiversity as reflected by the fast growth in SILVA database (Yilmaz et al. 2014) and (ii) some novel species may be present in the EFs (Cai et al. 2014). Nevertheless, the relative proportion of the human gut associated taxa significantly decreased from IFs to EFs (Figs. 4 and 5), which was partially consistent with the previous findings, where the efficiency of WWTPs was attributed for the potential Fig. 5 A linear relationship (log-transformed) between a daily dataset and a season dataset for the relative importance of deterministic processes controlling the turnover of the whole communities and dominant prokaryotic taxa from IFs to EFs in WWTPs of Xiamen, China. ...
Article
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Wastewater treatment plants (WWTPs) rely mainly on the microbial assemblages to contribute significantly for the removal of organic pollutants and nutrients. However, limited information is available on the ecological driving forces underlying the turnover of prokaryotic communities across wastewater treatment processes (i.e., from influents (IFs) and effluents (EFs)) within WWTPs. Here, we used a combination of the 16S rRNA gene amplicon sequencing and a quantitative ecological null model analysis to explore the ecological processes governing the turnover of the prokaryotic communities and the dominant taxonomic taxa across wastewater treatment processes of five full-scale WWTPs in China. Our results indicated that a significant variation in the composition of prokaryotic communities and the dominant taxa between IFs and EFs. The analysis of the environmental sources of indicator OTUs showed that a relatively lower abundance of the sludge/sewage and human guts associated OTUs in EFs than in IFs. Ecological null models revealed that among the ecological processes, deterministic processes were dominant in controlling the turnover of the overall communities from IFs to EFs, whereas the relative importance of deterministic processes varied among the dominant taxa (i.e., Bacteroidetes > Proteobacteria > Gammaproteobacteria > Firmicutes > Betaproteobacteria). However, the assembly of IF and EF communities was influenced mainly by the deterministic and stochastic processes, respectively. In addition, our results indicated that EF communities have a higher phylogenetic diversity than those of the IF communities, but the abundance of prokaryotic 16S rRNA genes was lower in EFs than in IFs. Overall, our study provides a novel insight of the assembly mechanisms underlying the turnover of prokaryotic communities during wastewater treatment processes.
... Moreover, the analyses of spaces with limited occupant density and diversity compared to public spaces, where the diversity and density of occupants is likely to be higher, over different time and spatial scales could better define the limits of indoor microbiome heterogeneity. This would likely highlight clearer trends and global patterns by essentially averaging the microbial input from different occupants, similar to what has been recently observed in sewage [27,107,108]. Studies examining spatial and temporal variation in the indoor microbiome, combined with epidemiological records, will also shed light on relationships between the indoor microbiome, building features, and health outcomes. ...
Article
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The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide “healthy” building design.
... The bacterial community of WW is usually composed of human commensal bacteria and environmental bacteria, which might have been exposed to antimicrobial substances from private households, clinical and agricultural settings (Cai et al., 2014). Both Enterobacteriaceae and Pseudomonas spp. ...
Article
Wastewater treatment plants (WWTP) play a key role in the dissemination of antibiotic resistance and analyzing the abundance of antibiotic resistance genes (ARGs) and resistant bacteria is necessary to evaluate the risk of proliferation caused by WWTPs. Since few studies investigated the seasonal variation of antibiotic resistance, this study aimed to determine the abundance of beta-lactamase and mcr genes and to characterize phenotypic resistant strains in a WWTP in Germany over the seasons. Wastewater, sewage sludge and effluent samples were collected over a one year period and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using VITEK 2. The results show a significantly higher occurrence of nearly all investigated ARGs in the wastewater compared to sewage sludge and effluent. ARG abundance and temperature showed a negative correlation in wastewater and significant differences between ARG abundance during warmer and colder seasons were determined, indicating a seasonal effect. Co-occurrence of mcr-1 and carbapenemase genes in a multi-drug resistant Enterobacter cloacae and Escherichia coli producing extended-spectrum beta-lactamase (ESBL) was determined. To the best of our knowledge, this is the first detection of mcr-1, blaVIM and blaOXA-48 in an ESBL-producing E. coli. Although wastewater treatment reduced the abundance of ARGs and resistant strains, a dissemination into the river might be possible because carbapenemase-, CTX-M- and mcr-1-gene harboring strains were still present in the effluent.
... In particular sewage systems that collect and transport human waste from residential, commercial, and industrial toilets to wastewater treatment plants are integral to urban infrastructure while also serving as a reflection of urban ecology, but have been little studied. Some recent studies have demonstrated that the influent of these systems serves as a proxy of population-level fecal microbiota within a city, retaining microbial signatures of human inhabitants including both commensal taxa and pathogens [10][11][12][13]. Systems where the sewer and storm drains are combined accumulate further microbes from animal wastes and natural environments through groundwater and surface runoffs [6]. ...
Article
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Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.
... It is governed notably by the pH of the aqueous conditions. Combined available rC refers to chloramine (Cl • ) and dichloramine (Cl 2 •− ).Among them, free rC (hypochlorous acid) has the best sterilization effect and can also remove different target pollutants [34,35]. Overall, the amount of rC in the water sample will be affected after the electrocatalytic treatment. ...
Article
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Tap water contains some heavy metals and bio-organic substances with variety of concentration and these cannot be treated using regular physicochemical processes. So the present study, aims at evaluating the effectiveness of the sterilization using electrocatalytic technique with Escherichia coli (E. coli) as the observed index. The operational parameters such as anode material, voltage, inflow method, and electrode number are studied to understand the variation of pH, conductivity, E. coli, and residual chlorine of tap water. The outcome reveals that the maximum sterilization efficiency of E. coli is obtained using the titanium dioxide electrode, followed by ruthenium dioxide and graphite. A disinfection efficiency of 98% can be easily achieved. Also, the appropriate increase in the operating voltage can increase the sterilization efficiency and decrease the treatment time. The sterilization efficiency of the E. coli can reach 100% under the continuous inflow of tap water and the voltage of 60 V for 1 min, which meets the conventional standard of drinking water (6 CFU/100ml). The estimated operating cost of treatment of 1 ton of tap water is NTD 1.7. Graphic abstract
... E; 29 • 42 44 S) has also adopted the strategy for irrigation of agricultural crops including leaf, root, and bulb vegetables. However, studies advise that all treated municipal wastewater should be viewed as potential carriers of pathogens with the potential ability to serve as a source of contamination of the agricultural produce [9,10]. ...
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The current study investigated the distribution of microbial populations and diversity in treated wastewater used for irrigation at the University of Limpopo Experimental Farm (ULEF), from different stages of post treatment disposal at Mankweng Wastewater Treatment Plant (MWTP) in Limpopo Province, South Africa. The study was arranged in a 4 × 5 factorial experiment, which studied the interactive effects of four collection points and five months of sampling, with borehole water used as a reference point. Water samples were analyzed for bacteria, helminths, and protozoa. All data were transformed and subjected to factorial analysis of variance. The site–time interactions were significant for Salmonella spp. and Ascaris lumbricoides, whereas collection point was significant for all variables. In conclusion, movement and storage of water post treatment at MWTP were able to improve the microbial quality of the treated wastewater disposed for irrigation at ULEF.
... Other less predominant bacterial phyla such as Bacteroidetes, Chloroflexi, Epsilonbacteraeota, and Planctomycetes had a lower contribution (,10%) to the overall bacterial community. They have previously been detected in various wastewaters (28)(29)(30) and activated sludge (31). ...
Article
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The spatiotemporal variation of several carbapenemase-encoding genes (CRGs) was investigated in the influent and effluent of municipal WWTPs, with or without hospital sewage input. Correlations among gene abundances, bacterial community composition, and wastewater quality parameters were tested to identify possible predictors of CRGs presence. Also, the possible role of wastewaters in mirroring clinical resistance is discussed. The taxonomic groups and gene abundances showed an even distribution among wastewater types, meaning that hospital sewage does not influence the microbial diversity and the CRG pool. The bacterial community was composed mainly of Proteobacteria, Firmicutes, Actinobacteria, Patescibacteria, and Bacteroidetes. Acinetobacter spp. was the most abundant group and had the majority of operational taxonomic units (OTUs) positively correlated with CRGs. This agrees with recent reports on clinical data. The influent samples were dominated by bla KPC , as opposed to effluent, where bla IMP was dominant. Also, bla IMP was the most frequent CRG family observed to correlate with bacterial taxa, especially with the Mycobacterium genus in effluent samples. Bacterial load, bla NDM , bla KPC , and bla OXA-48 abundances were positively correlated with BOD 5 , TSS, HEM, Cr, Cu, and Fe concentrations in wastewaters. When influent gene abundance values were converted into population equivalent (PE) data, the highest copies/1 PE were identified for bla KPC and bla OXA-48 , agreeing with previous studies regarding clinical isolates. Both hospital and non-hospital-type samples followed a similar temporal trend of CRG incidence, but with differences among gene groups. Colder seasons favored the presence of bla NDM , bla KPC and bla OXA-48 , whereas warmer temperatures show increased PE values for bla VIM and bla IMP. IMPORTANCE Wastewater-based epidemiology has recently been recognized as a valuable , cost-effective tool for antimicrobial resistance surveillance. It can help gain insights into the characteristics and distribution of antibiotic resistance elements at a local, national, and even global scale. In this study, we investigated the possible use of municipal wastewaters in the surveillance of clinically relevant carbapenemase-encoding genes (CRGs), seen as critical antibiotic resistance determinants. In this matter, our results highlight positive correlations among CRGs, microbial diversity, and wastewater physical and chemical parameters. Identified predictors can provide valuable data regarding the level of raw and treated wastewater contamination with these important antibiotic resistance genes. Also, wastewater-based gene abundances were used for the first time to observe possible spatiotemporal trends of CRGs incidence in the general population. Therefore, possible hot spots of carbapenem resistance could be easily identified at the community level, surpassing the limitations of health care-associated settings.
... The high abundance of the genus Arcobacter in the Sewage treatment group may be due to the low BOD content (Table 1) (Hubert et al. 2012). Moreover, an earlier study suggested the genus Arcobacter was oftenly present in raw sewage water (Cai et al. 2014). The findings of the present work suggest that high amount of organic matter (BOD) along with treatment of fish farms with lime may be the reason for the sharp decline of this genus. ...
Article
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Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world’s largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0–50%), Pseudomonas (0–15%), Sulfurospirillum (0–9%), Cloacibacterium (0–6%), hgcI clade (7–29%), C39 (0–9%), V6 (3–36%), Fluiivicola (1–6%) and Cyanobium (3–8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.
... Previous work has already demonstrated energy consumption of the AOP-PPT will vary significantly for disinfection (7-80 kWh/m 3 ) depending on the level of contamination of the water source (Singh et al., 2019). Regardless, any reductions are unlikely to be significant given the high pathogen contamination that is characteristic of municipal wastewater (Odjadjare et al., 2010;Cai et al., 2014). ...
Article
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Emerging contaminants continue to pose a threat to environmental quality that warrant mitigation. Novel technologies are being investigated that offer promise in their removal, yet it is important that the environmental costs of these treatments do not overshadow their benefits. With sustainability a key priority in global infrastructure development, insights into the environmental impact of new technologies is necessitated. In the present work, the environmental burden of three novel GBM (graphene-based material) filters (porous graphene, graphene oxide-based foam and hybrid combination) are quantified and compared at a flow rate of 1 m³/d by way of life cycle impact assessment with an alternative solution, an AOP-PPT (advanced oxidation process by pulsed power treatment). Initial results demonstrated negligible differences in overall environmental impact between the three GBM filter formats (7.7–7.9 pt), while significant asymmetry was observed with the AOP-PPT that incurred a total impact score of 67.9 pt. This disparity was attributed to the high energy demand of the AOP-PPT that was a key predictor of environmental cost in an India context due to the high proportion of non-renewable energy sourced. The GBM filters were also considered at a range of breakthrough times and contrasted against the AOP-PPT. Results showed that differences between GBM filters were negligible at all breakthrough periods and that multiple breakthroughs a day would be required before the AOP-PPT became environmentally favourable. Finally, due to the AOP-PPT affording inclusive disinfection, the environmental burden of a GBM filter was compared under different scenarios of incorporated disinfection. The total impact of the AOP-PPT achieving full disinfection was found to be 242.5 pt compared to only 26.8 pt for the GBM filter coupled with UV254 (ultraviolet 254 nm) treatment and 13.9 pt when incorporating chlorination/de-chlorination. These findings should support sustainable development goals when combating prevailing emerging contaminants in municipal wastewater.
... Testing of SS at the wastewater treatment plant (WWTP) of Hong Kong showed that the influent sewage bacterial profile reflected the human microbiome. Moreover, most potentially pathogenic bacteria were still present in the effluent, although at a very low level (Cai et al., 2014). In this respect, thermal recycling of SS was suggested as a possible option to fulfil the requirements of sustainable development (Fels, 2003). ...
Article
Recently, sewage sludge (SS) disposal has become one of the greatest global challenges. In this study, we aimed to evaluate the effect of faba bean straw (Straw-B), wheat straw (Straw-W), and wood-chip pellets (WCP) amended to SS, as well as bioaugmentation (BA), on the physicochemical characteristics and structure of the microbial community of the treated SS. Sixteen days of incubation of SS-containing mixtures revealed the highest efficiency of Straw-W(BA) in terms of SS stabilisation, i.e., the highest and most stable respiration intensity, the lowest ammonia emission, and the highest stimulation effect on the cress seedling growth. Shotgun sequencing data analysis showed that Proteobacteria dominated in the raw SS with 60.17% reads, which consisted of 16.40%, 29.18%, and 12.33% of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, respectively. All treated samples were characterised by an increased abundance of Firmicutes (32.70–53.84%). A remarkable increase in virus abundance (0.34% reads) was detected in the treated SS, which was incubated without C amendment and bioaugmentation. The addition of C sources to the SS changed some physicochemical characteristics of the mixture. All of these findings provide novel insights toward a mechanistic understanding of the fate of the human sewage microbiome in wastewater and other environments.
... In the presented study, bacteria from the Firmicutes phylum occurred in higher numbers at the initial stages of the treatment process and their percentage in wastewater decreased over the subsequent stages of the treatment process. Bacteria belonging to the human gastrointestinal biota, including the Firmicutes phylum, often shape the taxonomic structure of inflowing wastewater, while at the later stages of treatment, their percentage is effectively reduced (Cai et al., 2014). ...
Article
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The diversity of beta-lactam antibiotic resistance genes, with particular emphasis on carbapenemase genes, during the treatment process at two wastewater treatment plants (WWTPs) with different levels of hospital wastewater inflow was investigated using high-throughput sequencing. An additional aspect of the study was to determine the taxonomic diversity of microorganisms in the studied samples. The obtained results suggest that bacteria of the Fusobacteriaceae family, not associated to date with this phenomenon, may be involved in the spread of antibiotic resistance in the environment. In samples from both wastewater treatment plants, the dominant beta-lactamase genes included blaOXA, blaGES, blaBEL, blaCfxA, and blaTEM. It is worth noting that the blaKPC and blaNDM genes were only found in untreated municipal wastewater with a higher hospital wastewater content. Moreover, an increase in the abundance of the blaIMP gene after the biological treatment stage in the studied treatment plants was found. In wastewater characterized by a higher proportion of hospital wastewater, 94 correlations were observed, while in wastewater with its lower proportion, 41 correlations were noted. Considering the above, the current research indicates that the inflow of hospital wastewater contributes to the spread of antibiotic resistance in the aquatic environment.
... This could be accounted for during wastewater epidemiology studies if it were found to be sufficient to impact results of observations taken at different locations within the collection system. The shift in community structure from the fresh gut microbiome to wastewater [70,71] indicates this may be possible. Of interest is the potential for sewers to serve as selective environments for growth of ARG-carrying microbes, selection, and/or horizonal gene transfer. ...
Article
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Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, blaTEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.
... Molecular biology and computational biology tools are now being widely used for investigating microbial communities (Dinsdale et al., 2008;Fresia et al., 2018), while PICRUSt2 (Douglas et al., 2020) annotates the functional features, among which the ARGs (Šamanić et al., 2021), expanding the possibility for a comprehensive study of the vast environmental resistance reservoirs associated to wastewaters (Cai et al., 2014;García-Aljaro et al., 2019;Narciso-da-Rocha et al., 2018;Port et al., 2012). ...
Article
Wastewater treatment plant (WWTP) effluents are pointed as hotspots for the introduction of both commensal and pathogenic bacteria as well as their antibiotic resistance genes (ARGs) in receiving water bodies. For the first time, the effect of partially treated submarine effluents was explored at the bottom and surface of the water column to provide a comprehensive overview of the structure of the microbiome and associated AR, and to assess environmental factors leading to their alteration. Seawater samples were collected over a 5-month period from submarine outfalls in central Adriatic Sea, Croatia. 16S rRNA amplicon sequencing was used to establish taxonomic and resistome profiles of the bacterial communities. The community differences observed between the two discharge areas, especially in the abundance of Proteobacteria and Firmicutes, could be due to the origin of wastewaters treated in WWTPs and the limiting environmental conditions such as temperature and nutrients. PICRUSt2 analysis inferred the total content of ARGs in the studied microbiomes and showed the highest abundance of resistance genes encoding multidrug efflux pumps, such as MexAB-OprM, AcrEF-TolC and MdtEF-TolC, followed by the modified peptidoglycan precursors, transporter genes encoding tetracycline, macrolide and phenicol resistance, and the bla operon conferring β-lactam resistance. A number of pathogenic genera introduced by effluents, including Acinetobacter, Arcobacter, Bacteroides, Escherichia-Shigella, Klebsiella, Pseudomonas, and Salmonella, were predicted to account for the majority of efflux pump-driven multidrug resistance, while Acinetobacter, Salmonella, Bacteroides and Pseudomonas were also shown to be the predominant carriers of non-efflux ARGs conferring resistance to most of nine antibiotic classes. Taken together, we evidenced the negative impact of submarine discharges of treated effluents via alteration of physico-chemical characteristics of the water column and enrichment of bacterial community with nonindigenous taxa carrying an arsenal of ARGs, which could contribute to the further propagation of the AR in the natural environment.
... Some genera in Cluster A were also abundant before the incubation (e.g., Lawsonia and Oscillospira), but these are also anaerobic bacteria found in human or animal intestines (Gophna et al., 2017). They are potentially carried by wastewater and remained in the activated sludge (Cai et al., 2014;Guo et al., 2019), indicating their ability to survive in various conditions. Cluster B genera were generally at low abundances on day 0, and increase in abundance by day 7 of anaerobic incubation except in the sample with only ED treatment (i.e., not ED plus filtrate addition). ...
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Residual biosolids can be land applied if they meet microbiological requirements at the time of application. Electro-dewatering technology is shown to reduce biosolids bacterial counts to detection limits with little potential for bacterial regrowth during incubations. Here, we investigated the impacts on Escherichia coli regrowth and microbial communities of biosolids pH, removed nutrients via the filtrate, and produced inhibitory compounds in electro-dewatered biosolids. Findings suggest pH as the primary mechanism impacting E. coli regrowth in electro-dewatered biosolids. Propidium monoazide treatments were effective to remove DNA from dead cells based on the removal of obligate anaerobes observed after anaerobic incubation. Analyses of high throughput sequenced data showed lower alpha-diversities associated with electro-dewatering treatment and incubation time. Moreover, biosolids pH and incubation period were the main factors contributing to the variations in microbial community compositions after incubation. Results highlight the role of biosolids pH on regrowing culturable bacteria and overall microbial communities.
... Further bolstering the SourceTracker results, the abundant taxa in the microbial communities revealed a distinct sewage plume assemblage that contrasted with the coastal ocean assemblage. Acidovorax, Bacteroides, Cloacibacterium, Comamonas, Macellibacteroides, and potentially pathogenic genera Acinetobacter, Aeromonas, and Arcobacter, the most abundant taxa in this sewage plume assemblage, have been consistently reported to be abundant taxa in sewage 16S rRNA microbiomes throughout the world (e.g., McLellan et al., 2010;Vandewalle et al., 2012;Shanks et al., 2013;Cai et al., 2014;Newton et al., 2015;Ahmed et al., 2017;Numberger et al., 2019). In contrast, the most abundant taxa identified in the coastal ocean assemblage were typical of the environmental marine microbiome and have all been identified previously as abundant in southern California coastal ocean communities: Alphaproteobacteria including the ubiquitous SAR11 clade, Amylibacter, Planktomarina, Planktotalea, and the coastal HIMB11 Roseobacter group, Flavobacteriaceae marine groups NS4 and NS5, and Synechococcus CC9902, a ubiquitous marine cyanobacterium (Morris et al., 2002;Fuhrman et al., 2006;Dufresne et al., 2008;Giebel et al., 2009;Steele et al., 2011;Cram et al., 2015). ...
Article
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Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multiple microbial source tracking tools were employed to characterize the impact and reach of an ocean wastewater treatment facility discharge in Mexico northward along the coast and across the Southwest United States- Mexico Border. Water samples were evaluated for fecal indicator bacteria (FIB), Enterococcus by culture-based methods, and human-associated genetic marker (HF183) and Enterococcus by droplet digital polymerase chain reaction (ddPCR). In addition, 16S rRNA gene sequence analysis was performed and the SourceTracker algorithm was used to characterize the bacterial community of the wastewater treatment plume and its contribution to beach waters. Sampling dates were chosen based on ocean conditions associated with northern currents. Evidence of a gradient in human fecal pollution that extended north from the wastewater discharge across the United States/Mexico border from the point source was observed using human-associated genetic markers and microbial community analysis. The spatial extent of fecal contamination observed was largely dependent on swell and ocean conditions. These findings demonstrate the utility of a combination of molecular tools for understanding and tracking specific pollutant sources in dynamic coastal water environments.
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The surveillance of tuberculosis infections has largely depended on clinical diagnostics and hospitalization data. The advancement in molecular methods creates an opportunity for the adoption of alternative surveillance systems, such as wastewater-based epidemiology. This study presents the use of conventional and advanced polymerase chain reaction techniques (droplet digital PCR) to determine the occurrence and concentration of total mycobacteria and members of the Mycobacterium tuberculosis complex (MTBC) in treated and untreated wastewater. Wastewater samples were taken from three wastewater treatment plants (WWTPs) in the city of Durban, South Africa, known for a high burden of TB/MDR-TB due to HIV infections. All untreated wastewater samples contained total mycobacteria and MTBC at varying percentages per WWTP studied. Other members of the MTBC related to tuberculosis infection in animals, M. bovis and M. caprae were also detected. The highest median concentration detected in untreated wastewater was up to 4.9(±0.2) Log10 copies/ml for total mycobacteria, 4.0(±0.85) Log10 copies/ml for MTBC, 3.9(±0.54) Log10 copies/ml for M. tuberculosis, 2.7(±0.42) Log10 copies/ml for M. africanum, 4.0(±0.29) Log10 copies/ml for M. bovis and 4.5(±0.52) Log10 copies/ml for M. caprae. Lower concentrations were detected in the treated wastewater, with a statistically significant difference (P-value ≤ 0.05) in concentrations observed. The log reduction achieved for these bacteria in the respective WWTPs was not statistically different, indicating that the treatment configuration did not have an impact on their removal. The detection of M. africanum in wastewater from South Africa shows that it is possible that some of the TB infections in the community could be caused by this mycobacterium. This study, therefore, highlights the potential of wastewater-based epidemiology for monitoring tuberculosis infections.
Thesis
Wasser ist lebensnotwendig und somit eine essentielle Ressource. Jedoch sind unsere Süßwasser-Ressourcen begrenzt und ihre Erhaltung daher besonders wichtig. Verschmutzungen mit Chemikalien und Krankheitserregern, die mit einer wachsenden Bevölkerung und Urbanisierung einhergehen, verschlechtern die Qualität unseres Süßwassers. Außerdem kann Wasser als Übertragungsvektor für Krankheitserreger dienen und daher wasserbürtige Krankheiten verursachen. Der Leibniz-Forschungsverbund INFECTIONS‘21 untersuchte innerhalb der interdisziplinären Forschungsgruppe III - „Wasser", Gewässer als zentralen Mittelpunkt für Krankheiterreger. Dabei konzentrierte man sich auf Clostridioides difficile sowie aviäre Influenza A-Viren, von denen angenommen wird, dass sie in die Gewässer ausgeschieden werden. Ein weiteres Ziel bestand darin, die bakterielle Gemeinschaften eines Klärwerkes der deutschen Hauptstadt Berlin zu charakterisieren, um anschließend eine Bewertung des potentiellen Gesundheitsrisikos geben zu können. Bakterielle Gemeinschaften des Roh- und Klarwassers aus dem Klärwerk unterschieden sich signifikant voneinander. Der Anteil an Darm-/Fäkalbakterien war relativ niedrig und potentielle Darmpathogene wurden größtenteils aus dem Rohwasser entfernt. Ein potentielles Gesundheitsrisiko konnte allerdings von potentiell pathogenen Legionellen wie L. lytica festgestellt werden, deren relative Abundanz im Klarwasser höher war als im Rohwasser. Es wurden außerdem drei C. difficile-Isolate aus den Klärwerk-Rohwasser und einem städtischen Badesee in Berlin (Weisser See) gewonnen und sequenziert. Die beiden Isolate aus dem Klärwerk tragen keine Toxin-Gene, wohingegen das Isolat aus dem See Toxin-Gene besitzt. Alle drei Isolate sind sehr nah mit humanen Stämmen verwandt. Dies deutet auf ein potentielles, wenn auch sporadisches Gesundheitsrisiko hin. (Aviäre) Influenza A-Viren wurden in 38.8% der untersuchten Sedimentproben mittels PCR detektiert, aber die Virusisolierung schlug fehl. Ein Experiment mit beimpften Wasser- und Sedimentproben zeigte, dass für die Isolierung aus Sedimentproben eine relativ hohe Viruskonzentration nötig ist. In Wasserproben ist jedoch ein niedriger Titer an Influenza A-Viren ausreichend, um eine Infektion auszulösen. Es konnte zudem auch festgestellt werden, dass sich „Madin-Darby Canine Kidney (MDCK)―-Zellkulturen im Gegensatz zu embryonierten Hühnereiern besser eignen, um Influenza A-Viren aus Sediment zu isolieren. Zusammenfassend lässt sich sagen, dass diese Arbeit mögliche Gesundheitsrisiken aufgedeckt hat, wie etwa durch Legionellen im untersuchten Berliner Klärwerk, deren relative Abundanz in geklärtem Abwasser höher ist als im Rohwasser. Desweiteren wird indiziert, dass Abwasser und Gewässer als Reservoir und Vektor für pathogene Organismen dienen können, selbst für nicht-typische Wasser-Pathogene wie C. difficile.
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Chapter
This chapter describes the current knowledge about the entry routes of antibiotics and antimicrobial resistance in the environment. It starts with an overview of the most important entry routes being wastewater and sludge from urban wastewater treatment plants, and natural fertilizers like pig slurry and cow manure and fertilizer from poultry farming. These sites are referred to as hotspots for antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB), including bacteria pathogenic for humans and animals, also those mentioned on the WHO priority list of global priority pathogens and of antibiotic-resistant bacteria. All these entry routes, manure, wastewater, and aquacultures, are characterized in terms of general sources of antibiotics, ARB, and ARGs. We also analyze the European Surveillance of Veterinary Antimicrobial Consumption report on the sale of antibacterials for veterinary. Furthermore, the EU guidelines to reduce the sales of veterinary antimicrobials across Europe under the umbrella of the EU One-Health Action Plan against Antimicrobial Resistance are mentioned. In the last section we point the need to develop and standardize the guidelines and method protocols for surveillance of AMR which need to be practicable, comparable, simple, and cost-effective so that they can be applied globally.
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Chapter
The term microbiome refers to the collection of microorganisms or their hereditary material from a specific biological system. Microbiomes are widespread and inescapable and contemporary in the soil, water, air, and in/on other living beings. Changes in the microbiome can conflict the wellbeing of the natural specialty where they occupy. In order to collect more comprehensive knowledge about these microbial communities, various measures have been pursued. Exploration of natural microbiome can be of a specific interest for revelation of novel creatures or novel gene or new microbial metabolites. Technologies that explore the roles, relationships, or characteristics of biomolecules of cells, such as DNA, RNA, proteins, or small metabolites, named by conjoin suffix—“omics”, as in genomics, transcriptomics, proteomics, or metabolomics, respectively. Genomics and transcriptomics research has elevated because of advances in microarray technology. Fast advancement in “omics”—metagenomics, metatranscriptomics, metaproteomics, metabolomics leading to a greater understanding of the patterns, processes, and mechanisms governing the structure and dynamics of microbiomes. Albeit each “omics” technology gives a valuable data independently yet when they use in consolidated structure, they delineate an increasingly extensive picture. The omics technologies have critical commitment to comprehend ecological bioremediation mechanisms. Omics advancements help in discovering of genes involved in biodegradation, to find out the functions of missing genes and to explore the metabolic pathways of bioremediation. Genomics has been used to study pure cultures with regard to bioremediation. Proteomics-based examinations have been helpful in elaborating changes in the structure and function of proteins as well as in the identification of key proteins associated with the physiological reaction of microorganisms when presented to anthropogenic contaminations. Transcriptomic or metatranscriptomics apparatuses are utilized to increase utilitarian bits of knowledge into the exercises of ecological microbial networks by considering their mRNA transcriptional profiles.
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The aim of this study was to investigate the presence of colistin- and/or tigecycline-resistant Klebsiella spp. in influents from four wastewater treatment plants (WWTPs), which partly reflect the gut microbiome of human populations. Colistin- and tigecycline-resistant Klebsiella pneumoniae isolates (K30/ST29) were detected four times from the WWTP A during a period of 3 months. Disruptions of the mgrB and ramR genes by ISEc68 and ISKpn21, respectively, were identified in those four isolates. They also shared the IncL/M 86,197-bp plasmids carrying a blaCTX-M-3 and Tn1548-associated armA [IS26-IntI1-dfrA12-gucF-aadA2-qacEΔ1-sul1-ISCR1-ISEc28-armA-ISEc29-msr(E)-mph(E)-IS26]. Those isolates formed a distinct cluster within wgMLST clusters of ST29 K30 public reference strains of human origin and were unique due to harboring of Tn21-like mercury resistance operon transposons in addition to silver, copper, and arsenic resistance determinants. Five K. pneumoniae strains with different STs and 1 Klebsiella quasipneumoniae strain, exhibiting colistin resistance, were detected in WWTPs B, C, and D. For these isolates, disruptions of mgrB by ISEc68 (three isolates) or ISEcl1 (one isolate), insertion of IS2 in the mgrB promoter region (one isolate), and inactivation of MgrB by a nonsense mutation (one isolate) were identified. Close monitoring of these mcr-negative colistin- and/or tigecycline-resistant bacteria in wastewater influents is imperative to avoid further limiting of treatment options.
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Municipal wastewater consists of a downstream collection of flushed sewage (without solid waste), other household runoffs, industrial runoffs, hospital runoffs and agricultural runoffs through an underground pipe before treatment. A runoff collection system called the wastewater treatment plant (WWTPs) treats such wastewater before release into environment following specific regulatory standards. This years-long practice has been improved upon by adding end-to-end pipe technologies with a view to enhancing the quality of effluent released. However, effluents released into the environment from design/application of WWTPs appear to contain emerging contaminants of both biotic and abiotic nature. The observation of chemical contaminants, antibiotic resistant bacteria (ARB), antibiotic resistant genes (ARGs) and diverse pathogenic bacteria genera in wastewater works release further affirm the abundance of such emerging contaminants. As a result, the government and water regulatory organizations in various part of the world are considering the removal of water reuse act from recycling policy/process. Current global debate is focused on questions about sustenance of any improved additional treatment level; effect of energy consumption by added treatment stage and its impact on the environmental wellness as contaminants borne wastewater is consistently released. Technological advancement/research suggests implementation of newer innovative infrastructural systems (NIIS) such as Mobbing Bed Biofilm Rector (MBBR), for wastewater effluent management which involve addition of newer wastewater treatment stages. This review addressed current pitfalls including wastewater microbiota of high epidemiological/public health relevance and affirms the need for such improvement which requires modification of ongoing institutional framework with a view to encourage implementation of NIIS for an improved effluent release. Exploiting the advances of microbial biofilming and the potentials of microbial biofueling as discussed in various section promises a future of robust environmental system, stable operational standard, release of quality effluent and sustainable management of wastewater works. Application of the aforementioned would enhance quality WWTPs release and in-defacto reduces spread of ARB/ARGs as well as impacts both the environment wellness and public health.
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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.
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Poorly operating wastewater treatment plants (WWTPs) result in faecal pollution of receiving waters, posing a health risk to humans and animals. The aim of this study was to determine the antimicrobial resistance patterns and presence of virulent genes in Enterococcus spp. isolated from three WWTPs final effluent and receiving waters in the North West Province, South Africa. Sixty-three Enterococcus spp. were identified and their antimicrobial susceptibility, as well as the presence of five virulence genes, determined. The antibiotic inhibition zone diameter data were subject to cluster analysis. Sixty-eight percent of the screened Enterococcus spp. were resistant to three or more antibiotics and harboured plasmids. Five virulence genes were detected and six multi-virulence profiles observed. Cluster analysis indicated groupings of isolates from all three effluents points downstream together, and between plants 1 and 2 together. The findings of this study have demonstrated that Enterococcus spp. harbouring virulence factors and plasmids that mediate multiple antibiotic resistance are present in effluent and receiving water systems that support various social needs. This is a cause for concern and it is recommended that Enterococcus be used as an additional faecal indicator when microbiological quality of water is assessed.
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The bacterial diversity and corresponding biological significance revealed by high-throughput sequencing contribute massive information to source tracking of fecal contamination. The performances of classification models on predicting the fecal source of geographical local and foreign samples were examined herein, by applying support vector machine (SVM) algorithm. Random forest (RF) and Adaboost were applied for comparison as well. Discriminatory sequences were selected from Clostridiale, Bacteroidales, or Lactobacillales bacterial groups using extremely randomized trees (ExtraTrees). 1.51–12.64% of the unique sequences in the original library composed the representative markers, and they contributed 70% of the discrepancies between source microbiomes. The overall accuracy of the SVM model and the RF model on local samples was 96.08% and 98.04%, respectively, higher than that of the Adaboost (90.20%). As for the non-local samples, the SVM assigned most of the fecal samples into the correct category while several false-positive judgments occurred in closely related groups. The results in this paper suggested that the SVM was a time-saving and accurate method for fecal source tracking in contaminated water body with the potential capability of executing tasks based on geographically unassociated samples, and underlined the necessity of qPCR analysis for accurate detection of human source pollution.
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Mammals, born with a near-sterile intestinal tract, are inoculated with their mothers’ microbiome during birth. Thereafter, extrinsic and intrinsic factors shape their intestinal microbe assemblage. Wastewater treatment works (WWTW), sites synonymous with pollutants and pathogens, receive influent from domestic, agricultural and industrial sources. The high nutrient content of wastewater supports abundant populations of chironomid midges (Diptera), which transfer these toxicants and potential pathogens to their predators, such as the banana bat Neoromicia nana (Vespertilionidae), thereby influencing their intestinal microbial assemblages. We used next generation sequencing and 16S rRNA gene profiling to identify and compare intestinal bacteria of N. nana at two reference sites and two WWTW sites. We describe the shared intestinal microbiome of the insectivorous bat, N. nana, consisting of seven phyla and eleven classes. Further, multivariate analyses revealed that location was the most significant driver (sex, body size and condition were not significant) of intestinal microbiome diversity. Bats at WWTW sites exhibited greater intestinal microbiota diversity than those at reference sites, likely due to wastewater exposure, stress and/or altered diet. Changes in their intestinal microbiota assemblages may allow these bats to cope with concomitant stressors.
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The raw sewage that flows through sewage systems contains a complex microbial community whose main source is the human gut microbiome, with bacteriophages being as abundant as bacteria or even more so. Phages that infect common strains of the human gut bacteriome and transient bacterial pathogens have been isolated in raw sewage, as have other phages corresponding to non-sewage inputs. Although human gut phages do not seem to replicate during their transit through the sewers, they predominate at the entrance of wastewater treatment plants, inside which the dominant populations of bacteria and phages undergo a swift change. The sheer abundance of phages in the sewage virome prompts several questions, some of which are addressed in this review. There is growing concern about their potential role in the horizontal transfer of genes, including those related with bacterial pathogenicity and antibiotic resistance. On the other hand, some phages that infect human gut bacteria are being used as indicators of fecal/viral water pollution and as source tracking markers and have been introduced in water quality legislation. Other potential applications of enteric phages to control bacterial pathogens in sewage or undesirable bacteria that impede the efficacy of wastewater treatments, including biofilm formation on membranes, are still being researched.
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On-site wastewater treatment systems are gaining popularity in areas where centralized wastewater treatment is not available. In the current case study a domestic activated sludge system was investigated, where treated effluent was stored in a short-term (1 week turn-over time) and a long-term (over 2-3 months) storage tank and was then used for irrigation. This design provided a unique opportunity to assess the chemical and microbial changes of the effluent upon storage. Long-term storage greatly improved both the chemical quality and the degradation efficiency of most organic micropollutants examined, including petroleum hydrocarbons and the pesticide diethyltoluamide. Taxonomic profile of the core microbiome of the effluent was also influenced upon storage. Relative abundance values of the members of Azoarcus and Thauera genera, which are important in degrading polycyclic aromatic hydrocarbons compounds, clearly indicated the biodegrading activity of these microbes across samples. The abundance of xenobiotics degradation functions correlated with the observed organic micropollutant degradation values indicating efficient microbial decomposition of these contaminants. Functions related to infectious diseases also had the highest abundance in the short-term storage tank corresponding well with the relative abundance of indicator organisms and implying to the significance of storage time in the elimination of pathogens. Based on these results, small, on-site wastewater treatment systems could benefit from long-term storage of wastewater effluent.
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Microbial sewage communities consist of a combination of human fecal microorganisms and non-fecal microorganisms, which may be residents of urban sewer infrastructure or flow-through originating from gray water or rainwater inputs. Together these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e. non-fecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal-derived, while 81.4% were consistently associated with the sewage infrastructure. The composition of fecal-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States.
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In recent years, PCR-based pyrosequencing of 16S rRNA genes has continuously increased our understanding of complex microbial communities in various environments of the Earth. However, there is always concern on the potential biases of diversity determination using different 16S rRNA gene primer sets and covered regions. Here, we first report how bacterial 16S rRNA gene pyrotags derived from a series of different primer sets resulted in the biased diversity metrics. In total, 14 types of pyrotags were obtained from two-end pyrosequencing of 7 amplicon pools generated by 7 primer sets paired by 1 of 4 forward primers (V1F, V3F, V5F, and V7F) and 1 of 4 reverse primers (V2R, V4R, V6R, and V9R), respectively. The results revealed that: i) the activated sludge exhibited a large bacterial diversity that represented a broad range of bacterial populations and served as a good sample in this methodology research; ii) diversity metrics highly depended on the selected primer sets and covered regions; iii) paired pyrotags obtained from two-end pyrosequencing of each short amplicon displayed different diversity metrics; iv) relative abundance analysis indicated the sequencing depth affected the determination of rare bacteria but not abundant bacteria; v) the primer set of V1F and V2R significantly underestimated the diversity of activated sludge; and vi) the primer set of V3F and V4R was highly recommended for future studies due to its advantages over other primer sets. All of these findings highlight the significance of this methodology research and offer a valuable reference for peer researchers working on microbial diversity determination.
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As Rocky Mountain Spotted Fever is the most common tick-borne disease in South America, the presence of Rickettsia sp. in Amblyomma ticks is a possible indication of its endemicity in certain geographic regions. In the present work, bacterial DNA sequences related to Rickettsia amblyommii genes in A. dubitatum ticks, collected in the Brazilian state of Mato Grosso, were discovered. Simultaneously, Paracoccus sp. was detected in aproximately 77% of A. cajennense specimens collected in Rio de Janeiro, Brazil. This is the first report of Paracoccus sp. infection in a specific tick population, and raises the possibility of these bacteria being maintained and/or transmitted by ticks. Whether Paracoccus sp. represents another group of pathogenic Rhodobacteraceae or simply plays a role in A. cajennense physiology, is unknown. The data also demonstrate that the rickettsial 16S rRNA specific primers used forRickettsia spp. screening can also detect Paracoccus alpha-proteobacteria infection in biological samples. Hence, a PCR-RFLP strategy is presented to distinguish between these two groups of bacteria.
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Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.
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In this study fecal microflora of human infants born through vaginal delivery (VB) and through cesarean section (CB) was investigated using culture independent 16S rDNA cloning and sequencing approach. The results obtained clearly revealed that fecal microbiota of VB infants distinctly differ from their counterpart CB infants. The intestinal microbiota of infants delivered by cesarean section appears to be more diverse, in terms of bacteria species, than the microbiota of vaginally delivered infants. The most abundant bacterial species present in VB infants were Acinetobacter sp., Bifidobacterium sp. and Staphylococcus sp. However, CB infant's fecal microbiota was dominated with Citrobacter sp., Escherichia coli and Clostridium difficile. The intestinal microbiota of cesarean section delivered infants in this study was also characterized by an absence of Bifidobacteria species. An interesting finding of our study was recovery of large number of Acinetobacter sp consisting of Acinetobacter pittii (former Acinetobacter genomic species 3), Acinetobacter junii and Acinetobacter baumannii in the VB infants clone library. Among these Acinetobacter baumannii is a known nosocomial pathogen and Acinetobacter pittii (gen. sp. 3) is recently recognized as clinically important taxa within the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex. Though, none of the infants had shown any sign of clinical symptoms of disease, this observation warrant a closer look.
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Standardization of DNA extraction is a fundamental issue of fidelity and comparability in investigations of environmental microbial communities. Commercial kits for soil or feces are often adopted for studies of activated sludge because of a lack of specific kits, but they have never been evaluated regarding their effectiveness and potential biases based on high throughput sequencing. In this study, seven common DNA extraction kits were evaluated, based on not only yield/purity but also sequencing results, using two activated sludge samples (two sub-samples each, i.e. ethanol-fixed and fresh, as-is). The results indicate that the bead-beating step is necessary for DNA extraction from activated sludge. The two kits without the bead-beating step yielded very low amounts of DNA, and the least abundant operational taxonomic units (OTUs), and significantly underestimated the Gram-positive Actinobacteria, Nitrospirae, Chloroflexi, and Alphaproteobacteria and overestimated Gammaproteobacteria, Deltaproteobacteria, Bacteroidetes, and the rare phyla whose cell walls might have been readily broken. Among the other five kits, FastDNA SPIN Kit for Soil extracted the most and the purest DNA. Although the number of total OTUs obtained using this kit was not the highest, the abundant OTUs and abundance of Actinobacteria demonstrated its efficiency. The three MoBio kits and one ZR kit produced fair results, but had a relatively low DNA yield and/or less Actinobacteria-related sequences. Moreover, the 50 % ethanol fixation increased the DNA yield, but did not change the sequenced microbial community in a significant way. Based on the present study, the FastDNA SPIN kit for Soil is recommended for DNA extraction of activated sludge samples. More importantly, the selection of the DNA extraction kit must be done carefully if the samples contain dominant lysing-resistant groups, such as Actinobacteria and Nitrospirae.
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Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary.
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Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.
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