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Girón-Guzmán I, Cuevas-Ferrando E, Barranquero R, Díaz-Reolid A, Puchades-Colera P, Falcó I, Pérez-Cataluña A, Sánchez G. Urban wastewater-based epidemiology for multi-viral pathogen surveillance in the Valencian region, Spain. WATER RESEARCH 2024; 255:121463. [PMID: 38537489 DOI: 10.1016/j.watres.2024.121463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/24/2024]
Abstract
Wastewater-based epidemiology (WBE) has lately arised as a promising tool for monitoring and tracking viral pathogens in communities. In this study, we analysed WBE's role as a multi-pathogen surveillance strategy to detect the presence of several viral illness causative agents. Thus, an epidemiological study was conducted from October 2021 to February 2023 to estimate the weekly levels of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Respiratory Syncytial virus (RSV), and Influenza A virus (IAV) in influent wastewater samples (n = 69). In parallel, a one-year study (October 2021 to October 2022) was performed to assess the presence of pathogenic human enteric viruses. Besides, monitoring of proposed viral fecal contamination indicators crAssphage and Pepper mild mottle virus (PMMoV) was also assessed, along with plaque counting of somatic coliphages. Genetic material of rotavirus (RV), human astrovirus (HAStV), and norovirus genogroup I (GI) and GII was found in almost all samples, while hepatitis A and E viruses (HAV and HEV) only tested positive in 3.77 % and 22.64 % of the samples, respectively. No seasonal patterns were overall found for enteric viruses, although RVs had a peak prevalence in the winter months. All samples tested positive for SARS-CoV-2 RNA, with a mean concentration of 5.43 log genome copies per liter (log GC/L). The tracking of the circulating SARS-CoV-2 variants of concern (VOCs) was performed by both duplex RT-qPCR and next generation sequencing (NGS). Both techniques reliably showed how the dominant VOC transitioned from Delta to Omicron during two weeks in Spain in December 2021. RSV and IAV viruses peaked in winter months with mean concentrations 6.40 and 4.10 log GC/L, respectively. Moreover, the three selected respiratory viruses strongly correlated with reported clinical data when normalised by wastewater physico-chemical parameters and presented weaker correlations when normalising sewage concentration levels with crAssphage or somatic coliphages titers. Finally, predictive models were generated for each respiratory virus, confirming high reliability on WBE data as an early-warning system and communities illness monitoring system. Overall, this study presents WBE as an optimal tool for multi-pathogen tracking reflecting viral circulation and diseases trends within a selected area, its value as a multi-pathogen early-warning tool stands out due to its public health interest.
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Affiliation(s)
- Inés Girón-Guzmán
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Enric Cuevas-Ferrando
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
| | - Regino Barranquero
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Azahara Díaz-Reolid
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Pablo Puchades-Colera
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Irene Falcó
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Alba Pérez-Cataluña
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain
| | - Gloria Sánchez
- Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, Valencia 46980, Spain.
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2
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Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
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Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
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Suh SH, Lee JS, Kim SH, Vinjé J, Kim SH, Park GW. Evaluation of crAssphages as a potential marker of human viral contamination in environmental water and fresh leafy greens. Front Microbiol 2024; 15:1374568. [PMID: 38618485 PMCID: PMC11010641 DOI: 10.3389/fmicb.2024.1374568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/04/2024] [Indexed: 04/16/2024] Open
Abstract
CrAssphages are human gut bacteriophages with potential use as an indicator of human fecal contamination in water and other environmental systems. We determined the prevalence and abundance of crAssphages in water, food, and fecal samples and compared these estimates with the prevalence of norovirus. Samples were tested using two crAssphage-specific qPCR assays (CPQ056 and TN201-203) and for norovirus using TaqMan realtime RT-PCR. CrAssphage was detected in 40% of human fecal specimens, 61% of irrigation water samples, 58.5% of stream water samples, and 68.5% of fresh leafy greens samples. Interestingly, across all sample categories, crAssphage concentrations were 2-3 log10 higher than norovirus concentrations. The correlation of detection of crAssphage and norovirus was significant for the irrigation water samples (r = 0.74, p = 7.4e-06). Sequences obtained from crAssphage positive samples from human fecal and stream water samples phylogenetically clustered with genotype I crAssphages, whereas sequences derived from irrigation water samples clustered differently from other genotypes. Our data show that crAssphages were prevalent in norovirus-positive water samples and in fresh leafy green samples, there was a strong correlation between the presence of crAssphage and norovirus. CrAssphage genomic copies were consistently higher than norovirus copies in all sample types. Overall, our findings suggest that crAssphages could be used as reliable indicators to monitor fecal-borne virus contamination within the food safety chain.
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Affiliation(s)
- Soo Hwan Suh
- Division of Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si, Republic of Korea
| | - Jeong Su Lee
- Division of Emerging Virus Vector Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si, Republic of Korea
| | - Seung Hwan Kim
- Division of Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si, Republic of Korea
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Soon Han Kim
- Division of Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si, Republic of Korea
| | - Geun Woo Park
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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4
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Babkin IV, Tikunov AY, Baykov IK, Morozova VV, Tikunova NV. Genome Analysis of Epsilon CrAss-like Phages. Viruses 2024; 16:513. [PMID: 38675856 PMCID: PMC11054128 DOI: 10.3390/v16040513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.
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Affiliation(s)
- Igor V. Babkin
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Artem Y. Tikunov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Ivan K. Baykov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
- Shared Research Facility “Siberian Circular Photon Source” (SRF “SKIF”) of Boreskov Institute of Catalysis SB RAS, 630090 Novosibirsk, Russia
| | - Vera V. Morozova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Nina V. Tikunova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
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5
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Geissler M, Mayer R, Helm B, Dumke R. Food and Environmental Virology: Use of Passive Sampling to Characterize the Presence of SARS-CoV-2 and Other Viruses in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:25-37. [PMID: 38117471 DOI: 10.1007/s12560-023-09572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/18/2023] [Indexed: 12/21/2023]
Abstract
Fecal shedding of SARS-CoV-2 leads to a renaissance of wastewater-based epidemiology (WBE) as additional tool to follow epidemiological trends in the catchment of treatment plants. As alternative to the most commonly used composite samples in surveillance programs, passive sampling is increasingly studied. However, the many sorbent materials in different reports hamper the comparison of results and a standardization of the approach is necessary. Here, we compared different cost-effective sorption materials (cheesecloths, gauze swabs, electronegative filters, glass wool, and tampons) in torpedo-style housings with composite samples. Despite a remarkable variability of the concentration of SARS-CoV-2-specific gene copies, analysis of parallel-deposited passive samplers in the sewer demonstrated highest rate of positive samples and highest number of copies by using cheesecloths. Using this sorption material, monitoring of wastewater of three small catchments in the City of Dresden resulted in a rate of positive samples of 50% in comparison with composite samples (98%). During the investigation period, incidence of reported cases of SARS-CoV-2 in the catchments ranged between 16 and 170 per 100,000 persons and showed no correlation with the measured concentrations of E gene in wastewater. In contrast, constantly higher numbers of gene copies in passive vs. composite samples were found for human adenovirus and crAssphage indicating strong differences of efficacy of methods concerning the species investigated. Influenza virus A and B were sporadically detected allowing no comparison of results. The study contributes to the further understanding of possibilities and limits of passive sampling approaches in WBE.
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Affiliation(s)
- Michael Geissler
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Robin Mayer
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Dresden, Germany
| | - Björn Helm
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, Dresden, Germany
| | - Roger Dumke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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6
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Farkas K, Mannion F, Sorby R, Winterbourn B, Allender S, Gregory CGM, Holding P, Thorpe JM, Malham SK, Le Vay L. Assessment of wastewater derived pollution using viral monitoring in two estuaries. MARINE POLLUTION BULLETIN 2024; 200:116081. [PMID: 38354589 DOI: 10.1016/j.marpolbul.2024.116081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/16/2024]
Abstract
Human wastewater-derived pollution of the environment is an emerging health risk that increases the number of waterborne and foodborne illnesses globally. To better understand and mitigate such health risks, we investigated the prevalence of faecal indicator bacteria, Escherichia coli, and indicator virus (crAssphage) along with human and animal enteric viruses (adenoviruses, noroviruses, sapoviruses, hepatitis E virus) in shellfish and water samples collected from two shellfish harvesting areas in the UK. Human noroviruses were detected at higher detection rates in oyster and water samples compared to mussels with peaks during the autumn-winter seasons. Human enteric viruses were sporadically detected during the warmer months, suggesting potential introduction by tourists following the relaxation of COVID-19 lockdown measures. Our results suggest that viral indicators are more suitable for risk assessment and source tracking than E. coli. The detection of emerging hepatitis and sapoviruses, support the need for comprehensive viral monitoring in shellfish harvesting areas.
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Affiliation(s)
- Kata Farkas
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK; School of Environment & Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, UK.
| | - Finn Mannion
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Rees Sorby
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Ben Winterbourn
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Susan Allender
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Charlie G M Gregory
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK; School of Environment & Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, UK
| | - Phoebe Holding
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Jamie M Thorpe
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
| | - Lewis Le Vay
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
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7
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Remesh AT, Viswanathan R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09584-5. [PMID: 38413544 DOI: 10.1007/s12560-024-09584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.
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8
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Gao FZ, He LY, Liu YS, Zhao JL, Zhang T, Ying GG. Integrating global microbiome data into antibiotic resistance assessment in large rivers. WATER RESEARCH 2024; 250:121030. [PMID: 38113599 DOI: 10.1016/j.watres.2023.121030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Rivers are important in spreading antimicrobial resistance (AMR). Assessing AMR risk in large rivers is challenged by large spatial scale and numerous contamination sources. Integrating river resistome data into a global framework may help addressing this difficulty. Here, we conducted an omics-based assessment of AMR in a large river (i.e. the Pearl River in China) with global microbiome data. Results showed that antibiotic resistome in river water and sediment was more diversified than that in other rivers, with contamination levels in some river reaches higher than global baselines. Discharge of WWTP effluent and landfill waste drove AMR prevalence in the river, and the resistome level was highly associated with human and animal sources. Detection of 54 risk rank I ARGs and emerging mobilizable mcr and tet(X) highlighted AMR risk in the river reaches with high human population density and livestock pollution. Florfenicol-resistant floR therein deserved priority concerns due to its high detection frequency, dissimilar phylogenetic distance, mobilizable potential, and presence in multiple pathogens. Co-sharing of ARGs across taxonomic ranks implied their transfer potentials in the community. By comparing with global genomic data, we found that Burkholderiaceae, Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae were important potential ARG-carrying bacteria in the river, and WHO priority carbapenem-resistant Enterobacteriaceae, A. baumannii and P. aeruginosa should be included in future surveillance. Collectively, the findings from this study provide an omics-benchmarked assessment strategy for public risk associated with AMR in large rivers.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
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9
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Katayama YA, Hayase S, Iwamoto R, Kuroita T, Okuda T, Kitajima M, Masago Y. Simultaneous extraction and detection of DNA and RNA from viruses, prokaryotes, and eukaryotes in wastewater using a modified COPMAN. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167866. [PMID: 37863234 DOI: 10.1016/j.scitotenv.2023.167866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Wastewater surveillance can offer a comprehensive grasp of infectious disease prevalence and human health because wastewater contains various human-derived microbial pathogens, including viruses, bacteria, and fungi. However, methods capable of simultaneous detection of multiple groups of targets in the automated systems and large-scale surveillance are still under development. Here, we demonstrated the modification, involving the addition of bead-beating, to the existing COPMAN (COagulation and Proteolysis method using MAgnetic beads for detection of Nucleic acids in wastewater) enabled enhanced detection of various microorganisms, including SARS-CoV-2. The modified method, termed bead-beating COPMAN (BB-COPMAN), was evaluated through spike-and-recovery experiments and comparative analysis against three previously reported methods for simultaneous DNA/RNA detection. Our study targeted a range of microorganisms, including enveloped and non-enveloped RNA viruses (SARS-CoV-2, PMMoV), a DNA virus (crAssphage), archaea, gram-negative and gram-positive bacteria (E. coli, Lachnospiraceae), antibiotic resistance gene (ampC), and fungi (Candida albicans). The recovery rates of BB-COPMAN for gram-negative and gram-positive bacteria were 17 and 2.1-fold higher, respectively, compared to the method for DNA/RNA detection. Additionally, BB-COPMAN exhibited the highest extraction efficiency among the tested methods, achieving 1.2-5.7 times more DNA and 1.1-69 times more RNA yield on average. BB-COPMAN allowed the detection of SARS-CoV-2 from all nine samples and PMMoV at concentrations 39-97 times higher than other methods. Moreover, BB-COPMAN detected larger amounts of DNA for four out of six DNA targets than the previously reported DNA/RNA detection method. These results demonstrated that BB-COPMAN enables enhanced detection of multiple targets in a single flow of nucleic acid extraction, making the method well-suited for automated systems. In conclusion, BB-COPMAN is a promising method in wastewater surveillance for assessing the prevalence of wide range of pathogenic microorganisms.
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Affiliation(s)
- Yuka Adachi Katayama
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Shin Hayase
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Ryo Iwamoto
- Shionogi & Co., Ltd., Head Office, 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan; AdvanSentinel Inc., 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Tomohiro Kuroita
- Shionogi & Co., Ltd., Head Office, 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan; AdvanSentinel Inc., 3-1-8 Doshomachi, Chuo-ku, Osaka 541-0045, Japan
| | - Tomohiko Okuda
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Yusaku Masago
- Shionogi & Co., Ltd., Pharmaceutical Research Center, 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.
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10
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Ramos-Barbero MD, Gómez-Gómez C, Sala-Comorera L, Rodríguez-Rubio L, Morales-Cortes S, Mendoza-Barberá E, Vique G, Toribio-Avedillo D, Blanch AR, Ballesté E, Garcia-Aljaro C, Muniesa M. Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution. Nat Commun 2023; 14:4295. [PMID: 37463935 PMCID: PMC10354031 DOI: 10.1038/s41467-023-40098-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Crassvirales (crAss-like phages) are an abundant group of human gut-specific bacteriophages discovered in silico. The use of crAss-like phages as human fecal indicators is proposed but the isolation of only seven cultured strains of crAss-like phages to date has greatly hindered their study. Here, we report the isolation and genetic characterization of 25 new crAss-like phages (termed crAssBcn) infecting Bacteroides intestinalis, belonging to the order Crassvirales, genus Kehishuvirus and, based on their genomic variability, classified into six species. CrAssBcn phage genomes are similar to ΦCrAss001 but show genomic and aminoacidic differences when compared to other crAss-like phages of the same family. CrAssBcn phages are detected in fecal metagenomes around the world at a higher frequency than ΦCrAss001. This study increases the known crAss-like phage isolates and their abundance and heterogeneity open the question of what member of the Crassvirales group should be selected as human fecal marker.
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Affiliation(s)
- María Dolores Ramos-Barbero
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Sara Morales-Cortes
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Elena Mendoza-Barberá
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Gloria Vique
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Daniel Toribio-Avedillo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Anicet R Blanch
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Elisenda Ballesté
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain.
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11
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Wu H, Juel MAI, Eytcheson S, Aw TG, Munir M, Molina M. Temporal and spatial relationships of CrAssphage and enteric viral and bacterial pathogens in wastewater in North Carolina. WATER RESEARCH 2023; 239:120008. [PMID: 37192571 PMCID: PMC10896230 DOI: 10.1016/j.watres.2023.120008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/20/2023] [Accepted: 04/27/2023] [Indexed: 05/18/2023]
Abstract
Enteric disease remains one of the most common concerns for public health, particularly when it results from human exposure to surface and recreational waters contaminated with wastewater. Characterizing the temporal and spatial variation of enteric pathogens prevalent in wastewater is critical to develop approaches to mitigate their distribution in the environment. In this study, we aim to characterize pathogen variability and test the applicability of the human-associated wastewater indicator crAssphage as an indicator of enteric viral and bacterial pathogens. We conducted weekly samplings for 14 months from four wastewater treatment plants in North Carolina, USA. Untreated wastewater samples were processed using hollow fiber ultrafiltration, followed by secondary concentration methods. Adenovirus, norovirus, enterovirus, Salmonella, Shiga toxin 2 (stx2), Campylobacter, and crAssphage were measured by quantitative polymerase chain reaction (qPCR) and reverse transcriptase (rt)-qPCR. Our results revealed significant correlations between crAssphage and human adenovirus, enterovirus, norovirus, Salmonella, and Campylobacter (p<0.01). Pathogens and crAssphage concentrations in untreated wastewater showed distinct seasonal patterns, with peak concentrations of crAssphage and viral pathogens in fall and winter, while bacterial pathogens showed peaked concentrations in either winter (Campylobacter), fall (Salmonella), or summer (stx2). This study enhances the understanding of crAssphage as an alternative molecular indicator for both bacterial and viral pathogens. The findings of this study can also inform microbial modeling efforts for the prediction of the impact of wastewater pathogens on surface waters due to increased flooding events and wastewater overflows associated with climate change.
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Affiliation(s)
- Huiyun Wu
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, 27709, USA; Oak Ridge Institute for Science and Education, PO Box 117, Oak Ridge, Tennessee 37831 USA; Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, USA
| | - Md Ariful Islam Juel
- Department of Civil and Environmental Engineering, University of North Carolina Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Stephanie Eytcheson
- Oak Ridge Institute for Science and Education, PO Box 117, Oak Ridge, Tennessee 37831 USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, USA
| | - Mariya Munir
- Department of Civil and Environmental Engineering, University of North Carolina Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Marirosa Molina
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, 27709, USA.
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12
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Ariyadasa S, Taylor W, Weaver L, McGill E, Billington C, Pattis I. Nonbacterial Microflora in Wastewater Treatment Plants: an Underappreciated Potential Source of Pathogens. Microbiol Spectr 2023; 11:e0048123. [PMID: 37222623 PMCID: PMC10269893 DOI: 10.1128/spectrum.00481-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Wastewater treatment plants (WWTPs) receive and treat large volumes of domestic, industrial, and urban wastewater containing pathogenic and nonpathogenic microorganisms, chemical compounds, heavy metals, and other potentially hazardous substances. WWTPs play an essential role in preserving human, animal, and environmental health by removing many of these toxic and infectious agents, particularly biological hazards. Wastewater contains complex consortiums of bacterial, viral, archaeal, and eukaryotic species, and while bacteria in WWTP have been extensively studied, the temporal and spatial distribution of nonbacterial microflora (viruses, archaea, and eukaryotes) is less understood. In this study, we analyzed the viral, archaeal, and eukaryotic microflora in wastewater throughout a treatment plant (raw influent, effluent, oxidation pond water, and oxidation pond sediment) in Aotearoa (New Zealand) using Illumina shotgun metagenomic sequencing. Our results suggest a similar trend across many taxa, with an increase in relative abundance in oxidation pond samples compared to influent and effluent samples, except for archaea, which had the opposite trend. Additionally, some microbial families, such as Podoviridae bacteriophages and Apicomplexa alveolates, appeared largely unaffected by the treatment process, with their relative abundance remaining stable throughout. Several groups encompassing pathogenic species, such as Leishmania, Plasmodium, Toxoplasma, Apicomplexa, Cryptococcus, Botrytis, and Ustilago, were identified. If present, these potentially pathogenic species could be a threat to human and animal health and agricultural productivity; therefore, further investigation is warranted. These nonbacterial pathogens should be considered when assessing the potential for vector transmission, distribution of biosolids to land, and discharge of treated wastewater to waterways or land. IMPORTANCE Nonbacterial microflora in wastewater remain understudied compared to their bacterial counterparts despite their importance in the wastewater treatment process. In this study, we report the temporal and spatial distributions of DNA viruses, archaea, protozoa, and fungi in raw wastewater influent, effluent, oxidation pond water, and oxidation pond sediments by using shotgun metagenomic sequencing. Our study indicated the presence of groups of nonbacterial taxa which encompass pathogenic species that may have potential to cause disease in humans, animals, and agricultural crops. We also observed higher alpha diversity in viruses, archaea, and fungi in effluent samples than in influent samples. This suggests that the resident microflora in the wastewater treatment plant may be making a greater contribution to the diversity of taxa observed in wastewater effluent than previously thought. This study provides important insights to better understand the potential human, animal, and environmental health impacts of discharged treated wastewater.
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Affiliation(s)
- Sujani Ariyadasa
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - William Taylor
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Erin McGill
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Craig Billington
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Isabelle Pattis
- Institute of Environmental Science and Research, Christchurch, New Zealand
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13
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Sresung M, Paisantham P, Ruksakul P, Kongprajug A, Chyerochana N, Gallage TP, Srathongneam T, Rattanakul S, Maneein S, Surasen C, Passananon S, Mongkolsuk S, Sirikanchana K. Microbial source tracking using molecular and cultivable methods in a tropical mixed-use drinking water source to support water safety plans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162689. [PMID: 36898534 DOI: 10.1016/j.scitotenv.2023.162689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Microbial contamination deteriorates source water quality, posing a severe problem for drinking water suppliers worldwide and addressed by the Water Safety Plan framework to ensure high-quality and reliable drinking water. Microbial source tracking (MST) is used to examine different microbial pollution sources via host-specific intestinal markers for humans and different types of animals. However, the application of MST in tropical surface water catchments that provide raw water for drinking water supplies is limited. We analyzed a set of MST markers, namely, three cultivable bacteriophages and four molecular PCR and qPCR assays, together with 17 microbial and physicochemical parameters, to identify fecal pollution from general, human-, swine-, and cattle-specific sources. Seventy-two river water samples at six sampling sites were collected over 12 sampling events during wet and dry seasons. We found persistent fecal contamination via the general fecal marker GenBac3 (100 % detection; 2.10-5.42 log10 copies/100 mL), with humans (crAssphage; 74 % detection; 1.62-3.81 log10 copies/100 mL) and swine (Pig-2-Bac; 25 % detection; 1.92-2.91 log10 copies/100 mL). Higher contamination levels were observed during the wet season (p < 0.05). The conventional PCR screening used for the general and human markers showed 94.4 % and 69.8 % agreement with the respective qPCR results. Specifically, in the studied watershed, coliphage could be a screening parameter for the crAssphage marker (90.6 % and 73.7 % positive and negative predictive values; Spearman's rank correlation coefficient = 0.66; p < 0.001). The likelihood of detecting the crAssphage marker significantly increased when total and fecal coliforms exceeded 20,000 and 4000 MPN/100 mL, respectively, as Thailand Surface Water Quality Standards, with odds ratios and 95 % confidence intervals of 15.75 (4.43-55.98) and 5.65 (1.39-23.05). Our study confirms the potential benefits of incorporating MST monitoring into water safety plans, supporting the use of this approach to ensure high-quality drinking water supplies worldwide.
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Affiliation(s)
- Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Phongsawat Paisantham
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Pacharaporn Ruksakul
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Natcha Chyerochana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Tharindu Pollwatta Gallage
- Program in Environmental Toxicology, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Thitima Srathongneam
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Siriwara Maneein
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Chatsinee Surasen
- Water Resources and Environment Department, Metropolitan Waterworks Authority, Bangkok 10210, Thailand
| | - Somsak Passananon
- Line of Deputy Governor (Water Production), Metropolitan Waterworks Authority, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand.
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14
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Andrianjakarivony FH, Bettarel Y, Desnues C. Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments. J Microbiol 2023:10.1007/s12275-023-00052-6. [PMID: 37261715 DOI: 10.1007/s12275-023-00052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.
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Affiliation(s)
- Felana Harilanto Andrianjakarivony
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, 13005, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 13009, Marseille, France
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, 34090, Montpellier, France.
| | - Christelle Desnues
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, 13005, Marseille, France
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15
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Ahmed W, Smith WJM, Sirikanchana K, Kitajima M, Bivins A, Simpson SL. Influence of membrane pore-size on the recovery of endogenous viruses from wastewater using an Adsorption-Extraction method. J Virol Methods 2023; 317:114732. [PMID: 37080396 PMCID: PMC10111872 DOI: 10.1016/j.jviromet.2023.114732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/22/2023] [Accepted: 04/14/2023] [Indexed: 04/22/2023]
Abstract
The ongoing COVID-19 pandemic has emphasized the significance of wastewater-based epidemiology (WBE) in monitoring and tracking the spread of infectious diseases, including SARS-CoV-2. The WBE approach relies on detecting genetic material from viruses in wastewater, which could provide an early warning of outbreaks in communities. In this study, we evaluated the recovery of four types of endogenous viruses, including non-enveloped DNA (crAssphage and human adenovirus 40/41), non-enveloped RNA (enterovirus), and enveloped RNA (SARS-CoV-2) viruses, from wastewater samples using the adsorption-extraction (AE) method with electronegative membranes of different pore sizes (0.22, 0.45, and 0.8 μm). Our findings showed that the membrane with a pore size of 0.80 μm performed similarly to the membrane with a pore size of 0.45 μm for virus capture (repeated measurement one-way ANOVA; p >0.05), indicating that larger pore size membranes could process larger sample volumes while maintaining similar virus capture efficiency. We determined the recovery efficiencies of indigenous crAssphage and pepper mild mottle virus, which showed recovery efficiencies ranging from 50% to 94% and from 20% to 62%, respectively. Our results suggest that the AE method is a cost-effective and efficient approach for virus recovery in wastewater, and the use of larger pore size membranes may be beneficial for processing larger sample volumes, particularly for environmental waters containing low concentrations of viruses. This study provides valuable information for optimizing the AE method for virus recovery from wastewater, which is essential for monitoring and tracking infectious diseases in communities.
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Affiliation(s)
- Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Wendy J M Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060 -8628, Japan
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA
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16
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Hamza IA, Abd-Elmaksoud S. Applicability of crAssphage as a performance indicator for viral reduction during activated sludge wastewater treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50723-50731. [PMID: 36800087 PMCID: PMC10104927 DOI: 10.1007/s11356-023-25824-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/05/2023] [Indexed: 04/16/2023]
Abstract
A major threat to water quality is the discharge of human-derived wastewater, which can cause waterborne illnesses associated with enteric viruses. A poor association exists between fecal indicator bacteria and virus fate in the environment, especially during wastewater treatment. In the current study, the potential of using a novel human gut bacteriophage crAssphage as a wastewater treatment process indicator was evaluated. Using qPCR, influent and effluent wastewater samples of two wastewater treatment plants were analyzed for crAssphage and human viruses including human bocavirus (HBoV), human adenovirus (HAdV), and human polyomavirus (HPyV). All samples were positive for crAssphage. The annual crAssphage concentrations varied between 1.45E + 04 and 2.39E + 08 gc/l in influent samples and from 1.25E + 04 to 7.88E + 06 gc/l in effluent samples. Human viruses concentrations were some orders of magnitude lower than that of crAssphage. Data demonstrated a significant correlation between crAssphage, HAdV, and HPyV during the wastewater treatment process, suggesting that crAssphage and human viral pathogens have similar removal mechanisms. Ultimately, this work concludes that crAssphage could be a performance indicator for viral reduction in the wastewater treatment process.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, 33 El Buhouth St., Giza, 12622, Dokki, Egypt.
| | - Sherif Abd-Elmaksoud
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, 33 El Buhouth St., Giza, 12622, Dokki, Egypt
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17
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Gomi R, Haramoto E, Wada H, Sugie Y, Ma CY, Raya S, Malla B, Nishimura F, Tanaka H, Ihara M. Development of two microbial source tracking markers for detection of wastewater-associated Escherichia coli isolates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:160952. [PMID: 36549531 DOI: 10.1016/j.scitotenv.2022.160952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Escherichia coli has been used as an indicator of fecal pollution in environmental waters. However, its presence in environmental waters does not provide information on the source of water pollution. Identifying the source of water pollution is paramount to be able to effectively reduce contamination. The present study aimed to identify E. coli microbial source tracking (MST) markers that can be used to identify domestic wastewater contamination in environmental waters. We first analyzed wastewater E. coli genomes sequenced by us (n = 50) and RefSeq animal E. coli genomes of fecal origin (n = 82), and identified 144 candidate wastewater-associated marker genes. The sensitivity and specificity of the candidate marker genes were then assessed by screening the genes in 335 RefSeq wastewater E. coli genomes and 3318 RefSeq animal E. coli genomes. We finally identified two MST markers, namely W_nqrC and W_clsA_2, which could be used for detection of wastewater-associated E. coli isolates. These two markers showed higher performance than the previously developed human wastewater-associated E. coli markers H8 and H12. When used in combination, W_nqrC and W_clsA_2 showed specificity of 98.9 % and sensitivity of 25.7 %. PCR assays to detect W_nqrC and W_clsA_2 were also developed and validated. The developed PCR assays are potentially useful for detecting E. coli isolates of wastewater origin in environmental waters, though users should keep in mind that the sensitivity of these markers is not high. Further studies are needed to assess the applicability of the developed markers to a culture-independent approach.
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Affiliation(s)
- Ryota Gomi
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, 615-8540 Kyoto, Japan.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, 400-8511 Yamanashi, Japan
| | - Hiroyuki Wada
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Yoshinori Sugie
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Chih-Yu Ma
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, Kofu, 400-8511 Yamanashi, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, 400-8511 Yamanashi, Japan
| | - Fumitake Nishimura
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu 520-0811, Shiga, Japan; Faculty of Agriculture and Marine Science, Kochi University, Nankoku 783-8502, Kochi, Japan.
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18
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CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water. mSystems 2023; 8:e0128222. [PMID: 36744944 PMCID: PMC9948693 DOI: 10.1128/msystems.01282-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Viruses are the most biologically abundant entities and may be ideal indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic ecosystem changes in rivers, leading to substantial shifts in chemical and biological attributes. Here, we evaluate the viability of using the presence of crAssphage as indicators of fecal contamination in South African rivers. Shotgun analysis revealed diverse crAssphage viruses in these rivers, which are impacted by chemical and biological pollution. Overall, the diversity and relative abundances of these viruses was higher in contaminated sites compared to pristine locations. In contrast to fecal coliform counts, crAssphage sequences were detected in pristine rivers, supporting the assertion that the afore mentioned marker may be a more accurate indicator of fecal contamination. Our data demonstrate the presence of diverse putative hosts which includes members of the phyla Bacteroidota, Pseudomonadota, Verrucomicrobiota, and Bacillota. Phylogenetic analysis revealed novel subfamilies, suggesting that rivers potentially harbor distinct and uncharacterized clades of crAssphage. These data provide the first insights regarding the diversity, distribution, and functional roles of crAssphage in rivers. Taken together, the results support the potential application of crAssphage as viable markers for water quality monitoring. IMPORTANCE Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. Waterborne viral outbreaks have been reported even after fecal indicator bacteria (FIB) were suggested to be absent or below regulated levels of coliforms. This indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination in two South African rivers. We assess the abundance, distribution, and diversity of these viruses in sites that had been predicted pristine or contaminated by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies were unrepresented in our data, suggesting that the diversity of these viruses may reflect geographic locality and dependence.
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19
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Jantharadej K, Kongprajug A, Mhuantong W, Limpiyakorn T, Suwannasilp BB, Mongkolsuk S, Sirikanchana K. Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157652. [PMID: 35905960 DOI: 10.1016/j.scitotenv.2022.157652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %-0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %-58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %-27.5 %), aminoglycoside (94 subtypes; 9.6 %-15.3 %), tetracycline (80 subtypes; 15.6 %-20.2 %), and macrolide (79 subtypes; 14.5 %-32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.
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Affiliation(s)
- Krittayapong Jantharadej
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Akechai Kongprajug
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, Enzyme Technology Research Team, Pathum Thani, Thailand
| | - Tawan Limpiyakorn
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, Bangkok, Thailand; Biotechnology for Wastewater Engineering Research Group, Chulalongkorn University, Bangkok, Thailand
| | - Benjaporn Boonchayaanant Suwannasilp
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, Bangkok, Thailand; Biotechnology for Wastewater Engineering Research Group, Chulalongkorn University, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand.
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20
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Dumke R, Geissler M, Skupin A, Helm B, Mayer R, Schubert S, Oertel R, Renner B, Dalpke AH. Simultaneous Detection of SARS-CoV-2 and Influenza Virus in Wastewater of Two Cities in Southeastern Germany, January to May 2022. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192013374. [PMID: 36293955 PMCID: PMC9603229 DOI: 10.3390/ijerph192013374] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 05/06/2023]
Abstract
Dependent on the excretion pattern, wastewater monitoring of viruses can be a valuable approach to characterizing their circulation in the human population. Using polyethylene glycol precipitation and reverse transcription-quantitative PCR, the occurrence of RNA of SARS-CoV-2 and influenza viruses A/B in the raw wastewater of two treatment plants in Germany between January and May 2022 was investigated. Due to the relatively high incidence in both exposal areas (plant 1 and plant 2), SARS-CoV-2-specific RNA was determined in all 273 composite samples analyzed (concentration of E gene: 1.3 × 104 to 3.2 × 106 gc/L). Despite a nation-wide low number of confirmed infections, influenza virus A was demonstrated in 5.2% (concentration: 9.8 × 102 to 8.4 × 104 gc/L; plant 1) and in 41.6% (3.6 × 103 to 3.0 × 105 gc/L; plant 2) of samples. Influenza virus B was detected in 36.0% (7.2 × 102 to 8.5 × 106 gc/L; plant 1) and 57.7% (9.6 × 103 to 2.1 × 107 gc/L; plant 2) of wastewater samples. The results of the study demonstrate the frequent detection of two primary respiratory viruses in wastewater and offer the possibility to track the epidemiology of influenza by wastewater-based monitoring.
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Affiliation(s)
- Roger Dumke
- Institute of Medical Microbiology und Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Correspondence:
| | - Michael Geissler
- Institute of Medical Microbiology und Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Annett Skupin
- Institute of Medical Microbiology und Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Björn Helm
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, 01069 Dresden, Germany
| | - Robin Mayer
- Institute of Urban and Industrial Water Management, Technische Universität Dresden, 01069 Dresden, Germany
| | - Sara Schubert
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Institute of Hydrobiology, Technische Universität Dresden, 01217 Dresden, Germany
| | - Reinhard Oertel
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Bertold Renner
- Institute of Clinical Pharmacology, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Alexander H. Dalpke
- Institute of Medical Microbiology und Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, 69120 Heidelberg, Germany
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