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Sala-Comorera L, Muniesa M, Rodríguez-Rubio L. Detection and Quantification of Bacteriophages in Wastewater Samples by Culture and Molecular Methods. Methods Mol Biol 2024; 2738:155-173. [PMID: 37966598 DOI: 10.1007/978-1-0716-3549-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Bacteriophages are promising tools for the detection of fecal pollution in water bodies and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages are perfect surrogates for the study of the fate and transport of enteric viruses, generally better than any other group of indicators.Different groups of bacteriophages, such as somatic coliphages, F-specific RNA bacteriophages, and bacteriophages infecting selected strains of Bacteroides, have been comprehensively tested as indicators of fecal pollution. Somatic coliphages and F-specific RNA bacteriophages can be used as indicators of general fecal contamination, whereas Bacteroides phages can be used to detect a particular fecal source, for instance, human, bovine, porcine, or poultry fecal contamination.Feasible and cost-effective protocols standardized by the International Standardization Organization and the United States Environmental Protection Agency for the detection of infectious bacteriophages belonging to these three groups are available. Molecular methods for the detection of some particular phages have also been developed. Here we introduce those methods for the detection, enumeration, and isolation of bacteriophages in wastewater samples.
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Affiliation(s)
- Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.
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2
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Kelmer GAR, Ramos ER, Dias EHO. Coliphages as viral indicators in municipal wastewater: A comparison between the ISO and the USEPA methods based on a systematic literature review. WATER RESEARCH 2023; 230:119579. [PMID: 36640612 DOI: 10.1016/j.watres.2023.119579] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 12/18/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The use of traditional faecal indicator bacteria as surrogate organisms for pathogenic viruses in domestic wastewater has been noted as a problematic as concentrations and removal rates of bacteria and viruses do not seem to correlate. In this sense, bacteriophages (phages) emerge as potential viral indicators, as they are commonly found in wastewater in high levels, and can be quantified using simple, fast, low-cost methods. Somatic and F-specific coliphages comprise groups of phages commonly used as indicators of water quality. There are two internationally recognised methods to detect and enumerate coliphages in water samples, the International Standardization Organization (ISO) and the US Environmental Protection Agency (USEPA) methods. Both methods are based on the lysis of specific bacterial host strains infected by phages. Within this context, this systematic literature review aimed at gathering concentrations in raw and treated domestic wastewater (secondary, biological treatment systems and post-treatment systems), and removal efficiencies of somatic and F-specific coliphages obtained by ISO and USEPA methods, and then compare both methods. A total of 33 research papers were considered in this study. Results showed that the ISO method is more commonly applied than the USEPA method. Some discrepancies in terms of concentrations and removal efficiencies were observed between both methods. Higher removal rates were observed for both somatic and F-specific coliphages in activated sludge systems when using the USEPA method compared to the ISO method; in other secondary (biological) treatment systems, this was observed only for F-specific coliphages. The use of different standardised methods available might lead to difficulties in obtaining and comparing phage data in different conditions and locations. Future research comparing both ISO and USEPA methods as well as viral and bacterial pathogens and indicators in WWTP is recommended.
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Affiliation(s)
- Gisele A R Kelmer
- Postgraduate Programme in Civil Engineering (PEC), Faculty of Engineering, Federal University of Juiz de Fora (UFJF). Rua José Lourenço Kelmer, s/n, Campus UFJF. São Pedro, Juiz de Fora - MG, CEP 36036-900, Brazil
| | - Elloís R Ramos
- Environmental and Sanitary Engineering Course, Faculty of Engineering, Federal University of Juiz de Fora (UFJF). Rua José Lourenço Kelmer, s/n, Campus UFJF. São Pedro, Juiz de Fora - MG, CEP 36036-900, Brazil
| | - Edgard H O Dias
- Postgraduate Programme in Civil Engineering (PEC), Faculty of Engineering, Federal University of Juiz de Fora (UFJF). Rua José Lourenço Kelmer, s/n, Campus UFJF. São Pedro, Juiz de Fora - MG, CEP 36036-900, Brazil; Department of Sanitary and Environmental Engineering (ESA), Faculty of Engineering, Federal University of Juiz de Fora (UFJF). Rua José Lourenço Kelmer, s/n, Campus UFJF. São Pedro, Juiz de Fora - MG, CEP 36036-900, Brazil.
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3
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Ballesté E, Blanch AR, Muniesa M, García-Aljaro C, Rodríguez-Rubio L, Martín-Díaz J, Pascual-Benito M, Jofre J. Bacteriophages in sewage: abundance, roles, and applications. FEMS MICROBES 2022; 3:xtac009. [PMID: 37332509 PMCID: PMC10117732 DOI: 10.1093/femsmc/xtac009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/03/2022] [Accepted: 03/12/2022] [Indexed: 08/25/2023] Open
Abstract
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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Affiliation(s)
- Elisenda Ballesté
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Anicet R Blanch
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Cristina García-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Julia Martín-Díaz
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Miriam Pascual-Benito
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - J Jofre
- Reial Academia de Ciències i Arts de Barcelona, La Rambla, 115, 08002 Barcelona, Spain
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4
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Méndez J, García-Aljaro C, Muniesa M, Pascual-Benito M, Ballesté E, López P, Monleón A, Blanch AR, Lucena F. Modeling human pollution in water bodies using somatic coliphages and bacteriophages that infect Bacteroides thetaiotaomicron strain GA17. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 301:113802. [PMID: 34638039 DOI: 10.1016/j.jenvman.2021.113802] [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: 03/04/2021] [Revised: 09/08/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
The ability to detect human fecal pollution in water is of great importance when assessing the associated health risks. Many microbial source tracking (MST) markers have been proposed to determine the origin of fecal pollution, but their application remains challenging. A range of factors, not yet sufficiently analyzed, may affect MST markers in the environment, such as dilution and inactivation processes. In this work, a statistical framework based on Monte Carlo simulations and non-linear regression was used to develop a classification procedure for use in MST studies. The predictive model tested uses only two parameters: somatic coliphages (SOMCPH), as an index of general fecal pollution, and human host-specific bacteriophages that infect Bacteroides thetaiotaomicron strain GA17 (GA17PH). Taking into account bacteriophage dilution and differential inactivation, the threshold concentration of SOMCPH was calculated to be around 500 PFU/100 mL for a limit of detection of 10 PFU/100 mL. However, this threshold can be lowered by increasing the analyzed volume sample, which in turn lowers the limit of detection. The resulting model is sufficiently accurate for application in practical cases involving MST and could be easily used with markers other than those tested here.
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Affiliation(s)
- Javier Méndez
- Section of Microbiology. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain; BIOST3 Group. Section of Statistics. Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Cristina García-Aljaro
- Section of Microbiology. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Maite Muniesa
- Section of Microbiology. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Miriam Pascual-Benito
- Section of Microbiology. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Elisenda Ballesté
- Section of Microbiology. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Pere López
- Section of Statistics. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain; BIOST3 Group. Section of Statistics. Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Antonio Monleón
- Section of Statistics. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain; BIOST3 Group. Section of Statistics. Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Anicet R Blanch
- Section of Microbiology. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Francisco Lucena
- Section of Microbiology. Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain; BIOST3 Group. Section of Statistics. Department of Genetics, Microbiology and Statistics, University of Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
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5
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Runa V, Wenk J, Bengtsson S, Jones BV, Lanham AB. Bacteriophages in Biological Wastewater Treatment Systems: Occurrence, Characterization, and Function. Front Microbiol 2021; 12:730071. [PMID: 34803947 PMCID: PMC8600467 DOI: 10.3389/fmicb.2021.730071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Phage bacteria interactions can affect structure, dynamics, and function of microbial communities. In the context of biological wastewater treatment (BWT), the presence of phages can alter the efficiency of the treatment process and influence the quality of the treated effluent. The active role of phages in BWT has been demonstrated, but many questions remain unanswered regarding the diversity of phages in these engineered environments, the dynamics of infection, the determination of bacterial hosts, and the impact of their activity in full-scale processes. A deeper understanding of the phage ecology in BWT can lead the improvement of process monitoring and control, promote higher influent quality, and potentiate the use of phages as biocontrol agents. In this review, we highlight suitable methods for studying phages in wastewater adapted from other research fields, provide a critical overview on the current state of knowledge on the effect of phages on structure and function of BWT bacterial communities, and highlight gaps, opportunities, and priority questions to be addressed in future research.
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Affiliation(s)
- Viviane Runa
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom
| | - Jannis Wenk
- Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
| | | | - Brian V Jones
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ana B Lanham
- Centre for Sustainable and Circular Technologies, University of Bath, Bath, United Kingdom.,Department of Chemical Engineering, University of Bath, Bath, United Kingdom.,Water Innovation and Research Centre, University of Bath, Bath, United Kingdom
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Monteiro S, Ebdon J, Santos R, Taylor H. Elucidation of fecal inputs into the River Tagus catchment (Portugal) using source-specific mitochondrial DNA, HAdV, and phage markers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147086. [PMID: 34088114 DOI: 10.1016/j.scitotenv.2021.147086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Determining the source of fecal contamination in a water body is important for the application of appropriate remediation measures. However, it has been suggested in the extant literature that this can best be achieved using a 'toolbox' of molecular- and culture-based methods. In response, this study deployed three indicators (Escherichia coli (EC), intestinal enterococci (IE) and somatic coliphages (SC)), one culture-dependent human marker (Bacteroides (GB-124) bacteriophage) and five culture-independent markers (human adenovirus (HAdV), human (HMMit), cattle (CWMit), pig (PGMit) and poultry (PLMit) mitochondrial DNA markers (mtDNA)) within the River Tagus catchment (n = 105). Water samples were collected monthly over a 13-month sampling campaign at four sites (impacted by significant specific human and non-human inputs and influenced by differing degrees of marine and freshwater mixing) to determine the dominant fecal inputs and assess geographical, temporal, and meteorological (precipitation, UV, temperature) fluctuations. Our results revealed that all sampling sites were not only highly impacted by fecal contamination but that this contamination originated from human and from a range of agricultural animal sources. HMMit was present in a higher percentage (83%) and concentration (4.20 log GC/100 mL) than HAdV (32%, 2.23 log GC/100 mL) and GB-124 bacteriophage with the latter being detected once. Animal mtDNA markers were detected, with CWMit found in 73% of samples with mean concentration of 3.74 log GC/100 mL. Correlation was found between concentrations of fecal indicators (EC, IE and SC), CWMit and season. Levels of CWMit were found to be related to physico-chemical parameters, such as temperature and UV radiation, possibly as a result of the increasing presence of livestock outside in warmer months. This study provides the first evaluation of such a source-associated 'toolbox' for monitoring surface water in Portugal, and the conclusions may inform future implementation of surveillance and remediation strategies for improving water quality.
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Affiliation(s)
- S Monteiro
- School of Environment and Technology, University of Brighton, Brighton, UK; Laboratorio Analises, Instituto Superior Tecnico, Lisbon, Portugal.
| | - J Ebdon
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - R Santos
- Laboratorio Analises, Instituto Superior Tecnico, Lisbon, Portugal
| | - H Taylor
- School of Environment and Technology, University of Brighton, Brighton, UK
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7
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Bacteriophages as Fecal Pollution Indicators. Viruses 2021; 13:v13061089. [PMID: 34200458 PMCID: PMC8229503 DOI: 10.3390/v13061089] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages are promising tools for the detection of fecal pollution in different environments, and particularly for viral pathogen risk assessment. Having similar morphological and biological characteristics, bacteriophages mimic the fate and transport of enteric viruses. Enteric bacteriophages, especially phages infecting Escherichia coli (coliphages), have been proposed as alternatives or complements to fecal indicator bacteria. Here, we provide a general overview of the potential use of enteric bacteriophages as fecal and viral indicators in different environments, as well as the available methods for their detection and enumeration, and the regulations for their application.
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8
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Kapoor R, Ebdon J, Wadhwa A, Chowdhury G, Wang Y, Raj SJ, Siesel C, Durry SE, Mairinger W, Mukhopadhyay AK, Kanungo S, Dutta S, Moe CL. Evaluation of Low-Cost Phage-Based Microbial Source Tracking Tools for Elucidating Human Fecal Contamination Pathways in Kolkata, India. Front Microbiol 2021; 12:673604. [PMID: 34093494 PMCID: PMC8173070 DOI: 10.3389/fmicb.2021.673604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022] Open
Abstract
Phages, such as those infecting Bacteroides spp., have been proven to be reliable indicators of human fecal contamination in microbial source tracking (MST) studies, and the efficacy of these MST markers found to vary geographically. This study reports the application and evaluation of candidate MST methods (phages infecting previously isolated B. fragilis strain GB-124, newly isolated Bacteroides strains (K10, K29, and K33) and recently isolated Kluyvera intermedia strain ASH-08), along with non-source specific somatic coliphages (SOMCPH infecting strain WG-5) and indicator bacteria (Escherichia coli) for identifying fecal contamination pathways in Kolkata, India. Source specificity of the phage-based methods was first tested using 60 known non-human fecal samples from common animals, before being evaluated with 56 known human samples (municipal sewage) collected during both the rainy and dry season. SOMCPH were present in 40-90% of samples from different animal species and in 100% of sewage samples. Phages infecting Bacteroides strain GB-124 were not detected from the majority (95%) of animal samples (except in three porcine samples) and were present in 93 and 71% of the sewage samples in the rainy and dry season (Mean = 1.42 and 1.83 log10PFU/100mL, respectively), though at lower levels than SOMCPH (Mean = 3.27 and 3.02 log10PFU/100mL, respectively). Phages infecting strain ASH-08 were detected in 89 and 96% of the sewage samples in the rainy and dry season, respectively, but were also present in all animal samples tested (except goats). Strains K10, K29, and K30 were not found to be useful MST markers due to low levels of phages and/or co-presence in non-human sources. GB-124 and SOMCPH were subsequently deployed within two low-income neighborhoods to determine the levels and origin of fecal contamination in 110 environmental samples. E. coli, SOMCPH, and phages of GB-124 were detected in 68, 42, and 28% of the samples, respectively. Analyses of 166 wastewater samples from shared community toilets and 21 samples from sewage pumping stations from the same districts showed that SOMCPH were present in 100% and GB-124 phages in 31% of shared toilet samples (Median = 5.59 and <1 log10 PFU/100 mL, respectively), and both SOMCPH and GB-124 phages were detected in 95% of pumping station samples (Median = 5.82 and 4.04 log10 PFU/100 mL, respectively). Our findings suggest that GB-124 and SOMCPH have utility as low-cost fecal indicator tools which can facilitate environmental surveillance of enteric organisms, elucidate human and non-human fecal exposure pathways, and inform interventions to mitigate exposure to fecal contamination in the residential environment of Kolkata, India.
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Affiliation(s)
- Renuka Kapoor
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - James Ebdon
- Environment and Public Health Research and Enterprise Group (EPHREG), University of Brighton, Brighton, United Kingdom
| | - Ashutosh Wadhwa
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Goutam Chowdhury
- ICMR – National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
| | - Yuke Wang
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Suraja J. Raj
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Casey Siesel
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Sarah E. Durry
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Wolfgang Mairinger
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | | | - Suman Kanungo
- ICMR – National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
| | - Shanta Dutta
- ICMR – National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
| | - Christine L. Moe
- Center for Global Safe Water, Sanitation and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, United States
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Ballesté E, Blanch AR, Mendez J, Sala-Comorera L, Maunula L, Monteiro S, Farnleitner AH, Tiehm A, Jofre J, García-Aljaro C. Bacteriophages Are Good Estimators of Human Viruses Present in Water. Front Microbiol 2021; 12:619495. [PMID: 34012424 PMCID: PMC8128106 DOI: 10.3389/fmicb.2021.619495] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
The detection of fecal viral pathogens in water is hampered by their great variety and complex analysis. As traditional bacterial indicators are poor viral indicators, there is a need for alternative methods, such as the use of somatic coliphages, which have been included in water safety regulations in recent years. Some researchers have also recommended the use of reference viral pathogens such as noroviruses or other enteric viruses to improve the prediction of fecal viral pollution of human origin. In this work, phages previously tested in microbial source tracking studies were compared with norovirus and adenovirus for their suitability as indicators of human fecal viruses. The phages, namely those infecting human-associated Bacteroides thetaiotaomicron strain GA17 (GA17PH) and porcine-associated Bacteroides strain PG76 (PGPH), and the human-associated crAssphage marker (crAssPH), were evaluated in sewage samples and fecal mixtures obtained from different animals in five European countries, along with norovirus GI + GII (NoV) and human adenovirus (HAdV). GA17PH had an overall sensitivity of ≥83% and the highest specificity (>88%) for human pollution source detection. crAssPH showed the highest sensitivity (100%) and specificity (100%) in northern European countries but a much lower specificity in Spain and Portugal (10 and 30%, respectively), being detected in animal wastewater samples with a high concentration of fecal indicators. The correlations between GA17PH, crAssPH, or the sum of both (BACPH) and HAdV or NoV were higher than between the two human viruses, indicating that bacteriophages are feasible indicators of human viral pathogens of fecal origin and constitute a promising, easy to use and affordable alternative to human viruses for routine water safety monitoring.
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Affiliation(s)
- Elisenda Ballesté
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Anicet R. Blanch
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Javier Mendez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Leena Maunula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Silvia Monteiro
- Laboratório Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisbon, Portugal
| | - Andreas H. Farnleitner
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Vienna, Austria
- Research Division Water Quality and Health, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Andreas Tiehm
- Department of Microbiology and Molecular Biology, DVGW-Technologiezentrum Wasser, Karlsruhe, Germany
| | - Joan Jofre
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Cristina García-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
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10
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Tariq MA, Newberry F, Haagmans R, Booth C, Wileman T, Hoyles L, Clokie MRJ, Ebdon J, Carding SR. Genome Characterization of a Novel Wastewater Bacteroides fragilis Bacteriophage (vB_BfrS_23) and its Host GB124. Front Microbiol 2020; 11:583378. [PMID: 33193224 PMCID: PMC7644841 DOI: 10.3389/fmicb.2020.583378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
Bacteroides spp. are part of the human intestinal microbiota but can under some circumstances become clinical pathogens. Phages are a potentially valuable therapeutic treatment option for many pathogens, but phage therapy for pathogenic Bacteroides spp. including Bacteroides fragilis is currently limited to three genome-sequenced phages. Here we describe the isolation from sewage wastewater and genome of a lytic phage, vB_BfrS_23, that infects and kills B. fragilis strain GB124. Transmission electron microscopy identified this phage as a member of the Siphoviridae family. The phage is stable when held at temperatures of 4 and 60°C for 1 h. It has a very narrow host range, only infecting one host from a panel of B. fragilis strains (n = 8). Whole-genome sequence analyses of vB_BfrS_23 determined it is double-stranded DNA phage and is circularly permuted, with a genome of 48,011 bp. The genome encodes 73 putative open reading frames. We also sequenced the host bacterium, B. fragilis GB124 (5.1 Mb), which has two plasmids of 43,923 and 4,138 bp. Although this phage is host specific, its isolation together with the detailed characterization of the host B. fragilis GB124 featured in this study represent a useful starting point from which to facilitate the future development of highly specific therapeutic agents. Furthermore, the phage could be a novel tool in determining water (and water reuse) treatment efficacy, and for identifying human fecal transmission pathways within contaminated environmental waters and foodstuffs.
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Affiliation(s)
- Mohammad A. Tariq
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Fiona Newberry
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Rik Haagmans
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Catherine Booth
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Tom Wileman
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, Leicester University, Leicester, United Kingdom
| | - James Ebdon
- Environment and Public Health Research Group, School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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11
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Hernández S, Vives MJ. Phages in Anaerobic Systems. Viruses 2020; 12:E1091. [PMID: 32993161 PMCID: PMC7599459 DOI: 10.3390/v12101091] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of phages in 1915, these viruses have been studied mostly in aerobic systems, or without considering the availability of oxygen as a variable that may affect the interaction between the virus and its host. However, with such great abundance of anaerobic environments on the planet, the effect that a lack of oxygen can have on the phage-bacteria relationship is an important consideration. There are few studies on obligate anaerobes that investigate the role of anoxia in causing infection. In the case of facultative anaerobes, it is a well-known fact that their shifting from an aerobic environment to an anaerobic one involves metabolic changes in the bacteria. As the phage infection process depends on the metabolic state of the host bacteria, these changes are also expected to affect the phage infection cycle. This review summarizes the available information on phages active on facultative and obligate anaerobes and discusses how anaerobiosis can be an important parameter in phage infection, especially among facultative anaerobes.
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Affiliation(s)
- Santiago Hernández
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia;
| | - Martha J. Vives
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia;
- School of Sciences, Universidad de los Andes, Bogotá 111711, Colombia
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12
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Farkas K, Walker DI, Adriaenssens EM, McDonald JE, Hillary LS, Malham SK, Jones DL. Viral indicators for tracking domestic wastewater contamination in the aquatic environment. WATER RESEARCH 2020; 181:115926. [PMID: 32417460 PMCID: PMC7211501 DOI: 10.1016/j.watres.2020.115926] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 05/13/2023]
Abstract
Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.
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Affiliation(s)
- Kata Farkas
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK.
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, DT4 8UB, UK
| | | | - James E McDonald
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Luke S Hillary
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
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13
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Blanco-Picazo P, Fernández-Orth D, Brown-Jaque M, Miró E, Espinal P, Rodríguez-Rubio L, Muniesa M, Navarro F. Unravelling the consequences of the bacteriophages in human samples. Sci Rep 2020; 10:6737. [PMID: 32317653 PMCID: PMC7174282 DOI: 10.1038/s41598-020-63432-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. To unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. In addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. This method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs.
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Affiliation(s)
- Pedro Blanco-Picazo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Dietmar Fernández-Orth
- European Genome-phenome Archive, Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028, Barcelona, Spain.
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041, Barcelona, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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14
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Ballesté E, Belanche-Muñoz LA, Farnleitner AH, Linke R, Sommer R, Santos R, Monteiro S, Maunula L, Oristo S, Tiehm A A, Stange C, Blanch AR. Improving the identification of the source of faecal pollution in water using a modelling approach: From multi-source to aged and diluted samples. WATER RESEARCH 2020; 171:115392. [PMID: 31865126 DOI: 10.1016/j.watres.2019.115392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 05/20/2023]
Abstract
The last decades have seen the development of several source tracking (ST) markers to determine the source of pollution in water, but none of them show 100% specificity and sensitivity. Thus, a combination of several markers might provide a more accurate classification. In this study Ichnaea® software was improved to generate predictive models, taking into account ST marker decay rates and dilution factors to reflect the complexity of ecosystems. A total of 106 samples from 4 sources were collected in 5 European regions and 30 faecal indicators and ST markers were evaluated, including E. coli, enterococci, clostridia, bifidobacteria, somatic coliphages, host-specific bacteria, human viruses, host mitochondrial DNA, host-specific bacteriophages and artificial sweeteners. Models based on linear discriminant analysis (LDA) able to distinguish between human and non-human faecal pollution and identify faecal pollution of several origins were developed and tested with 36 additional laboratory-made samples. Almost all the ST markers showed the potential to correctly target their host in the 5 areas, although some were equivalent and redundant. The LDA-based models developed with fresh faecal samples were able to differentiate between human and non-human pollution with 98.1% accuracy in leave-one-out cross-validation (LOOCV) when using 2 molecular human ST markers (HF183 and HMBif), whereas 3 variables resulted in 100% correct classification. With 5 variables the model correctly classified all the fresh faecal samples from 4 different sources. Ichnaea® is a machine-learning software developed to improve the classification of the faecal pollution source in water, including in complex samples. In this project the models were developed using samples from a broad geographical area, but they can be tailored to determine the source of faecal pollution for any user.
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Affiliation(s)
- Elisenda Ballesté
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain.
| | | | - Andreas H Farnleitner
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Getreidemarkt 9/166, 1060, Vienna, Austria; Karl Landsteiner University of Health Sciences, Research Division Water Quality and Health, Dr.-Karl-Dorrek-Straße 30, 3500, Krems an der Donau, Austria
| | - Rita Linke
- Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Getreidemarkt 9/166, 1060, Vienna, Austria
| | - Regina Sommer
- Unit of Water Hygiene, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Ricardo Santos
- Laboratório Analises, Instituto Superior Tecnico. Universidade Lisboa, Lisbon, Portugal
| | - Silvia Monteiro
- Laboratório Analises, Instituto Superior Tecnico. Universidade Lisboa, Lisbon, Portugal
| | - Leena Maunula
- Dept. Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Satu Oristo
- Dept. Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Andreas Tiehm A
- Dept. Microbiology and Molecular Biology, DVGW-Technologiezentrum Wasser, Germany
| | - Claudia Stange
- Dept. Microbiology and Molecular Biology, DVGW-Technologiezentrum Wasser, Germany
| | - Anicet R Blanch
- Dept. Genetics, Microbiology and Statistics, University of Barcelona, Catalonia, Spain
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15
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Sánchez-Alfonso AC, Venegas C, Díez H, Méndez J, Blanch AR, Jofre J, Campos C. Microbial indicators and molecular markers used to differentiate the source of faecal pollution in the Bogotá River (Colombia). Int J Hyg Environ Health 2020; 225:113450. [PMID: 31962274 DOI: 10.1016/j.ijheh.2020.113450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 10/25/2022]
Abstract
Intestinal pathogenic microorganisms are introduced into the water by means of faecal contamination, thus creating a threat to public health and to the environment. Detecting these contaminants has been difficult due to such an analysis being costly and time-intensive; as an alternative, microbiological indicators have been used for this purpose, although they cannot differentiate between human or animal sources of contamination because these indicators are part of the digestive tracts of both. To identify the sources of faecal pollution, the use of chemical, microbiological and molecular markers has been proposed. Currently available markers present some geographical specificity. The aim of this study was to select microbial and molecular markers that could be used to differentiate the sources of faecal pollution in the Bogotá River and to use them as tools for the evaluation and identification of the origin of discharges and for quality control of the water. In addition to existing microbial source markers, a phage host strain (PZ8) that differentiates porcine contamination was isolated from porcine intestinal content. The strain was identified biochemically and genotypically as Bacteroides. The use of this strain as a microbial source tracking indicator was evaluated in bovine and porcine slaughterhouse wastewaters, raw municipal wastewaters and the Bogotá River. The results obtained indicate that the selected microbial and molecular markers enable the determination of the source of faecal contamination in the Bogotá River by using different algorithms to develop prediction models.
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Affiliation(s)
- Andrea C Sánchez-Alfonso
- Department of Microbiology, Pontifical Xavierian University, Carrera 7 No. 43 - 82, Bogotá, Colombia
| | - Camilo Venegas
- Department of Microbiology, Pontifical Xavierian University, Carrera 7 No. 43 - 82, Bogotá, Colombia
| | - Hugo Díez
- Department of Microbiology, Pontifical Xavierian University, Carrera 7 No. 43 - 82, Bogotá, Colombia
| | - Javier Méndez
- Department of Microbiology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain.
| | - Anicet R Blanch
- Department of Microbiology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Joan Jofre
- Department of Microbiology, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Claudia Campos
- Department of Microbiology, Pontifical Xavierian University, Carrera 7 No. 43 - 82, Bogotá, Colombia
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16
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Ballesté E, Pascual-Benito M, Martín-Díaz J, Blanch AR, Lucena F, Muniesa M, Jofre J, García-Aljaro C. Dynamics of crAssphage as a human source tracking marker in potentially faecally polluted environments. WATER RESEARCH 2019; 155:233-244. [PMID: 30851594 DOI: 10.1016/j.watres.2019.02.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 05/26/2023]
Abstract
Recent studies have shown that crAssphage is abundant in human faecal samples worldwide. It has thus been postulated as a potential microbial source tracking (MST) marker to detect human faecal pollution in water. However, an effective implementation of crAssphage in water management strategies will depend on an understanding of its environmental dynamics. In this work, the abundance and temporal distribution of crAssphage was analysed in the effluent of wastewater treatment plants using different sewage treatments, and in two rivers (water and sediments) that differ in pollution impact and flow regime. Additionally, the influence of environmental conditions (temperature and rainfall) on the removal of the marker was studied along a river section, and natural inactivation was assessed by a mesocosms approach. Molecular and culture-based tools were used to compare crAssphage abundance and dynamics with those of bacteria and bacteriophages currently applied as global indicators (E. coli, somatic coliphages, Bacteroides GA17 bacteriophages, and the human-associated MST markers HF183 and HMBif). CrAssphage concentrations in sewage effluent and river samples were similar to those of HF183 and HMBif and higher than other general and/or culture-based indicators (by 2-3 orders of magnitude). Measurement of crAssphage abundance revealed no temporal variability in the effluent, although rainfall events affected the dynamics, possibly through the mobilisation of sediments, where the marker was detected in high concentrations, and an increase in diffuse and point pollution. Another factor affecting crAssphage inactivation was temperature. Its persistence was longer compared with other bacterial markers analysed by qPCR but lower than culturable markers. The results of this study support the use of crAssphage as a human source tracking marker of faecal pollution in water, since it has similar abundances to other molecular human MST markers, yet with a longer persistence in the environment. Nevertheless, its use in combination with infectious bacteriophages is probably advisable.
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Affiliation(s)
- E Ballesté
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain.
| | - M Pascual-Benito
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - J Martín-Díaz
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - A R Blanch
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - F Lucena
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - M Muniesa
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - J Jofre
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
| | - C García-Aljaro
- Department of Genetics, Microbiology and Statistics, Microbiology Section, Faculty of Biology, University of Barcelona, Diagonal 643, E-08028, Barcelona, Spain
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17
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Gencay YE, Gambino M, Prüssing TF, Brøndsted L. The genera of bacteriophages and their receptors are the major determinants of host range. Environ Microbiol 2019; 21:2095-2111. [PMID: 30888719 DOI: 10.1111/1462-2920.14597] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 01/21/2023]
Abstract
The host range of phages is a key to understand their impact on bacterial ecology and evolution. Because of the complexity of phage-host interactions, the variables that determine the breadth of a phage host range remain poorly understood. Here, we propose a novel holistic approach to identify the host range determinants of a new collection of phages infecting Salmonella, isolated from animal, environmental and wastewater samples that were able to infect 58 of the 71 Salmonella strains in our collection. By using a set of statistic approaches (non-metric dimensional scaling, Bray-Curtis distance, PERMANOVA), we analysed phenotypic (host range on wild-type and receptor mutants) and genetic data (taxonomic assignment and receptor binding proteins) to evaluate the impact of isolation strain and niche, phage receptor and genus on the host range. Statistical analysis revealed that two phage characteristics influence the host range by explaining the most variance: the receptor by 45% and the genus by 51%. Interestingly, phage genus and receptor in combination explained 79% of the variance, establishing these characteristics as the major determinants of the host range. This study demonstrates the power and the novelty of applying statistical approaches to phenotypic and genetic data to investigate the ecology of phage-host interactions.
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Affiliation(s)
- Yilmaz Emre Gencay
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Tessa From Prüssing
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
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18
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Trajano Gomes da Silva D, Dias E, Ebdon J, Taylor H. Assessment of recommended approaches for containment and safe handling of human excreta in emergency settings. PLoS One 2018; 13:e0201344. [PMID: 30048542 PMCID: PMC6062132 DOI: 10.1371/journal.pone.0201344] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 07/13/2018] [Indexed: 11/17/2022] Open
Abstract
Ebola and cholera treatment centres (ETC and CTC) generate considerable quantities of excreta that can further the transmission of disease amongst patients and health workers. Therefore, approaches for the safe handling, containment and removal of excreta within such settings are needed to minimise the likelihood of onward disease transmission. This study compared the performance and suitability of three chlorine-based approaches (0.5% HTH, NaDCC and NaOCl (domestic bleach)) and three lime-based approaches (10%, 20% and 30% Ca(OH)2). The experiments followed recent recommendations for Ebola Treatment Centres. Three excreta matrices containing either raw municipal wastewater, or raw municipal wastewater plus 10% or 20% (w/v) added faecal sludge, were treated in 14 litre buckets at a ratio of 1:10 (chlorine solutions or lime suspensions: excreta matrix). The effects of mixing versus non-mixing and increasing contact time (10 and 30 mins) were also investigated. Bacterial (faecal coliforms (FC) and intestinal enterococci (IE)) and viral (somatic coliphages (SOMPH), F+specific phages (F+PH) and Bacteroides fragilis phages (GB-124PH)) indicators were used to determine the efficacy of each approach. Lime-based approaches provided greater treatment efficacy than chlorine-based approaches, with lime (30% w/v) demonstrating the greatest efficacy (log reductions values, FC = 4.75, IE = 4.16, SOMPH = 2.85, F+PH = 5.13 and GB124PH = 5.41). There was no statistical difference in efficacy between any of the chlorine-based approaches, and the highest log reduction values were: FC = 2.90, IE = 2.36, SOMPH = 3.01, F+PH = 2.36 and GB124PH = 0.74. No statistical difference was observed with respect to contact time for any of the approaches, and no statistical differences were observed with respect to mixing for the chlorine-based approaches. However, statistically significant increases in the efficacy of some lime-based approaches were observed following mixing. These findings provide evidence and practical advice to inform safe handling and containment of excreta and ensure more effective health protection in future emergency settings.
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Affiliation(s)
- Diogo Trajano Gomes da Silva
- Environment and Public Health Research Group, School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Edgard Dias
- Department of Sanitary and Environmental Engineering, Faculty of Engineering, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - James Ebdon
- Environment and Public Health Research Group, School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Huw Taylor
- Environment and Public Health Research Group, School of Environment and Technology, University of Brighton, Brighton, United Kingdom
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19
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García-Aljaro C, Muniesa M, Jofre J. Isolation of Bacteriophages of the Anaerobic Bacteria Bacteroides. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1693:11-22. [PMID: 29119428 DOI: 10.1007/978-1-4939-7395-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Here we describe the detection, enumeration, and isolation of bacteriophages infecting Bacteroides. The method is based on the infection of Bacteroides host strains and the production of visible plaques in a confluent lawn of the host strain using the double-layer agar method. This is a straightforward methodology that can be applied for the detection, enumeration and isolation of bacteriophages for other anaerobic bacteria, using an appropriate host strain and culture conditions. In the case of bacteriophages of Bacteroides the results can be obtained in less than 24 h, although the time could vary depending on the growth rate of the host strain.
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Affiliation(s)
- Cristina García-Aljaro
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Maite Muniesa
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Juan Jofre
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain.
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20
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Booncharoen N, Mongkolsuk S, Sirikanchana K. Comparative persistence of human sewage-specific enterococcal bacteriophages in freshwater and seawater. Appl Microbiol Biotechnol 2018; 102:6235-6246. [DOI: 10.1007/s00253-018-9079-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 04/07/2018] [Accepted: 05/07/2018] [Indexed: 01/17/2023]
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21
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Prado T, Bruni ADC, Barbosa MRF, Bonanno VMS, Garcia SC, Sato MIZ. Distribution of human fecal marker GB-124 bacteriophages in urban sewage and reclaimed water of São Paulo city, Brazil. JOURNAL OF WATER AND HEALTH 2018; 16:289-299. [PMID: 29676764 DOI: 10.2166/wh.2017.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Bacteriophages infecting Bacteroides fragilis GB-124 have been described as potential markers of human fecal contamination in water sources. The aim of this study was to evaluate the occurrence of GB-124 phages in raw sewage, secondary effluents and reclaimed water of the São Paulo city using a low-cost microbial source tracking method. Samples were collected monthly from April 2015 to March 2016 in four municipal wastewater treatment plants that operate with activated sludge processes followed by different tertiary treatments (sand-anthracite filtration, membrane bioreactor/reverse osmosis) and final chlorination. GB-124 phages were detected in 100% of the raw sewage samples, with viral loads varying from 7.5 × 103 to 1.32 × 106 PFU/L. Virus removal efficiency in activated sludge processes ranged from 1.89 to 2.31 log10. Frequencies of phage detection were lower in reclaimed water samples (0-22.2%). The results indicated that GB-124 phage could be a complementary low-cost viral marker for the detection of human fecal pollution in waters impacted with urban sewage in this region. However, the datasets of tertiary effluents resulted in several samples with concentrations below the detection limit (DL ≤1 PFU/mL) suggesting the need to obtain analytical methods with lower DL for greater accuracy of negative results.
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Affiliation(s)
- Tatiana Prado
- Environmental Company of the São Paulo State (CETESB-SP), Av. Prof. Frederico Hermann Jr., 345, São Paulo, SP 05459-900, Brazil E-mail:
| | - Antônio de Castro Bruni
- Environmental Company of the São Paulo State (CETESB-SP), Av. Prof. Frederico Hermann Jr., 345, São Paulo, SP 05459-900, Brazil E-mail:
| | - Mikaela Renata Funada Barbosa
- Environmental Company of the São Paulo State (CETESB-SP), Av. Prof. Frederico Hermann Jr., 345, São Paulo, SP 05459-900, Brazil E-mail:
| | - Vilma Marques Santos Bonanno
- Environmental Company of the São Paulo State (CETESB-SP), Av. Prof. Frederico Hermann Jr., 345, São Paulo, SP 05459-900, Brazil E-mail:
| | - Suzi Cristina Garcia
- Environmental Company of the São Paulo State (CETESB-SP), Av. Prof. Frederico Hermann Jr., 345, São Paulo, SP 05459-900, Brazil E-mail:
| | - Maria Inês Zanoli Sato
- Environmental Company of the São Paulo State (CETESB-SP), Av. Prof. Frederico Hermann Jr., 345, São Paulo, SP 05459-900, Brazil E-mail:
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Diston D, Robbi R, Baumgartner A, Felleisen R. Microbial source tracking in highly vulnerable karst drinking water resources. JOURNAL OF WATER AND HEALTH 2018; 16:138-149. [PMID: 29424727 DOI: 10.2166/wh.2017.215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Water resources situated in areas with underlying karst geology are particularly vulnerable to fecal pollution. In such vulnerable systems, microbial source tracking (MST) methods are useful tools to elucidate the pathways of both animal and human fecal pollution, leading to more accurate water use risk assessments. Here, we describe the application of a MST toolbox using both culture-dependent bacteriophage and molecular-dependent 16S rRNA assays at spring and well sites in the karstic St Imier Valley, Switzerland. Culture-dependent and molecular-dependent marker performance varied significantly, with the 16S rRNA assays displaying greater sensitivity than their phage counterpart; HF183 was the best performing human wastewater-associated marker while Rum2Bac was the best performing ruminant marker. Differences were observed in pollution regimes between the well and spring sampling sites, with the spring water being more degraded than the well site. Our results inform the choice of marker selection for MST studies and highlight differences in microbial water quality between well and spring karst sites.
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Affiliation(s)
- D Diston
- Federal Food Safety and Veterinary Office FSVO, Sector Laboratories, Schwarzenburgstrasse 165, 3003 Bern, Switzerland E-mail:
| | - R Robbi
- Cantonal Laboratory, Bern, Switzerland
| | - A Baumgartner
- Federal Food Safety and Veterinary Office FSVO, Sector Laboratories, Schwarzenburgstrasse 165, 3003 Bern, Switzerland E-mail:
| | - R Felleisen
- Federal Food Safety and Veterinary Office FSVO, Sector Laboratories, Schwarzenburgstrasse 165, 3003 Bern, Switzerland E-mail:
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Ogilvie LA, Nzakizwanayo J, Guppy FM, Dedi C, Diston D, Taylor H, Ebdon J, Jones BV. Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking. ISME JOURNAL 2017; 12:942-958. [PMID: 29259289 PMCID: PMC5864186 DOI: 10.1038/s41396-017-0015-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/06/2017] [Accepted: 11/11/2017] [Indexed: 12/28/2022]
Abstract
Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.
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Affiliation(s)
- Lesley A Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK.
| | | | - Fergus M Guppy
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - Cinzia Dedi
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - David Diston
- Mikrobiologische & Biotechnologische Risiken Bundesamt für Gesundheit BAG, 3003, Bern, Switzerland
| | - Huw Taylor
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - James Ebdon
- School of Environment and Technology, University of Brighton, Brighton, UK
| | - Brian V Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK.
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24
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The human gut virome: form and function. Emerg Top Life Sci 2017; 1:351-362. [PMID: 33525769 DOI: 10.1042/etls20170039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 01/15/2023]
Abstract
Advances in next-generation sequencing technologies and the application of metagenomic approaches have fuelled an exponential increase in our understanding of the human gut microbiome. These approaches are now also illuminating features of the diverse and abundant collection of viruses (termed the virome) subsisting with the microbial ecosystems residing within the human holobiont. Here, we focus on the current and emerging knowledge of the human gut virome, in particular on viruses infecting bacteria (bacteriophage or phage), which are a dominant component of this viral community. We summarise current insights regarding the form and function of this 'human gut phageome' and highlight promising avenues for future research. In doing so, we discuss the potential for phage to drive ecological functioning and evolutionary change within this important microbial ecosystem, their contribution to modulation of host-microbiome interactions and stability of the community as a whole, as well as the potential role of the phageome in human health and disease. We also consider the emerging concepts of a 'core healthy gut phageome' and the putative existence of 'viral enterotypes' and 'viral dysbiosis'.
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25
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García-Aljaro C, Ballesté E, Muniesa M, Jofre J. Determination of crAssphage in water samples and applicability for tracking human faecal pollution. Microb Biotechnol 2017; 10:1775-1780. [PMID: 28925595 PMCID: PMC5658656 DOI: 10.1111/1751-7915.12841] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/15/2022] Open
Abstract
In recent decades, considerable effort has been devoted to finding microbial source-tracking (MST) markers that are suitable to assess the health risks of faecally polluted waters, with no universal marker reported so far. In this study, the abundance and prevalence of a crAssphage-derived DNA marker in wastewaters of human and animal origins were studied by a new qPCR assay with the ultimate aim of assessing its potential as an MST marker. crAssphage showed up to 106 GC/ml in the sewage samples of human origin, in both the total DNA and the viral DNA fraction. In wastewaters containing animal faecal remains, 39% of the samples were negative for the presence of the crAssphage sequence, while those showing positive results (41% of the samples) were at least 1 log10 unit lower than the samples of human origin. Noteworthy, the log10 values of the ratio (R) crAssphage (GC/ml)/Escherichia coli (CFU/ml) varied significantly depending on the human or animal origin (R > 1.5 for human samples and R < -1.5 for animal wastewater samples. This study opens the way for further research to explore if different specific animal variants of crAssphage exist and whether other zones of the crAssphage genome are better suited to source discrimination.
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Affiliation(s)
- Cristina García-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Elisenda Ballesté
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028, Barcelona, Spain
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McMinn BR, Ashbolt NJ, Korajkic A. Bacteriophages as indicators of faecal pollution and enteric virus removal. Lett Appl Microbiol 2017; 65:11-26. [PMID: 28304098 PMCID: PMC6089083 DOI: 10.1111/lam.12736] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 01/17/2023]
Abstract
Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer morphological and biological properties. Based on a review of published data, we summarize densities of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in individual human waste, raw wastewater, ambient fresh and marine waters and removal through wastewater treatment processes utilizing traditional treatments. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the aquatic environment and provide an overview of the environmental factors affecting their survival. In summary, concentrations of bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Overall, our investigation indicates that bacteriophages may be adequate viral surrogates, especially in built systems, such as wastewater treatment plants. SIGNIFICANCE AND IMPACT OF THE STUDY Bacteriophage are alternative fecal indicators that may be better surrogates for viral pathogens than fecal indicator bacteria (FIB). This report offers a summary of the existing literature concerning the utility of bacteriophage as indicators of viral presence (fecal sources and surface waters) and persistence (in built infrastructure and aquatic environments). Our findings indicate that bacteriophage levels in all matrices examined are consistently lower than FIB, but similar to viral pathogens. Furthermore, in built infrastructure (e.g. wastewater treatment systems) bacteriophage closely mimic viral pathogen persistence suggesting they may be adequate sentinels of enteric virus removal.
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Affiliation(s)
- Brian R. McMinn
- National Exposure Research Laboratory, Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268 United States
| | - Nicholas J. Ashbolt
- University of Alberta, School of Public Health, 3-57D South Academic Building, Edmonton, AB T6G 2G7, Canada
| | - Asja Korajkic
- National Exposure Research Laboratory, Office of Research and Development, United States Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH 45268 United States
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Yahya M, Blanch AR, Meijer WG, Antoniou K, Hmaied F, Ballesté E. Comparison of the Performance of Different Microbial Source Tracking Markers among European and North African Regions. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:760-766. [PMID: 28783792 DOI: 10.2134/jeq2016.11.0432] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microbial source tracking (MST) has been extensively used to detect the sources of fecal pollution in water. The inclusion of MST in water management strategies improves the ecological status of the ecosystem and human and animal health under interdisciplinary analysis in all aspects of health care for humans, animals, and the environment (One Health approach). In this study, the performance of MST markers targeting host-specific Bacteroidales (HF183 and Rum-2-Bac) and species (HMBif and CWBif) were evaluated in raw sewage collected from human, ruminant, swine, and poultry sources in Tunisia, Cyprus, Ireland, and Spain. In addition, the ratio between somatic coliphages and bacteriophages infecting GA17 (SOMCPH/GA17PH) was measured in Tunisia and Spain. The obtained results showed variability of the bacterial markers between the four countries, suggesting that their usefulness could be affected by several conditions (dietary habits, agricultural practices, and climatic conditions) that differ between countries. The Rum-2-Bac marker stood out as a valid MST tool, particularly in Ireland, whereas CWBif was the best option in Tunisia, Spain, and Cyprus. The human-specific HMBif marker showed good sensitivity and specificity in Tunisia, Spain, and Ireland, whereas HF183 showed a low specificity. However, HF183 was suggested as a good human marker in Ireland and Cyprus because of its higher concentration than HMBif. Regarding viral markers, the ratio of SOMCPH/GA17PH showed a clear discrimination between human and nonhuman samples. The combined use of molecular bacterial markers and the ratio of SOMCPH/GA17PH may improve the success of MST.
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Leknoi Y, Mongkolsuk S, Sirikanchana K. Assessment of swine-specific bacteriophages of Bacteroides fragilis in swine farms with different antibiotic practices. JOURNAL OF WATER AND HEALTH 2017; 15:251-261. [PMID: 28362306 DOI: 10.2166/wh.2016.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We assessed the occurrence and specificity of bacteriophages of Bacteroides fragilis in swine farms for their potential application in microbial source tracking. A local B. fragilis host strain, SP25 (DSM29413), was isolated from a pooled swine feces sample taken from a non-antibiotic farm. This strain was highly specific to swine fecal materials because it did not detect bacteriophages in any samples from human sewage, sheep, goats, cattle, dogs, and cats. The reference B. fragilis strain, RYC2056, could detect phages in swine samples but also detected phages in most human sewage and polluted urban canal samples. Phages of SP25 exist in the proximity of certain swine farms, regardless of their antibiotic use (p > 0.05). B. fragilis strain SP25 exhibited relatively high resistance to most of the veterinary antimicrobial agents tested. Interestingly, most farms that were positive for SP25 phages were also positive for RYC2056 phages. In conclusion, the swine-specific SP25 strain has the potential to indicate swine fecal contamination in certain bodies of water. Bacterial isolates with larger distributions are being studied and validated. This study highlights the importance of assessing the abundance of phages in local swine populations before determining their potential applicability for source tracking in local surface waters.
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Affiliation(s)
- Yuranan Leknoi
- Inter-University Program on Environmental Toxicology, Technology and Management, Asian Institute of Technology, Chulabhorn Research Institute and Mahidol University, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Department of Biotechnology and Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok, Thailand 10400; Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand 10210 and Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand 10400 E-mail:
| | - Kwanrawee Sirikanchana
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand 10210 and Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand 10400 E-mail:
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29
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Venegas C, Diez H, Blanch AR, Jofre J, Campos C. Microbial source markers assessment in the Bogotá River basin (Colombia). JOURNAL OF WATER AND HEALTH 2015; 13:801-10. [PMID: 26322765 DOI: 10.2166/wh.2015.240] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The microbiological indicators traditionally used to assess fecal contamination are insufficient to identify the source. The aim of this study was to detect microbial markers to identify the source of fecal pollution in the Bogotá River (Colombia). For this, we determined non-discriminating indicators such as Escherichia coli, somatic coliphages and phages infecting strain RYC2056 of Bacteroides, and potential source tracking markers as phages infecting strains GA17, HB13, and CA8 of Bacteroides, sorbitol-fermenting bifidobacteria, and molecular markers of Bifidobacterium adolescentis, Bifiodobacterium dentium, and Bacteroidetes in raw municipal wastewaters, slaughterhouse wastewaters, and the Bogotá River. Bacteriophages infecting Bacteroides strain GA17 and the molecular markers identified the wastewater sources. In contrast, sorbitol-fermenting bifidobacteria failed regarding specificity. In the Bogotá River, phages infecting strain GA17 were detected in all samples downstream of Bogotá, whereas they should be concentrated from 1 l samples in upstream samples containing less than 10(3) E. coli/100 ml to be detected. In the river water, the fraction of positive detections of molecular markers was lower than that of phages infecting strain GA17. The ratio SOMCPH/GA17PH was shown also to be a good marker. These results provide information that will allow focusing measures for sanitation of the Bogotá River.
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Affiliation(s)
- Camilo Venegas
- Department of Microbiology, Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, Colombia E-mail:
| | - Hugo Diez
- Department of Microbiology, Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, Colombia E-mail:
| | - Anicet R Blanch
- Department of Microbiology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Juan Jofre
- Department of Microbiology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Claudia Campos
- Department of Microbiology, Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Bogotá, Colombia E-mail:
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30
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Diston D, Wicki M. Occurrence of bacteriophages infecting Bacteroides host strains (ARABA 84 and GB-124) in fecal samples of human and animal origin. JOURNAL OF WATER AND HEALTH 2015; 13:654-61. [PMID: 26322751 DOI: 10.2166/wh.2014.199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bacteriophage-based microbial source-tracking studies are an economical and simple way of identifying fecal sources in polluted water systems. Recently isolated Bacteroides spp. strains ARABA 84, and GB-124 have been shown to detect bacteriophages exclusively in aquatic systems impacted by human fecal material. To date, limited examination of the occurrence or concentration of phages capable of infecting Bacteroides fragilis strain GB-124 or B. thetaiotaomicron strain ARABA 84 in human and animal feces has been carried out. This study reports the prevalence rates and concentrations of phages infecting ARABA 84 and GB-124 host strains in human and a range of animal feces. Discrete human fecal samples (n=55) and pooled animal samples (n=46, representing the feces of over 230 animals) were examined for phages infecting the host strains ARABA 84, GB-124, and E. coli strain WG5. Both human Bacteroides host strains were highly specific (95% and 100% for ARABA 84 and GB-124, respectively), challenging results from previous studies. This study supports the use of Bacteroides strains GB-124 and ARABA 84 in fecal source tracking studies for the detection of human fecal contamination.
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Affiliation(s)
- David Diston
- Federal Food Safety and Veterinary Office, 3003 Bern, Switzerland
| | - Melanie Wicki
- University Hospital Basel, CTU, 4031 Basel, Switzerland E-mail:
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Diston D, Sinreich M, Zimmermann S, Baumgartner A, Felleisen R. Evaluation of molecular- and culture-dependent MST markers to detect fecal contamination and indicate viral presence in good quality groundwater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7142-51. [PMID: 25871525 DOI: 10.1021/acs.est.5b00515] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Microbial contamination of groundwater represents a significant health risk to resource users. Culture-dependent Bacteroides phage and molecular-dependent Bacteroidales 16S rRNA assays are employed in microbial source tracking (MST) studies globally, however little is known regarding how these important groups relate to each other in the environment and which is more suitable to indicate the presence of waterborne fecal pollution and human enteric viruses. This study addresses this knowledge gap by examining 64 groundwater samples from sites with varying hydrogeological properties using a MST toolbox containing two bacteriophage groups (phage infecting GB-124 and ARABA-84), and two Bacteroidales 16S rRNA markers (Hf183 and BacR); those were compared to fecal indicator bacteria, somatic coliphage, Bacteroidales 16S rRNA marker AllBac, four human enteric viruses (norovirus GI and II, enterovirus and group A rotavirus) and supplementary hydrogeological/chemical data. Bacteroidales 16S rRNA indicators offered a more sensitive assessment of both human-specific and general fecal contamination than phage indicators, but may overestimate the risk from enteric viral pathogens. Comparison with hydrogeological and land use site characteristics as well as auxiliary microbiological and chemical data proved the plausibility of the MST findings. Sites representing karst aquifers were of significantly worse microbial quality than those with unconsolidated or fissured aquifers, highlighting the vulnerability of these hydrogeological settings.
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Affiliation(s)
- D Diston
- †Federal Food Safety and Veterinary Office FSVO, Bern 3003, Switzerland
| | - M Sinreich
- ‡Federal Office for the Environment FOEN, Bern 3003, Switzerland
| | - S Zimmermann
- ‡Federal Office for the Environment FOEN, Bern 3003, Switzerland
| | - A Baumgartner
- †Federal Food Safety and Veterinary Office FSVO, Bern 3003, Switzerland
| | - R Felleisen
- †Federal Food Safety and Veterinary Office FSVO, Bern 3003, Switzerland
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32
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Wicki M, Auckenthaler A, Felleisen R, Karabulut F, Niederhauser I, Tanner M, Baumgartner A. Assessment of source tracking methods for application in spring water. JOURNAL OF WATER AND HEALTH 2015; 13:473-88. [PMID: 26042979 DOI: 10.2166/wh.2014.255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
For discriminating between human and animal faecal contamination in water, microbial source tracking (MST) approaches using different indicators have been employed. In the current study, a range of 10 such MST indicators described in the scientific literature were comparatively assessed. Bacteriophages infecting host strains of Bacteroides (GA-17, GB-124 and ARABA 84) as well as sorbitol-fermenting bifidobacteria proved useful for indicating human faecal contamination while Rhodococcus coprophilus was associated with animal-derived faecal contamination. These potential source indicators were present in samples of faecal origin, i.e. either in human wastewater or animal waste, from many different regions in Switzerland and therefore showed a geographic stability. In addition, the MST indicators were abundant in surface water and were even sensitive enough to detect faecal contamination in spring water from two study areas in Switzerland. This is the first study that has compared and successfully applied MST methods in spring water.
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Affiliation(s)
- Melanie Wicki
- University Hospital Basel, 4031 Basel, Switzerland E-mail:
| | - Adrian Auckenthaler
- Office of Environmental Protection and Energy, Basel-Landschaft, 4410 Liestal, Switzerland
| | | | | | | | - Marcel Tanner
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland; University of Basel, 4000 Basel, Switzerland
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Wangkahad B, Bosup S, Mongkolsuk S, Sirikanchana K. Occurrence of bacteriophages infecting Aeromonas, Enterobacter, and Klebsiella in water and association with contamination sources in Thailand. JOURNAL OF WATER AND HEALTH 2015; 13:613-624. [PMID: 26042992 DOI: 10.2166/wh.2014.204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The co-residence of bacteriophages and their bacterial hosts in humans, animals, and environmental sources directed the use of bacteriophages to track the origins of the pathogenic bacteria that can be found in contaminated water. The objective of this study was to enumerate bacteriophages of Aeromonas caviae (AecaKS148), Enterobacter sp. (EnspKS513), and Klebsiella pneumoniae (KlpnKS648) in water and evaluate their association with contamination sources (human vs. animals). Bacterial host strains were isolated from untreated wastewater in Bangkok, Thailand. A double-layer agar technique was used to detect bacteriophages. All three bacteriophages were detected in polluted canal samples, with likely contamination from human wastewater, whereas none was found in non-polluted river samples. AecaKS148 was found to be associated with human fecal sources, while EnspKS513 and KlpnKS648 seemed to be equally prevalent in both human and animal fecal sources. Both bacteriophages were also present in polluted canals that could receive contamination from other fecal sources or the environment. In conclusion, all three bacteriophages were successfully monitored in Bangkok, Thailand. This study provided an example of bacteriophages for potential use as source identifiers of pathogen contamination. The results from this study will assist in controlling sources of pathogen contamination, especially in developing countries.
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Affiliation(s)
| | - Suchada Bosup
- Inter-University Program on Environmental Toxicology, Technology and Management, Asian Institute of Technology, Chulabhorn Research Institute, Mahidol University, Bangkok 10210, Thailand
| | - Skorn Mongkolsuk
- Department of Biotechnology and Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University, Bangkok 10400, Thailand and Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Bangkok 10400, Thailand E-mail:
| | - Kwanrawee Sirikanchana
- Center of Excellence on Environmental Health and Toxicology, Ministry of Education, Bangkok 10400, Thailand E-mail: ; Translational Research Unit, Chulabhorn Research Institute, Bangkok 10210, Thailand
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Panasiuk O, Hedström A, Marsalek J, Ashley RM, Viklander M. Contamination of stormwater by wastewater: a review of detection methods. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 152:241-50. [PMID: 25662485 DOI: 10.1016/j.jenvman.2015.01.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 01/19/2015] [Accepted: 01/31/2015] [Indexed: 05/20/2023]
Abstract
Even in separate sewer systems, wastewater may find its way into the receiving waters through stormwater sewers. The main reasons for this are cross-connections, illicit connections, overflows and leakages through broken sewers. Such discharges may affect receiving water quality and increase risks to public health and aquatic organisms. Detecting wastewater contamination and locating its points of ingress into storm sewer systems can be a challenging task, which should be addressed using proper methods and indicator parameters. A number of detection methods have already been proposed in this area, yet there is a lack of a general overview of such methods. This literature review summarizes and evaluates the methods used for detecting wastewater in stormwater, including those recently developed. The advantages, weaknesses and limitations of individual methods are discussed. It is concluded that while no single method can as yet produce results in a precise, fast and inexpensive way, the use of human waste specific chemical and microbiological markers, and their innovative sampling, offer the way forward. Guidance for selecting the most effective combinations of detection methods, under specific conditions, is also provided.
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Affiliation(s)
- Oleksandr Panasiuk
- Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 97187 Luleå, Sweden.
| | - Annelie Hedström
- Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 97187 Luleå, Sweden
| | - Jiri Marsalek
- Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 97187 Luleå, Sweden
| | - Richard M Ashley
- Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 97187 Luleå, Sweden
| | - Maria Viklander
- Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 97187 Luleå, Sweden
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35
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Yahya M, Hmaied F, Jebri S, Jofre J, Hamdi M. Bacteriophages as indicators of human and animal faecal contamination in raw and treated wastewaters from Tunisia. J Appl Microbiol 2015; 118:1217-25. [DOI: 10.1111/jam.12774] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 12/01/2022]
Affiliation(s)
- M. Yahya
- Unité de Microbiologie et Biologie moléculaire; CNSTN, Biotech Pole Sidi Thabet; Sidi Thabet Tunisia
| | - F. Hmaied
- Unité de Microbiologie et Biologie moléculaire; CNSTN, Biotech Pole Sidi Thabet; Sidi Thabet Tunisia
| | - S. Jebri
- Unité de Microbiologie et Biologie moléculaire; CNSTN, Biotech Pole Sidi Thabet; Sidi Thabet Tunisia
| | - J. Jofre
- Department of Microbiology; Barcelona University; Diagonal 645, 08028 Barcelona Spain
| | - M. Hamdi
- Laboratoire Ecologie Technologie Microbienne; Institut National des Sciences Appliquées de Tunis; Université de Carthage; Tunis Tunisia
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Casanovas-Massana A, Gómez-Doñate M, Sánchez D, Belanche-Muñoz LA, Muniesa M, Blanch AR. Predicting fecal sources in waters with diverse pollution loads using general and molecular host-specific indicators and applying machine learning methods. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 151:317-25. [PMID: 25585145 DOI: 10.1016/j.jenvman.2015.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 12/03/2014] [Accepted: 01/03/2015] [Indexed: 05/22/2023]
Abstract
In this study we use a machine learning software (Ichnaea) to generate predictive models for water samples with different concentrations of fecal contamination (point source, moderate and low). We applied several MST methods (host-specific Bacteroides phages, mitochondrial DNA genetic markers, Bifidobacterium adolescentis and Bifidobacterium dentium markers, and bifidobacterial host-specific qPCR), and general indicators (Escherichia coli, enterococci and somatic coliphages) to evaluate the source of contamination in the samples. The results provided data to the Ichnaea software, that evaluated the performance of each method in the different scenarios and determined the source of the contamination. Almost all MST methods in this study determined correctly the origin of fecal contamination at point source and in moderate concentration samples. When the dilution of the fecal pollution increased (below 3 log10 CFU E. coli/100 ml) some of these indicators (bifidobacterial host-specific qPCR, some mitochondrial markers or B. dentium marker) were not suitable because their concentrations decreased below the detection limit. Using the data from source point samples, the software Ichnaea produced models for waters with low levels of fecal pollution. These models included some MST methods, on the basis of their best performance, that were used to determine the source of pollution in this area. Regardless the methods selected, that could vary depending on the scenario, inductive machine learning methods are a promising tool in MST studies and may represent a leap forward in solving MST cases.
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Affiliation(s)
- Arnau Casanovas-Massana
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, Barcelona, Catalonia, Spain
| | - Marta Gómez-Doñate
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, Barcelona, Catalonia, Spain
| | - David Sánchez
- Department of Software, Technical University of Catalonia, Jordi Girona 1-3, Barcelona, Catalonia, Spain
| | - Lluís A Belanche-Muñoz
- Department of Software, Technical University of Catalonia, Jordi Girona 1-3, Barcelona, Catalonia, Spain
| | - Maite Muniesa
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, Barcelona, Catalonia, Spain
| | - Anicet R Blanch
- Department of Microbiology, University of Barcelona, Av. Diagonal 643, Barcelona, Catalonia, Spain.
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Indicators of Waterborne Viruses. ENVIRONMENTAL INDICATORS 2015. [PMCID: PMC7122105 DOI: 10.1007/978-94-017-9499-2_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Enteric viruses excreted by humans and animals may reach water resources and cause large outbreaks. Drinking water is one of the essential global life elements for humanity. However, some of our resources are contaminated with viruses and indicators for continuous monitoring have been developed. The classical ones are coliforms and fecal coliforms that are still the iron standard for water indicator monitoring (see Chap. 10.1007/978-94-017-9499-2_34). In the last decades, bacteriophages have been suggested as potential indicators of enteric viruses and many studies showed their potential as such mainly due to their comparable resistance to water processes such as disinfection. In this chapter, the indicator role of bacteriophages in water is critically reviewed and discussed.
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Sirikanchana K, Wangkahad B, Mongkolsuk S. The capability of non-native strains of Bacteroides bacteria to detect bacteriophages as faecal indicators in a tropical area. J Appl Microbiol 2014; 117:1820-9. [PMID: 25207866 DOI: 10.1111/jam.12646] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 09/04/2014] [Accepted: 09/06/2014] [Indexed: 11/28/2022]
Abstract
AIMS To evaluate the use of nonlocal, already-available strains of phages to indicate faecal contamination in Thailand waters. METHODS AND RESULTS Phages of Bacteroides fragilis strains ATCC 700786 (RYC2056PH) and ATCC 51477 (HSP40PH) were measured in 71 human and animal wastewater samples in Thailand using a double-layer agar assay. Bacteriophage RYC2056PH was detected at concentrations comparable to representative human and animal wastewater samples from European and Mediterranean countries, with 61·7 and 33·3% above the threshold value of 100 PFU 100 ml(-1) in wastewater samples of human and animal origins, respectively. On the other hand, HSP40PH was detected at low concentrations in both human- and animal-polluted wastewaters. Moreover, RYC2056PH was found in 12 canal waters with human-influenced pollution and was not detected in 6 nonpolluted river waters being tested in this study. CONCLUSIONS The presence of RYC2056PH could indicate nonsource-specific faecal contamination in Thailand. SIGNIFICANCE AND IMPACT OF THE STUDY This study provided the first evidence that bacteriophages of the European-isolated B. fragilis strain RYC2056 could be used as nonsource-specific faecal indicators in the Southeast Asian region. The results of this study support the worldwide use of Bacteroides phages as faecal indicators.
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Affiliation(s)
- K Sirikanchana
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
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Jofre J, Blanch AR, Lucena F, Muniesa M. Bacteriophages infecting Bacteroides as a marker for microbial source tracking. WATER RESEARCH 2014; 55:1-11. [PMID: 24583570 DOI: 10.1016/j.watres.2014.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/30/2014] [Accepted: 02/01/2014] [Indexed: 05/25/2023]
Abstract
Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination.
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Affiliation(s)
- Joan Jofre
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain.
| | - Anicet R Blanch
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
| | - Francisco Lucena
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
| | - Maite Muniesa
- Department of Microbiology, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain
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McMinn BR, Korajkic A, Ashbolt NJ. Evaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States. Lett Appl Microbiol 2014; 59:115-21. [PMID: 24725119 DOI: 10.1111/lam.12252] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/05/2014] [Accepted: 03/14/2014] [Indexed: 11/29/2022]
Abstract
UNLABELLED Phages infecting human-associated Bacteroides fragilis (GB-124 phages) have been employed in the European Union (EU) to identify human faecal pollution, but their utility for the United States was unclear. Primary sewage samples were collected seasonally from seven wastewater treatment plants (WWTP) across the continental United States, and more time-intensive sampling was conducted at local WWTPs. All samples were assayed for plaque-forming units (PFU) of GB-124 phages, somatic and FRNA-specific coliphages, as well as adenoviruses (by quantitative PCR [qPCR]). Animal faecal samples (>250) from 14 different species were tested for the presence of the three phage groups. GB-124 phages were consistently detected in sewage (10-10(2) PFU ml(-1) ), but not in animal faeces. While density estimates of both coliphages in sewage were approximately one order of magnitude higher than GB-124 phages, they were both randomly detected in animal faecal samples (10(2) -10(5) g(-1) dry weight). Stability of all three phages was inversely proportional to temperature; persistence was greatest at 5°C compared to 20 and 35°C, where no phages were detectable after a week. In summary, GB-124 phages appear to be a feasible alternative indicator organism and benefit from being sewage associated, while providing an inexpensive detection technique for infectious virions. SIGNIFICANCE AND IMPACT OF THE STUDY Bacteroides fragilis GB-124 phages appear to be restricted to human sewage sources in the United States, being absent from 264 animal faecal samples from 14 different species and present in approx. 90% (34/38) of primary sewage effluent samples collected across the country. Although somatic and F-specific coliphages were present in sewage samples at higher densities, unlike GB-124 phages, both coliphage types were also detected in animal faecal samples. Hence, GB-124 phages may prove to be a useful novel indicator group for human faecal pollution in the continental United States.
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Affiliation(s)
- B R McMinn
- National Exposure Research Laboratory, Office of Research and Development, United States Environmental Protection Laboratory, Cincinnati, OH, USA
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Diston D, Ebdon JE, Taylor HD. Inactivation of bacteriophage infecting Bacteroides strain GB124 using UV-B radiation. Photochem Photobiol 2014; 90:622-7. [PMID: 24329482 DOI: 10.1111/php.12223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/04/2013] [Indexed: 11/29/2022]
Abstract
Ultraviolet-B radiation (280-320 nm) has long been associated with the inactivation of microorganisms in the natural environment. Determination of the environmental inactivation kinetics of specific indicator organisms [used as tools in the field of microbial source tracking (MST)] is fundamental to their successful deployment, particularly in geographic regions subject to high levels of solar radiation. Phage infecting Bacteroides fragilis host strain GB124 (B124 phage) have been demonstrated to be highly specific indicators of human fecal contamination, but to date, little is known about their susceptibility to UV-B radiation. Therefore, B124 phage (n = 7) isolated from municipal wastewater effluent, were irradiated in a controlled laboratory environment using UV-B collimated beam experiments. All B124 phage suspensions possessed highly similar first order log-linear inactivation profiles and the mean fluence required to inactivate phage by 4 - log(10) was 320 mJ cm(-2). These findings suggest that phage infecting GB124 are likely to be inactivated when exposed to the levels of UV-B solar radiation experienced in a variety of environmental settings. As such, this may limit the utility of such methods for determining more remote inputs of fecal contamination in areas subject to high levels of solar radiation.
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Affiliation(s)
- David Diston
- Swiss Federal Food Safety and Veterinary Office, Köniz, Switzerland
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Casanovas-Massana A, Blanch AR. Determination of fecal contamination origin in reclaimed water open-air ponds using biochemical fingerprinting of enterococci and fecal coliforms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:3003-3010. [PMID: 23054766 DOI: 10.1007/s11356-012-1197-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 09/12/2012] [Indexed: 06/01/2023]
Abstract
Low levels of fecal indicator bacteria (FIB) were recently detected in two reclaimed water open-air ponds used to irrigate a golf course located in Northeastern Spain. The aim of this study was to evaluate the feasibility of a biochemical fingerprinting method to track the origin of fecal contamination in water with low FIB levels, as in the aforementioned ponds. We also aimed to determine whether FIB presence was due to regrowth of the reclaimed water populations or to a contribution of fecal matter whose source was in the golf facility. Three hundred and fifty enterococcal strains and 308 fecal coliform strains were isolated from the ponds and reclamation plant, and they were biochemically phenotyped. In addition, the inactivation of several microbial fecal pollution indicators (fecal coliforms, total bifidobacteria, sorbitol-fermenting bifidobacteria, somatic bacteriophages, and bacteriophages infecting Bacteroides thetaiotaomicron) was studied using a mesocosm in situ in order to obtain information about their decay rate. Although FIB concentration was low, the biochemical fingerprinting provided evidence that the origin of the fecal contamination in the ponds was not related to the reclaimed water. Biochemical fingerprinting thus proved to be a successful approach, since other microbial source-tracking methods perform poorly when dealing with low fecal load matrices. Furthermore, the mesocosm assays indicated that none of the microbial fecal indicators was able to regrow in the ponds. Finally, the study highlights the fact that reclaimed water may be recontaminated in open-air reservoirs, and therefore, its microbial quality should be monitored throughout its use.
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Affiliation(s)
- Arnau Casanovas-Massana
- Departament of Microbiology, University of Barcelona, Av. Diagonal, 643, 08028, Barcelona, Catalonia, Spain.
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43
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Marine and Freshwater Fecal Indicators and Source Identification. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Muniesa M, Lucena F, Blanch AR, Payán A, Jofre J. Use of abundance ratios of somatic coliphages and bacteriophages of Bacteroides thetaiotaomicron GA17 for microbial source identification. WATER RESEARCH 2012; 46:6410-6418. [PMID: 23039916 DOI: 10.1016/j.watres.2012.09.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 09/03/2012] [Accepted: 09/06/2012] [Indexed: 06/01/2023]
Abstract
Water contaminated with human faeces is a risk to human health and management of water bodies can be improved by determining the sources of faecal pollution. Field studies show that existing methods are insufficient and that different markers are required. This study proposes the combined use of two microbial indicators, the concentrations of which are presented as ratios. This provides a more reliable approach to identifying faecal sources as it avoids variation due to treatment or ageing of the contamination. Among other indicators, bacteriophages have been proposed as rapid and cheap indicators of faecal pollution. Samples analysed in this study were derived from wastewater treatment plants (raw sewage, secondary and tertiary effluents and raw sewage sludge) river water, seawater and animal related wastewater. The abundance ratios of faecal coliforms and Bacteroides phages, either strain RYC2056 (non-specific for faecal origin) or strain GA17 (specific for human pollution), and among somatic coliphages and phages infecting both Bacteroides strains, were evaluated. The results indicate that the ratio of somatic coliphages and phages infecting Bacteroides strain GA17, which is specific to human faecal sources, provides a robust method for discriminating samples, even those presenting different levels and ages of pollution, and allows samples polluted with human faeces to be distinguished from those containing animal faecal pollution. This method allows the generation of numerical data that can be further applied to numerical methods for faecal pollution discrimination.
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Affiliation(s)
- Maite Muniesa
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
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45
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New molecular quantitative PCR assay for detection of host-specific Bifidobacteriaceae suitable for microbial source tracking. Appl Environ Microbiol 2012; 78:5788-95. [PMID: 22685136 DOI: 10.1128/aem.00895-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bifidobacterium spp. belong to the commensal intestinal microbiota of warm-blooded animals. Some strains of Bifidobacterium show host specificity and have thus been proposed as host-specific targets to determine the origin of fecal pollution. Most strains have been used in microbial-source-tracking (MST) studies based on culture-dependent methods. Although some of these approaches have proved very useful, the low prevalence of culturable Bifidobacterium strains in the environment means that molecular culture-independent procedures could provide practical applications for MST. Reported here is a set of common primers and four Bifidobacterium sp. host-associated (human, cattle, pig, and poultry) probes for quantitative-PCR (qPCR) assessment of fecal source tracking. This set was tested using 25 water samples of diverse origin: urban sewage samples, wastewater from four abattoirs (porcine, bovine, and poultry), and water from a river with a low pollution load. The selected sequences showed a high degree of host specificity. There were no cross-reactions between the qPCR assays specific for each origin and samples from different fecal origins. On the basis of the findings, it was concluded that the host-specific qPCRs are sufficiently robust to be applied in environmental MST studies.
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46
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Ogilvie LA, Caplin J, Dedi C, Diston D, Cheek E, Bowler L, Taylor H, Ebdon J, Jones BV. Comparative (meta)genomic analysis and ecological profiling of human gut-specific bacteriophage φB124-14. PLoS One 2012; 7:e35053. [PMID: 22558115 PMCID: PMC3338817 DOI: 10.1371/journal.pone.0035053] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 03/08/2012] [Indexed: 12/30/2022] Open
Abstract
Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome.
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Affiliation(s)
- Lesley A. Ogilvie
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Jonathan Caplin
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Cinzia Dedi
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - David Diston
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Elizabeth Cheek
- School of Computing, Engineering and Mathematics, University of Brighton, Brighton, United Kingdom
| | - Lucas Bowler
- Sussex Proteomics Centre, University of Sussex, Brighton, United Kingdom
| | - Huw Taylor
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - James Ebdon
- School of Environment and Technology, University of Brighton, Brighton, United Kingdom
| | - Brian V. Jones
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- * E-mail:
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Ebdon JE, Sellwood J, Shore J, Taylor HD. Phages of Bacteroides (GB-124): a novel tool for viral waterborne disease control? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:1163-1169. [PMID: 22107174 DOI: 10.1021/es202874p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Current fecal indicator bacteria (FIB) and emerging microbial source tracking (MST) methods may indicate the presence and even the likely source of water contamination, but they are less effective at determining the potential risk to health from human enteric viruses. This paper investigates the presence of human-specific phages (detected using a low-cost MST method) in municipal wastewaters (MW) and assesses whether they may be used effectively to screen for the likely presence of human adenovirus (HAdV) and norovirus (NoV). The findings demonstrated that all samples positive for HAdV and/or NoV also contained phages infecting Bacteroides GB-124 (mean = 4.36 log(10) PFU/100 mL) and that GB-124 phages, HAdV, and NoV were absent from samples of nonhuman origin. HAdV and NoV were detected more frequently in MW samples containing higher levels of phages (e.g., >10(2)) and FIB (e.g., >10(3)). Interestingly, at one sewage treatment works (STW), the levels of GB-124 phages present in treated MW were not significantly lower (p = 0.001) than those in untreated MW. There was a positive correlation (R = 0.42) between the size of STW and the number of GB-124 phages present in the final treated effluent. Therefore, the detection of GB-124 phages by a simple phage-lysis method may have considerable potential as a low-cost surrogate for the detection of certain human pathogenic viruses in MW and receiving waters.
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Affiliation(s)
- James E Ebdon
- Environment & Public Health Research Unit, School of Environment and Technology, University of Brighton, Lewes Rd, Brighton BN2 4GJ, United Kingdom.
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48
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Purnell SE, Ebdon JE, Taylor HD. Bacteriophage lysis of Enterococcus host strains: a tool for microbial source tracking? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:10699-705. [PMID: 22047499 DOI: 10.1021/es202141x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This paper describes the isolation of Enterococcus host strains, for potential use as simple bacteriophage (phage)-based microbial source tracking (MST) tools. Presumptive Enterococcus host strains were isolated from cattle feces, raw municipal wastewater, agricultural runoff, and waters impacted by farms or wastewater treatment works (WWTW) in southern England, United Kingdom (UK). All enterococcal host strains (n = 390) were first screened for their ability to detect phage in samples of raw municipal wastewater and fecal material from cattle, pigs, and sheep. Host strains that detected phage (n = 147) were ranked according to both their specificity to a particular fecal source and also the number of phages (expressed as plaque-forming units, PFU) that they detected per milliliter of sample. Host strains that demonstrated host specificity and which detected phages at levels greater than 100 PFU/mL (n = 29) were further tested using additional fecal samples of human and nonhuman origin. The specificity and sensitivity of the enterococcal host strains were found to vary, ranging from 44 to 100% and from 17 to 83%, respectively. Most notably, seven strains exhibited 100% specificity to either cattle, human, or pig samples. Isolates exhibiting specificity to cattle were identified as belonging to the species Enterococcus casseliflavus , Enterococcus mundtii , or Enterococcus gallinarum , while human and pig isolates were members of either Enterococcus faecium or Enterococcus faecalis . The high specificity of phages infecting Enterococcus hosts and the simplicity and relatively low cost of the approach collectively indicate a strong potential for using this method as a tool in MST.
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Affiliation(s)
- Sarah E Purnell
- Environment & Public Health Research Unit, School of Environment and Technology, Cockcroft Building, University of Brighton, Lewes Road, Brighton, BN2 4GJ, United Kingdom.
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Nnane DE. Sustainable microbial water quality monitoring programme design using phage-lysis and multivariate techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2011; 409:5188-5195. [PMID: 21962927 DOI: 10.1016/j.scitotenv.2011.08.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 08/19/2011] [Accepted: 08/25/2011] [Indexed: 05/31/2023]
Abstract
Contamination of surface waters is a pervasive threat to human health, hence, the need to better understand the sources and spatio-temporal variations of contaminants within river catchments. River catchment managers are required to sustainably monitor and manage the quality of surface waters. Catchment managers therefore need cost-effective low-cost long-term sustainable water quality monitoring and management designs to proactively protect public health and aquatic ecosystems. Multivariate and phage-lysis techniques were used to investigate spatio-temporal variations of water quality, main polluting chemophysical and microbial parameters, faecal micro-organisms sources, and to establish 'sentry' sampling sites in the Ouse River catchment, southeast England, UK. 350 river water samples were analysed for fourteen chemophysical and microbial water quality parameters in conjunction with the novel human-specific phages of Bacteroides GB-124 (Bacteroides GB-124). Annual, autumn, spring, summer, and winter principal components (PCs) explained approximately 54%, 75%, 62%, 48%, and 60%, respectively, of the total variance present in the datasets. Significant loadings of Escherichia coli, intestinal enterococci, turbidity, and human-specific Bacteroides GB-124 were observed in all datasets. Cluster analysis successfully grouped sampling sites into five clusters. Importantly, multivariate and phage-lysis techniques were useful in determining the sources and spatial extent of water contamination in the catchment. Though human faecal contamination was significant during dry periods, the main source of contamination was non-human. Bacteroides GB-124 could potentially be used for catchment routine microbial water quality monitoring. For a cost-effective low-cost long-term sustainable water quality monitoring design, E. coli or intestinal enterococci, turbidity, and Bacteroides GB-124 should be monitored all-year round in this river catchment.
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Affiliation(s)
- Daniel Ekane Nnane
- Environment and Public Health Research Unit, School of Environment and Technology, University of Brighton, Cockcroft Building, Lewes Road, Brighton, BN2 4GJ, UK.
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50
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Gómez-Doñate M, Payán A, Cortés I, Blanch AR, Lucena F, Jofre J, Muniesa M. Isolation of bacteriophage host strains of Bacteroides species suitable for tracking sources of animal faecal pollution in water. Environ Microbiol 2011; 13:1622-31. [PMID: 21443742 DOI: 10.1111/j.1462-2920.2011.02474.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Microbial source tracking (MST) methods allow the identification of specific faecal sources. The aim is to detect the sources of faecal pollution in a water body to allow targeted, efficient and cost-effective remediation efforts in the catchment. Bacteriophages infecting selected host strains of Bacteroides species are used as markers to track faecal contaminants in water. By using a suitable Bacteroides host from a given faecal origin, it is possible to specifically detect bacteriophages of this faecal origin. It can thus be used to detect specific phages of Bacteroides for MST. With this objective, we isolated several Bacteroides strains from pig, cow and poultry faeces by applying a previously optimized methodology used to isolate the host strains from humans. The isolated strains belonged to Bacteroides fragilis and Bacteroides thetaiotaomicron. These strains, like most Bacteroides species, detected phages of the Siphoviridae morphology. Using the newly isolated host strains for phage enumeration in a range of samples, we showed that these detect phages in faecal sources that coincide with their own origin (70-100% of the samples), and show no detection or very low percentages of detection of phages from other animal origins (from 0 to 20% of the samples). Only strains isolated from pig wastewater detected phages in 50% of human sewage samples. Nevertheless, those strains detecting phages from faecal origins other than their own detected fewer phages (2-3 log₁₀ pfu·100 ml⁻¹) than the phages detected by the specific strain of the same origin. On the basis of our results, we propose that faecal source tracking with phages infecting specific Bacteroides host strains is a useful method for MST. In addition, the method presented here is feasible in laboratories equipped with only basic microbiological equipment, it is more rapid and cost-effective than other procedures and it does not require highly qualified staff.
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Affiliation(s)
- Marta Gómez-Doñate
- Department of Microbiology, University of Barcelona-Institut de l'aigua, Diagonal 645, E-08028, Barcelona, Spain
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