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Zhang Y, Huo Y, Zhang Z, Zhu S, Fan W, Wang X, Huo M. Deciphering the influence of multiple anthropogenic inputs on taxonomic and functional profiles of the microbial communities in Yitong River, Northeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:39973-39984. [PMID: 35112248 DOI: 10.1007/s11356-021-18386-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
We conducted the analysis of physicochemical parameters, 16S rRNA amplicon sequencing and real-time quantitative polymerase chain reaction to explore the impact of human inputs on the bacterioplankton communities within a tributary of the largest river flowing through a megacity in northeast China. Agriculture largely accounted for the alteration of diversity and functions of the microbial communities. Furthermore, nitrate and total phosphorus declined at the reservoir outlet. The WWTP effluent discharge caused a decrease of the relative abundance of Actinobacteria and Cyanobacteria, while the impact on the variation of alpha diversity of river microbial community was slight. Carbon fixation and nitrogen cycle varied with the change of land use type. The rare taxa contributed with a predominant role in the response to environmental variables and NH3-N as well as NO3--N were the main environmental factors that drove the shift in the bacterial community. The occurrence of the human-specific fecal indicator was mostly derived from agriculture, and its increase in relative abundance was observed in the WWTP effluent. Thus, our study provides guidance for ecological assessment and management of rivers by revealing the response pattern of river bacterioplankton to multiple types of anthropogenic stressors.
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Affiliation(s)
- Ying Zhang
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Yang Huo
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
- School of Physics, Northeast Normal University, Changchun, 130024, China.
| | - Zhiruo Zhang
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Changchun, 130118, China
| | - Suiyi Zhu
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Wei Fan
- School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Xianze Wang
- School of Environment, Northeast Normal University, Changchun, 130117, China
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China
| | - Mingxin Huo
- School of Environment, Northeast Normal University, Changchun, 130117, China.
- Science and Technology Innovation Center for Municipal Wastewater Treatment and Water Quality Protection, Northeast Normal University, Changchun, 130117, China.
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Microbial source tracking using metagenomics and other new technologies. J Microbiol 2021; 59:259-269. [DOI: 10.1007/s12275-021-0668-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 12/12/2022]
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Fuhrmeister E, Ercumen A, Pickering AJ, Jeanis KM, Crider Y, Ahmed M, Brown S, Alam M, Sen D, Islam S, Kabir MH, Islam M, Rahman M, Kwong LH, Arnold BF, Luby SP, Colford JM, Nelson KL. Effect of Sanitation Improvements on Pathogens and Microbial Source Tracking Markers in the Rural Bangladeshi Household Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4316-4326. [PMID: 32167305 PMCID: PMC7144219 DOI: 10.1021/acs.est.9b04835] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 05/19/2023]
Abstract
Diarrheal illnesses from enteric pathogens are a leading cause of death in children under five in low- and middle-income countries (LMICs). Sanitation is one way to reduce the spread of enteric pathogens in the environment; however, few studies have investigated the effectiveness of sanitation in rural LMICs in reducing pathogens in the environment. In this study, we measured the impact of a sanitation intervention (dual-pit latrines, sani-scoops, child potties delivered as part of a randomized control trial, WASH Benefits) in rural Bangladeshi household compounds by assessing prevalence ratios, differences, and changes in the concentration of pathogen genes and host-specific fecal markers. We found no difference in the prevalence of pathogenic Escherichia coli, norovirus, or Giardia genes in the domestic environment in the sanitation and control arms. The prevalence of the human fecal marker was lower on child hands and the concentration of animal fecal marker was lower on mother hands in the sanitation arm in adjusted models, but these associations were not significant after correcting for multiple comparisons. In the subset of households with ≥10 individuals per compound, the prevalence of enterotoxigenic E. coli genes on child hands was lower in the sanitation arm. Incomplete removal of child and animal feces or the compound (versus community-wide) scale of intervention could explain the limited impacts of improved sanitation.
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Affiliation(s)
- Erica
R. Fuhrmeister
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Ayse Ercumen
- School
of Public Health, University of California, Berkeley, California 94720, United States
- Department
of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Amy J. Pickering
- Civil
and Environmental Engineering, Tufts University, Medford, Massachusetts 02153, United States
| | - Kaitlyn M. Jeanis
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Yoshika Crider
- Energy
and Resources Group, University of California, Berkeley, California 94720, United States
| | - Mahaa Ahmed
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Sara Brown
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Mahfuja Alam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Debashis Sen
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Sharmin Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Mir Himayet Kabir
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Mahfuza Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Mahbubur Rahman
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka 1212, Bangladesh
| | - Laura H. Kwong
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Benjamin F. Arnold
- School
of Public Health, University of California, Berkeley, California 94720, United States
| | - Stephen P. Luby
- Woods
Institute for the Environment, Stanford
University, Stanford, California 94305, United States
| | - John M. Colford
- School
of Public Health, University of California, Berkeley, California 94720, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
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4
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Fuhrmeister E, Ercumen A, Pickering AJ, Jeanis KM, Ahmed M, Brown S, Arnold BF, Hubbard AE, Alam M, Sen D, Islam S, Kabir MH, Kwong LH, Islam M, Unicomb L, Rahman M, Boehm AB, Luby SP, Colford JM, Nelson KL. Predictors of Enteric Pathogens in the Domestic Environment from Human and Animal Sources in Rural Bangladesh. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10023-10033. [PMID: 31356066 PMCID: PMC6727619 DOI: 10.1021/acs.est.8b07192] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 05/19/2023]
Abstract
Fecal indicator organisms are measured to indicate the presence of fecal pollution, yet the association between indicators and pathogens varies by context. The goal of this study was to empirically evaluate the relationships between indicator Escherichia coli, microbial source tracking markers, select enteric pathogen genes, and potential sources of enteric pathogens in 600 rural Bangladeshi households. We measured indicators and pathogen genes in stored drinking water, soil, and on mother and child hands. Additionally, survey and observational data on sanitation and domestic hygiene practices were collected. Log10 concentrations of indicator E. coli were positively associated with the prevalence of pathogenic E. coli genes in all sample types. Given the current need to rely on indicators to assess fecal contamination in the field, it is significant that in this study context indicator E. coli concentrations, measured by IDEXX Colilert-18, provided quantitative information on the presence of pathogenic E. coli in different sample types. There were no significant associations between the human fecal marker (HumM2) and human-specific pathogens in any environmental sample type. There was an increase in the prevalence of Giardia lamblia genes, any E. coli virulence gene, and the specific E. coli virulence genes stx1/2 with every log10 increase in the concentration of the animal fecal marker (BacCow) on mothers' hands. Thus, domestic animals were important contributors to enteric pathogens in these households.
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Affiliation(s)
- Erica
R. Fuhrmeister
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Ayse Ercumen
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
- Department
of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Amy J. Pickering
- Civil
and Environmental Engineering, Tufts University, Medford, Massachusetts 02153, United States
| | - Kaitlyn M. Jeanis
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Mahaa Ahmed
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Sara Brown
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Benjamin F. Arnold
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Alan E. Hubbard
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Mahfuja Alam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Debashis Sen
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Sharmin Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Mir Himayet Kabir
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Laura H. Kwong
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Mahfuza Islam
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Leanne Unicomb
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Mahbubur Rahman
- Infectious
Disease Division, International Centre for
Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Alexandria B. Boehm
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Stephen P. Luby
- Woods
Institute for the Environment, Stanford
University, Stanford, California 94305, United States
| | - John M. Colford
- School
of Public Health, University of California, Berkeley, California 94720, Unites States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
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5
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Devane ML, Moriarty EM, Robson B, Lin S, Wood D, Webster-Brown J, Gilpin BJ. Relationships between chemical and microbial faecal source tracking markers in urban river water and sediments during and post-discharge of human sewage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:1588-1604. [PMID: 30360285 DOI: 10.1016/j.scitotenv.2018.09.258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
This study explores the relationships between faecal source tracking (FST) markers (quantitative Polymerase Chain Reaction (qPCR) markers and steroids), microbial indicators, the faecal ageing ratio of atypical colonies/total coliforms (AC/TC) and potential human pathogens (Giardia, Cryptosporidium and Campylobacter). Faecal source PCR markers tested were GenBac3, HumM3, HumBac (HF183-Bac708R); Bifidobacterium adolescentis, wildfowl and canine-associated markers. Sediment and water samples from the Avon River were collected during and post-discharge of untreated human sewage inputs, following a series of earthquakes, which severely damaged the Christchurch sewerage system. Significant, positive Spearman Ranks (rs) correlations were observed between human-associated qPCR markers and steroid FST markers and Escherichia coli and F-specific RNA bacteriophage (rs 0.57 to 0.84, p < 0.001) in water samples. These human source indicative FST markers demonstrated that they were also effective predictors of potentially pathogenic protozoa in water (rs 0.43-0.74, p ≤ 0.002), but correlated less well with Campylobacter. Human-associated qPCR and steroid markers showed significant, substantial agreement between the two FST methods (Cohen's kappa, 0.78, p = 0.023), suggesting that water managers could be confident in the results using either method under these contamination conditions. Low levels of fluorescent whitening agents (FWA) (mean 0.06 μg/L, range 0.01-0.40 μg/L) were observed in water throughout the study, but steroids and FWA appeared to be retained in river sediments, months after continuous sewage discharges had ceased. No relationship was observed between chemical FST markers in sediments and the overlying water, and few correlations in sediment between chemical FST markers and target microorganisms. The low values observed for the faecal ageing ratio, AC/TC in water, were significantly, negatively correlated with increasing pathogen detection. This study provides support for the use of the AC/TC ratio, and qPCR and steroid FST markers as indicators of health risks associated with the discharge of raw human sewage into a freshwater system.
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Affiliation(s)
- Megan L Devane
- Institute of Environmental Science and Research Limited, Christchurch Science Centre, PO Box 29-181, Christchurch, New Zealand.
| | - Elaine M Moriarty
- Institute of Environmental Science and Research Limited, Christchurch Science Centre, PO Box 29-181, Christchurch, New Zealand
| | - Beth Robson
- Institute of Environmental Science and Research Limited, Christchurch Science Centre, PO Box 29-181, Christchurch, New Zealand
| | - Susan Lin
- Institute of Environmental Science and Research Limited, Christchurch Science Centre, PO Box 29-181, Christchurch, New Zealand
| | - David Wood
- Institute of Environmental Science and Research Limited, Christchurch Science Centre, PO Box 29-181, Christchurch, New Zealand
| | - Jenny Webster-Brown
- Waterways Centre for Freshwater Management, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Brent J Gilpin
- Institute of Environmental Science and Research Limited, Christchurch Science Centre, PO Box 29-181, Christchurch, New Zealand
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6
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Stachler E, Akyon B, de Carvalho NA, Ference C, Bibby K. Correlation of crAssphage qPCR Markers with Culturable and Molecular Indicators of Human Fecal Pollution in an Impacted Urban Watershed. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7505-7512. [PMID: 29874457 DOI: 10.1021/acs.est.8b00638] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Environmental waters are monitored for fecal pollution to protect public health. Many previously developed human-specific fecal pollution indicators lack adequate sensitivity to be reliably detected in environmental waters or do not correlate well with viral pathogens. Recently, two novel human sewage-associated source tracking qPCR markers were developed based on the bacteriophage crAssphage, CPQ_056 and CPQ_064. These assays are highly human specific, abundant in sewage, and are viral-based, suggesting great promise for environmental application as human fecal pollution indicators. A 30-day sampling study was conducted in an urban stream impacted by combined sewer overflows to evaluate the crAssphage markers' performance in an environmental system. The crAssphage markers were present at concentrations of 4.02-6.04 log10 copies/100 mL throughout the study period, indicating their high abundance and ease of detection in polluted environmental waters. In addition, the crAssphage assays were correlated with rain events, molecular markers for human polyomavirus and HF183, as well as culturable E. coli, enterococci, and somatic coliphage. The CPQ_064 assay correlated strongly to a greater number of biological indicators than the CPQ_056 assay. This study is the first to evaluate both crAssphage qPCR assays in an extended environmental application of crAssphage markers for monitoring of environmental waters. It is also the first study to compare crAssphage marker concentration with other viral-based indicators.
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Affiliation(s)
- Elyse Stachler
- Department of Civil and Environmental Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Benay Akyon
- Department of Civil and Environmental Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Nathalia Aquino de Carvalho
- Department of Civil and Environmental Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Christian Ference
- Department of Civil and Environmental Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
| | - Kyle Bibby
- Department of Civil and Environmental Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
- Department of Civil and Environmental Engineering and Earth Sciences , University of Notre Dame , South Bend , Indiana 46556 , United States
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7
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Price JR, Ledford SH, Ryan MO, Toran L, Sales CM. Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:1104-1116. [PMID: 28954372 DOI: 10.1016/j.scitotenv.2017.09.162] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/30/2017] [Accepted: 09/16/2017] [Indexed: 05/20/2023]
Abstract
Through a combined approach using analytical chemistry, real-time quantitative polymerase chain reaction (qPCR), and targeted amplicon sequencing, we studied the impact of wastewater treatment plant effluent sources at six sites on two sampling dates on the chemical and microbial population regimes within the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, Pennsylvania, USA. These water bodies contribute flow to the Schuylkill River, one of the major drinking water sources for Philadelphia, Pennsylvania. Effluent was observed to be a significant source of nutrients, human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources, which we hypothesize is controlled by distance from effluent source. Antecedent moisture conditions were observed to impact overall microbial community diversity, with higher diversity occurring after rainfall. Finally, the efficacy of using a subset of the microbial community including the orders of Bifidobacteriales, Bacteroidales, and Clostridiales to estimate the degree of influence due to sewage and fecal sources was explored and verified.
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Affiliation(s)
- Jacob R Price
- Civil, Architectural, and Environmental Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, United States
| | - Sarah H Ledford
- Earth and Environmental Science, Temple University, 1901 N. 13th St, Philadelphia, PA 19122, United States
| | - Michael O Ryan
- Civil, Architectural, and Environmental Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, United States
| | - Laura Toran
- Earth and Environmental Science, Temple University, 1901 N. 13th St, Philadelphia, PA 19122, United States
| | - Christopher M Sales
- Civil, Architectural, and Environmental Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, United States.
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Impact of Some Ecological Factors on Fecal Contamination of Drinking Water by Diarrheagenic Antibiotic-Resistant Escherichia coli in Zagazig City, Egypt. Int J Microbiol 2016; 2016:6240703. [PMID: 27725834 PMCID: PMC5048019 DOI: 10.1155/2016/6240703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 07/02/2016] [Accepted: 08/04/2016] [Indexed: 12/05/2022] Open
Abstract
Fecal contamination of drinking water is a major health problem which accounts for many cases of diarrhea mainly in infants and foreigners. This contamination is a complex interaction of many parameters. Antibiotic resistance among bacterial isolates complicates the problem. The study was done to identify fecal contamination of drinking water by Diarrheagenic Antibiotic-Resistant Escherichia coli in Zagazig city and to trace reasons for such contamination, three hundred potable water samples were investigated for E. coli existence. Locations of E. coli positive samples were investigated in relation to population density, water source, and type of water pipe. Sixteen E. coli strains were isolated. Antibiotic sensitivity was done and enterotoxigenic, enteropathogenic, and enterohaemorrhagic virulence genes were investigated by PCR. Probability of fecal contamination correlated with higher population density, with increased distance from Zagazig water plant, and with asbestos cement water pipes. Resistance to at least one antimicrobial drug was found in all isolates. Virulence genes were detected in a rate of 26.27%, 13.13%, 20%, 6.67%, and 33.33% for LT, ST, stx1, stx2, and eae genes, respectively. This relatively high frequency of fecal contamination points towards the high risk of developing diarrhea by antibiotic resistant DEC in low socioeconomic communities particularly with old fashion distribution systems.
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Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii. Appl Environ Microbiol 2015; 82:1496-1503. [PMID: 26712546 DOI: 10.1128/aem.02456-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/16/2015] [Indexed: 11/20/2022] Open
Abstract
The coalescence of next-generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineation of host-microbe associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macroorganisms, but it remains unclear how the specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA genes amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). We investigated the interspecific abundance-occupancy relationship, where widespread taxa tend to be more abundant than narrowly distributed taxa, among operational taxonomic units (OTUs) within and among host species. In a separate analysis, we identified specialist OTUs that were highly abundant in a single host and rare in all other hosts by using a multinomial model without excluding undersampled OTUs a priori. We show that intestinal microbes in humans and other vertebrates display abundance-occupancy relationships, but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest that intestinal bacteria can be shared among diverse hosts in ways that resemble the distribution of "free-living" bacteria in the extraintestinal environment.
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Tan B, Ng C, Nshimyimana JP, Loh LL, Gin KYH, Thompson JR. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities. Front Microbiol 2015; 6:1027. [PMID: 26441948 PMCID: PMC4585245 DOI: 10.3389/fmicb.2015.01027] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/10/2015] [Indexed: 12/20/2022] Open
Abstract
Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.
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Affiliation(s)
- BoonFei Tan
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
| | - Charmaine Ng
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Jean Pierre Nshimyimana
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological UniversitySingapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological UniversitySingapore, Singapore
| | - Lay Leng Loh
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Karina Y.-H. Gin
- Department of Civil and Environmental Engineering, National University of SingaporeSingapore, Singapore
| | - Janelle R. Thompson
- Center for Environmental Sensing and Modelling, Singapore-MIT Alliance for Research and Technology CentreSingapore, Singapore
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, CambridgeMA, USA
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11
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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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12
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Molina M, Hunter S, Cyterski M, Peed LA, Kelty CA, Sivaganesan M, Mooney T, Prieto L, Shanks OC. Factors affecting the presence of human-associated and fecal indicator real-time quantitative PCR genetic markers in urban-impacted recreational beaches. WATER RESEARCH 2014; 64:196-208. [PMID: 25061692 DOI: 10.1016/j.watres.2014.06.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 06/25/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
Urban runoff can carry a variety of pollutants into recreational beaches, often including bacterial pathogens and indicators of fecal contamination. To develop complete recreational criteria and risk assessments, it is necessary to understand conditions under which human contamination could be present at beaches solely impacted by urban runoff. Accurately estimating risk requires understanding sources, concentrations, and transport mechanisms of microbial contaminants in these environments. By applying microbial source tracking methods and empirical modeling, we assessed the presence and level of human contamination at urban runoff impacted recreational beaches. We also identified environmental parameters and pollution sources that can influence the concentration and transport of culturable and molecular fecal indicator bacteria (FIB) in systems impacted solely by urban runoff. Water samples and physico-chemical parameters were collected from shoreline locations from three South Carolina (SC) beaches (five locations per beach) and two Florida (FL) beaches (three locations per beach). Each SC beach was directly impacted by swashes or tidal creeks receiving stormwater runoff from the urbanized area and therefore were designated as swash drain associated (SDA) beaches, while FL beaches were designated as non-swash drain associated (NSDA). Sampling in swash drains (SD; three sites per SD) directly impacting each SC beach was also conducted. Results indicate that although culturable (enterococci) and real-time quantitative polymerase chain reaction (qPCR) (EC23S857, Entero1, and GenBac3) FIB concentrations were, on average, higher at SD locations, SDA beaches did not have consistently higher molecular FIB signals compared to NSDA beaches. Both human-associated markers (HF183 and HumM2) were concomitantly found only at SDA beaches. Bacteroidales species-specific qPCR markers (BsteriF1 and BuniF2) identified differences in the Bacteroidales community, depending on beach type. The marker for general Bacteroidales was most abundant at SD locations and exhibited a high correlation with both culturable and other molecular markers. Combining molecular information with predictive modeling allowed us to identify both alongshore movement of currents and SD outflow as significant influences on the concentration of molecular and culturable indicators in the bathing zone. Data also suggests that combining methodologies is a useful and cost effective approach to help understand transport dynamics of fecal contamination and identify potential sources of contamination at marine beaches.
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Affiliation(s)
- Marirosa Molina
- USEPA, Office of Research and Development, National Exposure Research Laboratory, Athens, GA, USA.
| | - Shayla Hunter
- SSA Contractor to the USEPA, ORD, NERL, Athens, GA, USA
| | - Mike Cyterski
- USEPA, Office of Research and Development, National Exposure Research Laboratory, Athens, GA, USA
| | - Lindsay A Peed
- USEPA, ORD, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Catherine A Kelty
- USEPA, ORD, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Mano Sivaganesan
- USEPA, ORD, National Risk Management Research Laboratory, Cincinnati, OH, USA
| | - Thomas Mooney
- SSA Contractor to the USEPA, ORD, NRMRL, Cincinnati, OH, USA
| | - Lourdes Prieto
- USEPA, Office of Research and Development, National Exposure Research Laboratory, Athens, GA, USA
| | - Orin C Shanks
- USEPA, ORD, National Risk Management Research Laboratory, Cincinnati, OH, USA
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13
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Green HC, White KM, Kelty CA, Shanks OC. Development of rapid canine fecal source identification PCR-based assays. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:11453-61. [PMID: 25203917 DOI: 10.1021/es502637b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The extent to which dogs contribute to aquatic fecal contamination is unknown despite the potential for zoonotic transfer of harmful human pathogens. We used genome fragment enrichment (GFE) to identify novel nonribosomal microbial genetic markers potentially useful for detecting dog fecal contamination with PCR-based methods in environmental samples. Of the 679 sequences obtained from GFE, we used 84 for the development of PCR assays targeting putative canine-associated genetic markers. Twelve genetic markers were shown to be prevalent among dog fecal samples and were rarely found in other animals. Three assays, DG3, DG37, and DG72, performed best in terms of specificity and sensitivity and were used for the development of SYBR Green and TaqMan quantitative PCR (qPCR) assays. qPCR analysis of 244 fecal samples collected from a wide geographic range indicated that marker concentrations were below limits of detection in noncanine hosts. As a proof-of-concept, these markers were detected in urban stormwater samples, suggesting a future application of newly developed methods for water quality monitoring.
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Affiliation(s)
- Hyatt C Green
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, Cincinnati, Ohio 45268, United States
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14
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McLellan SL, Eren AM. Discovering new indicators of fecal pollution. Trends Microbiol 2014; 22:697-706. [PMID: 25199597 DOI: 10.1016/j.tim.2014.08.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/30/2014] [Accepted: 08/06/2014] [Indexed: 12/30/2022]
Abstract
Fecal pollution indicators are essential to identify and remediate contamination sources and protect public health. Historically, easily cultured facultative anaerobes such as fecal coliforms, Escherichia coli, or enterococci have been used but these indicators generally provide no information as to their source. More recently, molecular methods have targeted fecal anaerobes, which are much more abundant in humans and other mammals, and some strains appear to be associated with particular host sources. Next-generation sequencing and microbiome studies have created an unprecedented inventory of microbial communities associated with fecal sources, allowing reexamination of which taxonomic groups are best suited as informative indicators. The use of new computational methods, such as oligotyping coupled with well-established machine learning approaches, is providing new insights into patterns of host association. In this review we examine the basis for host-specificity and the rationale for using 16S rRNA gene targets for alternative indicators and highlight two taxonomic groups, Bacteroidales and Lachnospiraceae, which are rich in host-specific bacterial organisms. Finally, we discuss considerations for using alternative indicators for water quality assessments with a particular focus on detecting human sewage sources of contamination.
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Affiliation(s)
- Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
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15
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Walker TJ, Bachoon DS, Otero E, Ramsubhag A. Detection of verotoxin producing Escherichia coli in marine environments of the Caribbean. MARINE POLLUTION BULLETIN 2013; 76:406-410. [PMID: 24035427 DOI: 10.1016/j.marpolbul.2013.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/14/2013] [Accepted: 08/16/2013] [Indexed: 06/02/2023]
Abstract
The goal of this study was to determine the potential for Enterohemorrhagic Escherichia coli O157:H7 (EHEC) contamination in tropical marine waters. Samples were collected from urban, suburban, and rural sites around the islands of Puerto Rico and The Republic of Trinidad and Tobago. Quantification of E. coli and EHEC was evaluated using MI plates and qPCR. EHEC was detected in six sites in Puerto Rico: West of La Parguera Town, Boquilla, Oro Creek, Fishers Association, Joyuda Lagoon, and Boqueron Wetland Creek and in two rural sites in Trinidad: Balandra Bay and Quinam Bay. Plate count enumeration of E. coli was not a reliable indicator for the presence of EHEC. The sites where EHEC was detected on both islands are used for recreational bathing, water sports and recreational/commercial fisheries and therefore pose a public potential health risk.
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Affiliation(s)
- Trisha J Walker
- Department of Biological and Environmental Sciences, Georgia College and State University, Campus Box 81, Milledgeville, GA 31061-0490, USA
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16
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Lan Y, Morrison JC, Hershberg R, Rosen GL. POGO-DB--a database of pairwise-comparisons of genomes and conserved orthologous genes. Nucleic Acids Res 2013; 42:D625-32. [PMID: 24198250 PMCID: PMC3964953 DOI: 10.1093/nar/gkt1094] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
POGO-DB (http://pogo.ece.drexel.edu/) provides an easy platform for comparative microbial genomics. POGO-DB allows users to compare genomes using pre-computed metrics that were derived from extensive computationally intensive BLAST comparisons of >2000 microbes. These metrics include (i) average protein sequence identity across all orthologs shared by two genomes, (ii) genomic fluidity (a measure of gene content dissimilarity), (iii) number of ‘orthologs’ shared between two genomes, (iv) pairwise identity of the 16S ribosomal RNA genes and (v) pairwise identity of an additional 73 marker genes present in >90% prokaryotes. Users can visualize these metrics against each other in a 2D plot for exploratory analysis of genome similarity and of how different aspects of genome similarity relate to each other. The results of these comparisons are fully downloadable. In addition, users can download raw BLAST results for all or user-selected comparisons. Therefore, we provide users with full flexibility to carry out their own downstream analyses, by creating easy access to data that would normally require heavy computational resources to generate. POGO-DB should prove highly useful for researchers interested in comparative microbiology and benefit the microbiome/metagenomic communities by providing the information needed to select suitable phylogenetic marker genes within particular lineages.
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Affiliation(s)
- Yemin Lan
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA, Electrical & Computer Engineering Department, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA and Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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17
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Shen Z, Duan C, Zhang C, Carson A, Xu D, Zheng G. Using an intervening sequence of Faecalibacterium 16S rDNA to identify poultry feces. WATER RESEARCH 2013; 47:6415-6422. [PMID: 24011842 DOI: 10.1016/j.watres.2013.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 06/02/2023]
Abstract
This study was designed to identify poultry feces-specific marker(s) within sequences of Faecalibacterium 16S rDNA for detecting poultry fecal pollution in water. Bioinformatics tools were used in the comparative analysis of 7,458 sequences of Faecalibacterium 16S rDNA, reportedly associated with various poultry (chicken and turkey) and animal species. One intervening sequence (IVS) within between the hypervariable region 1 and the conserved region 2, designated as IVS-p, was found to be unique to poultry feces. Based on this sequence, a PCR assay (PCR-p) was developed. The PCR-p produced an amplicon of 132 bp only in the test when fecal or wastewater samples from poultry were used, but not when using fecal or wastewater samples from other sources. The non-poultry sources included feces of beef or dairy cattle, dog, horse, human, domestic or wild geese, seagull, sheep, swine, and wild turkey. These data indicate that IVS-p may prove to be a useful genetic marker for the specific identification of poultry fecal pollution in environmental waterways. Furthermore, results of data mining and PCR assay indicate that the IVS-p may have a broad geographic distribution. This report represents initial evidence of the potential utility of ribosomal intervening sequences as genetic markers for tracking host sources of fecal pollution in waterways.
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Affiliation(s)
- Zhenyu Shen
- Department of Agriculture and Environmental Sciences, Lincoln University, 904 Chestnut Street, Jefferson City, MO 65101, USA
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18
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Harwood VJ, Staley C, Badgley BD, Borges K, Korajkic A. Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes. FEMS Microbiol Rev 2013; 38:1-40. [PMID: 23815638 DOI: 10.1111/1574-6976.12031] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 05/08/2013] [Accepted: 06/25/2013] [Indexed: 01/22/2023] Open
Abstract
Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.
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Affiliation(s)
- Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
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19
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Krentz CA, Prystajecky N, Isaac-Renton J. Identification of fecal contamination sources in water using host-associated markers. Can J Microbiol 2013; 59:210-20. [DOI: 10.1139/cjm-2012-0618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In British Columbia, Canada, drinking water is tested for total coliforms and Escherichia coli, but there is currently no routine follow-up testing to investigate fecal contamination sources in samples that test positive for indicator bacteria. Reliable microbial source tracking (MST) tools to rapidly test water samples for multiple fecal contamination markers simultaneously are currently lacking. The objectives of this study were (i) to develop a qualitative MST tool to identify fecal contamination from different host groups, and (ii) to evaluate the MST tool using water samples with evidence of fecal contamination. Singleplex and multiplex polymerase chain reaction (PCR) were used to test (i) water from polluted sites and (ii) raw and drinking water samples for presence of bacterial genetic markers associated with feces from humans, cattle, seagulls, pigs, chickens, and geese. The multiplex MST assay correctly identified suspected contamination sources in contaminated waterways, demonstrating that this test may have utility for heavily contaminated sites. Most raw and drinking water samples analyzed using singleplex PCR contained at least one host-associated marker. Singleplex PCR was capable of detecting host-associated markers in small sample volumes and is therefore a promising tool to further analyze water samples submitted for routine testing and provide information useful for water quality management.
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Affiliation(s)
- Corinne A. Krentz
- The University of British Columbia, Room G227, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Natalie Prystajecky
- British Columbia Public Health Microbiology and Reference Laboratory, Provincial Health Service Authority, 655 W 12th avenue, Vancouver, BC V5Z 4R4, Canada
| | - Judith Isaac-Renton
- The University of British Columbia, Room G227, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
- British Columbia Public Health Microbiology and Reference Laboratory, Provincial Health Service Authority, 655 W 12th avenue, Vancouver, BC V5Z 4R4, Canada
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20
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McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML. Sewage reflects the distribution of human faecal Lachnospiraceae. Environ Microbiol 2013; 15:2213-27. [PMID: 23438335 DOI: 10.1111/1462-2920.12092] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/13/2013] [Accepted: 01/17/2013] [Indexed: 01/10/2023]
Abstract
Faecal pollution contains a rich and diverse community of bacteria derived from animals and humans, many of which might serve as alternatives to the traditional enterococci and Escherichia coli faecal indicators. We used massively parallel sequencing (MPS) of the 16S rRNA gene to characterize microbial communities from wastewater treatment plant (WWTP) influent sewage from 12 cities geographically distributed across the USA. We examined members of the Clostridiales, which included the families Clostridiaceae, Lachnospiraceae and Ruminococcaceae for their potential as sewage indicators. Lachnospiraceae was one of the most abundant groups of faecal bacteria in sewage, and several Lachnospiraceae high-abundance sewage pyrotags occurred in at least 46 of 48 human faecal samples. Clone libraries targeting Clostridium coccoides (C. coccoides) in sewage samples demonstrated that Lachnospiraceae-annotated V6 pyrotags encompassed the previously reported C. coccoides group. We used oligotyping to profile the genus Blautia within Lachnospiraceae and found oligotypes comprised of 24 entropy components that showed patterns of host specificity. These findings suggest that indicators based on Blautia might have the capacity to discriminate between different faecal pollution sources. Development of source-specific alternative indicators would enhance water quality assessments, which leads to improved ecosystem health and reduced human health risk due to waterborne disease.
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Affiliation(s)
- Sandra L McLellan
- Great Lakes Water Institute, School of Freshwater Sciences, University of Wisconsin-Milwaukee, 600 E. Greenfield Ave, Milwaukee, WI 53204, USA.
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21
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Johnston C, Byappanahalli MN, Gibson JM, Ufnar JA, Whitman RL, Stewart JR. Probabilistic analysis showing that a combination of Bacteroides and Methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:13621-8. [PMID: 24182330 DOI: 10.1021/es403753k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.
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Affiliation(s)
- Christopher Johnston
- Jardon and Howard Technologies Incorporated , Orlando, Florida 32826, United States
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22
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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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23
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Ishii S, Sadowsky MJ. Escherichia coli in the Environment: Implications for Water Quality and Human Health. Microbes Environ 2012; 23:101-8. [PMID: 21558695 DOI: 10.1264/jsme2.23.101] [Citation(s) in RCA: 259] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli is naturally present in the intestinal tracts of warm-blooded animals. Since E. coli is released into the environment through deposition of fecal material, this bacterium is widely used as an indicator of fecal contamination of waterways. Recently, research efforts have been directed towards the identification of potential sources of fecal contamination impacting waterways and beaches. This is often referred to as microbial source tracking. However, recent studies have reported that E. coli can become "naturalized" to soil, sand, sediments, and algae in tropical, subtropical, and temperate environments. This phenomenon raises issues concerning the continued use of this bacterium as an indicator of fecal contamination. In this review, we discuss the relationship between E. coli and fecal pollution and the use of this bacterium as an indicator of fecal contamination in freshwater systems. We also discuss recent studies showing that E. coli can become an active member of natural microbial communities in the environment, and how this bacterium is being used for microbial source tracking. We also discuss the impact of environmentally-"naturalized" E. coli populations on water quality.
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Affiliation(s)
- Satoshi Ishii
- Department of Soil, Water, and Climate, University of Minnesota
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24
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Genetic markers for rapid PCR-based identification of gull, Canada goose, duck, and chicken fecal contamination in water. Appl Environ Microbiol 2011; 78:503-10. [PMID: 22081573 DOI: 10.1128/aem.05734-11] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avian feces contaminate waterways but contribute fewer human pathogens than human sources. Rapid identification and quantification of avian contamination would therefore be useful to prevent overestimation of human health risk. We used subtractive hybridization of PCR-amplified gull fecal 16S RNA genes to identify avian-specific fecal rRNA gene sequences. The subtracters were rRNA genes amplified from human, dog, cat, cow, and pig feces. Recovered sequences were related to Enterobacteriaceae (47%), Helicobacter (26%), Catellicoccus (11%), Fusobacterium (11%), and Campylobacter (5%). Three PCR assays, designated GFB, GFC, and GFD, were based on recovered sequence fragments. Quantitative PCR assays for GFC and GFD were developed using SYBR green. GFC detected down to 0.1 mg gull feces/100 ml (corresponding to 2 gull enterococci most probable number [MPN]/100 ml). GFD detected down to 0.1 mg chicken feces/100 ml (corresponding to 13 Escherichia coli MPN/100 ml). GFB and GFC were 97% and 94% specific to gulls, respectively. GFC cross-reacted with 35% of sheep samples but occurred at about 100,000 times lower concentrations in sheep. GFD was 100% avian specific and occurred in gulls, geese, chickens, and ducks. In the United States, Canada, and New Zealand, the three markers differed in their geographic distributions but were found across the range tested. These assays detected four important bird groups contributing to fecal contamination of waterways: gulls, geese, ducks, and chickens. Marker distributions across North America and in New Zealand suggest that they will have broad applicability in other parts of the world as well.
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25
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Stewart JR, Fleming LE, Fleisher JM, Abdelzaher AM, Maille Lyons M. Waterborne Pathogens. MARINE POLLUTION AND HUMAN HEALTH 2011. [DOI: 10.1039/9781849732871-00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A variety of microorganisms occur in the marine environment which are capable of infecting humans. This chapter, focused on waterborne pathogens, summarizes the types of pathogens that are a threat to human health, as well as the fecal indicator bacteria that are commonly used as surrogates for pathogens in regulatory and research applications. Limitations and alternatives to traditional fecal indicator bacteria are explored, highlighting challenges and policy implications for protecting public health. Methodological advances and challenges are also reviewed, with an emphasis on research designed to fill gaps and provide scientific support for management of marine resources, particularly bathing beaches. Accordingly, recent and previous epidemiology studies linking microbial measures of water quality to health outcomes are discussed in detail. As an alternative to the measurement of individual water samples, modeling of pathogens in marine waters is introduced. Overall, this chapter provides an overview of the pathogens, microbial measures and policy implications important for protecting humans from exposure to pathogens in marine waters.
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26
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Peed LA, Nietch CT, Kelty CA, Meckes M, Mooney T, Sivaganesan M, Shanks OC. Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:5652-9. [PMID: 21662992 DOI: 10.1021/es2003167] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between human and other animal sources of fecal pollution making it difficult to identify diffuse pollution sources. Human-associated quantitative real-time PCR (qPCR) methods in combination with low-order headwatershed sampling, precipitation information, and high-resolution geographic information system land use data can be useful for identifying diffuse source of human fecal pollution in receiving waters. To test this assertion, this study monitored nine headwatersheds over a two-year period potentially impacted by faulty septic systems and leaky sanitary sewer lines. Human fecal pollution was measured using three different human-associated qPCR methods and a positive significant correlation was seen between abundance of human-associated genetic markers and septic systems following wet weather events. In contrast, a negative correlation was observed with sanitary sewer line densities suggesting septic systems are the predominant diffuse source of human fecal pollution in the study area. These results demonstrate the advantages of combining water sampling, climate information, land-use computer-based modeling, and molecular biology disciplines to better characterize diffuse sources of human fecal pollution in environmental waters.
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27
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Morales SE, Holben WE. Linking bacterial identities and ecosystem processes: can 'omic' analyses be more than the sum of their parts? FEMS Microbiol Ecol 2011; 75:2-16. [PMID: 20662931 DOI: 10.1111/j.1574-6941.2010.00938.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A major goal in microbial ecology is to link specific microbial populations to environmental processes (e.g. biogeochemical transformations). The cultivation and characterization of isolates using genetic, biochemical and physiological tests provided direct links between organisms and their activities, but did not provide an understanding of the process networks in situ. Cultivation-independent molecular techniques have extended capabilities in this regard, and yet, for two decades, the focus has been on monitoring microbial community diversity and population dynamics by means of rRNA gene abundances or rRNA molecules. However, these approaches are not always well suited for establishing metabolic activity or microbial roles in ecosystem function. The current approaches, microbial community metagenomic and metatranscriptomic techniques, have been developed as other ways to study microbial assemblages, giving rise to exponentially increasing collections of information from numerous environments. This review considers some advantages and limitations of nucleic acid-based 'omic' approaches and discusses the potential for the integration of multiple molecular or computational techniques for a more effective assessment of links between specific microbial populations and ecosystem processes in situ. Establishing such connections will enhance the predictive power regarding ecosystem response to parameters or perturbations, and will bring us closer to integrating microbial data into ecosystem- and global-scale process measurements and models.
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Affiliation(s)
- Sergio E Morales
- Microbial Ecology Program, Division of Biological Sciences, The University of Montana, Missoula, MT 59812-1006, USA.
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28
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Shanks OC, White K, Kelty CA, Sivaganesan M, Blannon J, Meckes M, Varma M, Haugland RA. Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:6281-8. [PMID: 20704227 DOI: 10.1021/es100311n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
There are numerous PCR-based assays available to characterize human fecal pollution in ambient waters. Each assay employs distinct oligonucleotides and many target different genes and microorganisms leading to potential variations in assay performance. Performance comparisons utilizing feces and raw sewage samples are needed to determine which assays are best suited for expensive and time-consuming field validation, fate, transport, and epidemiology studies. We report the assessment of five end-point PCR and 10 real-time quantitative PCR (qPCR) assays that target genes from presumptive Bacteroidales microorganisms reported to be associated with human feces. Each assay was tested against a reference collection of 54 primary influent sewage samples collected from different geographical locations across the United States and 174 fecal DNA extracts from 23 different animal sources. Experiments indicate that human-associated genetic markers are distributed across a broad range of human populations but show substantial differences in specificity for human feces suggesting that particular assays may be more suitable than others depending on the abundance of genetic marker required for detection and the animal sources impacting a particular watershed or beach of interest.
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Affiliation(s)
- Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, Ohio 45268, USA.
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Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales species and human fecal waste by qPCR. Syst Appl Microbiol 2010; 33:348-57. [PMID: 20655680 DOI: 10.1016/j.syapm.2010.06.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 06/03/2010] [Accepted: 06/11/2010] [Indexed: 11/24/2022]
Abstract
Molecular methods for quantifying defined Bacteroidales species from the human gastrointestinal tract may have important clinical and environmental applications, ranging from diagnosis of infections to fecal source tracking in surface waters. In this study, sequences from the V2 region of the small subunit ribosomal RNA gene were targeted in the development of qPCR assays to quantify DNA from six Bacteroides and one Prevotella species. In silico and experimental analyses suggested that each of the assays was highly discriminatory in detecting DNA from the intended species. Analytical sensitivity, precision and ranges of quantification were demonstrated for each assay by coefficients of variation of less than 2% for cycle threshold measurements over a range from 10 to 4×10(4) target sequence copies. The assays were applied to assess the occurrence and relative abundance of their target sequences in feces from humans and five animal groups as well as in 14 sewage samples from 13 different treatment facilities. Sequences from each of the species were detected at high levels (>10(3)copies/ng total extracted DNA) in human wastes. Sequences were also detected by each assay in all sewage samples and, with exception of the Prevotella sequences, showed highly correlated (R(2)≥0.7) variations in concentrations between samples. In contrast, the occurrence and relative abundance profiles of these sequences differed substantially in the fecal samples from each of the animal groups. These results suggest that analyses for multiple individual Bacteroidales species may be useful in identifying human fecal pollution in environmental waters.
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Zheng G, Yampara-Iquise H, Jones JE, Andrew Carson C. Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces. J Appl Microbiol 2010; 106:634-41. [PMID: 19200327 DOI: 10.1111/j.1365-2672.2008.04037.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS The focus of this study was to identify a bacterial 16S rRNA gene sequence, unique to microbiota in the human gut, for use in development of a dependable PCR assay to detect human faecal pollution in water. METHODS AND RESULTS Suppression subtractive hybridization (SSH) and bioinformatics were used to identify a genetic marker, within the 16S rRNA gene of Faecalibacterium, for the detection of human faeces. DNA sequencing analysis demonstrated that a majority (16) of 74 clones of the SSH library contained insertion sequences identified as Faecalibacterium 16S rRNA genes. Human faeces-specific sequences were derived and six PCR primer sets designed and tested against faecal DNA samples from human and nonhuman sources. One PCR primer set, HFB-F3 and HFB-R5, was exclusively associated with human faeces. These primers generated a human faeces-specific amplicon of 399 bp from 60.2% of human faecal samples and 100% of sewage samples. CONCLUSIONS The subject Faecalibacterium marker is specific for sewage. SIGNIFICANCE AND IMPACT OF THE STUDY This study represents the initial report of a Faecalibacterium marker for human faeces, which may prove useful for microbial source tracking.
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Affiliation(s)
- G Zheng
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
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Kent AD, Bayne ZL. Degraded water quality influences microbial community composition and perception of health risks in the Chattooga River. DNA Cell Biol 2010; 29:509-17. [PMID: 20230298 DOI: 10.1089/dna.2009.0988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacterial skin infections are a chronic problem among whitewater rafters on the Chattooga River in the southeastern United States; however, little is known about the source of such infections. The Chattooga River is a federally designated "Wild and Scenic" river, with a forested riparian buffer zone designed to protect water quality in the river. Riverine water quality can be negatively impacted by tributaries that are not protected by federal guidelines. Water quality in Stekoa Creek, a major tributary of the Chattooga River, is degraded by sediment that runs off from construction sites near the creek, as well as fecal coliform contamination from wastewater treatment facilities. Degraded water quality may impact the health of visitors recreating on the river, as well as recreation industry workers. We demonstrate that inputs from the impaired creek influence microbial community composition in Chattooga River waters. A survey of whitewater raft guides was conducted to collect data on incidence of skin infection, and to assess perceived health risk from recreation activities. Whitewater rafting guides working on the Chattooga River reported concerns about their personal health related to degraded water quality and microbial contamination from Stekoa Creek. Incidence of bacterial skin infection and perceived health risk was strongly correlated among the whitewater rafting guides (r = 0.67). Concerns about environmental quality appear to be shaped by the incidence of skin infection. Such concerns are also correlated with changes in recreation practices among whitewater rafting guides (r = 0.67).
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Affiliation(s)
- Angela D Kent
- Deparment of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois, USA
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Yampara-Iquise H, Zheng G, Jones JE, Carson CA. Use of a Bacteroides thetaiotaomicron-specific alpha-1-6, mannanase quantitative PCR to detect human faecal pollution in water. J Appl Microbiol 2010; 105:1686-93. [PMID: 19149766 DOI: 10.1111/j.1365-2672.2008.03895.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The aims of this work were to develop a quantitative test, based on Bacteroides thetaiotaomicron, for human faecal pollution in water and to evaluate test performance. METHODS AND RESULTS qPCR primers, based on the complete genomic sequence of B. thetaiotaomicron VPI 5482, were designed and tested. The single-copy putative mannanase homologue, alpha-1-6 mannanase, was selected as the particular target and sequences within this gene chosen as the qPCR primers by Blast search for specificity to B. thetaiotaomicron. The average concentration of B. thetaiotaomicron in human faeces was 1.39 x 10(8) cells per gram faeces and the detection limit was 9.3 B. thetaiotaomicron copies per qPCR procedure. Comparison of B. thetaiotaomicron content in sewage vs pooled nonhuman faecal samples indicated that the current assay is specific for sewage. CONCLUSION The subject assay is potentially useful for quantification of sewage pollution in water. SIGNIFICANCE AND IMPACT OF THE STUDY Bacteroides-associated markers, proposed for faecal source tracking, have exclusively been based on gene sequences related to generally classified and uncultured bacteria. However, genes associated with host-microbe interaction have been suggested as more specific markers. The present assay targets such a gene of B. thetaiotaomicron which is considered to be a symbiont in the human gut.
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Affiliation(s)
- H Yampara-Iquise
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
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33
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Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution. Appl Environ Microbiol 2010; 76:1359-66. [PMID: 20061457 DOI: 10.1128/aem.02033-09] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are numerous PCR-based assays available to characterize bovine fecal pollution in ambient waters. The determination of which approaches are most suitable for field applications can be difficult because each assay targets a different gene, in many cases from different microorganisms, leading to variation in assay performance. We describe a performance evaluation of seven end-point PCR and real-time quantitative PCR (qPCR) assays reported to be associated with either ruminant or bovine feces. Each assay was tested against a reference collection of DNA extracts from 247 individual bovine fecal samples representing 11 different populations and 175 fecal DNA extracts from 24 different animal species. Bovine-associated genetic markers were broadly distributed among individual bovine samples ranging from 39 to 93%. Specificity levels of the assays spanned 47.4% to 100%. End-point PCR sensitivity also varied between assays and among different bovine populations. For qPCR assays, the abundance of each host-associated genetic marker was measured within each bovine population and compared to results of a qPCR assay targeting 16S rRNA gene sequences from Bacteroidales. Experiments indicate large discrepancies in the performance of bovine-associated assays across different bovine populations. Variability in assay performance between host populations suggests that the use of bovine microbial source-tracking applications will require a priori characterization at each watershed of interest.
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Abstract
Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting Bacteroidales-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 x 10(6) copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total Bacteroidales and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.
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35
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Phylogenetic diversity and molecular detection of bacteria in gull feces. Appl Environ Microbiol 2008; 74:3969-76. [PMID: 18469128 DOI: 10.1128/aem.00019-08] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In spite of increasing public health concerns about the potential risks associated with swimming in waters contaminated with waterfowl feces, little is known about the composition of the gut microbial community of aquatic birds. To address this, a gull 16S rRNA gene clone library was developed and analyzed to determine the identities of fecal bacteria. Analysis of 282 16S rRNA gene clones demonstrated that the gull gut bacterial community is mostly composed of populations closely related to Bacilli (37%), Clostridia (17%), Gammaproteobacteria (11%), and Bacteriodetes (1%). Interestingly, a considerable number of sequences (i.e., 26%) were closely related to Catellicoccus marimammalium, a gram-positive, catalase-negative bacterium. To determine the occurrence of C. marimammalium in waterfowl, species-specific 16S rRNA gene PCR and real-time assays were developed and used to test fecal DNA extracts from different bird (n = 13) and mammal (n = 26) species. The results showed that both assays were specific to gull fecal DNA and that C. marimammalium was present in gull fecal samples collected from the five locations in North America (California, Georgia, Ohio, Wisconsin, and Toronto, Canada) tested. Additionally, 48 DNA extracts from waters collected from six sites in southern California, Great Lakes in Michigan, Lake Erie in Ohio, and Lake Ontario in Canada presumed to be impacted with gull feces were positive by the C. marimammalium assay. Due to the widespread presence of this species in gulls and environmental waters contaminated with gull feces, targeting this bacterial species might be useful for detecting gull fecal contamination in waterfowl-impacted waters.
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Leach MD, Broschat SL, Call DR. A discrete, stochastic model and correction method for bacterial source tracking. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:524-529. [PMID: 18284157 DOI: 10.1021/es070943x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have developed a model to test several underlying assumptions of bacterial source tracking (BST) when the BST method is based on detection of discrete genetic markers from source-specific bacteria. The model consists of an environment and discrete-time input signals that represent sources of contamination partitioned into marker-bearing and nonmarker-bearing units "shed" into the environment. Simulations run for different types of environmental contamination patterns indicate that if hosts shed different percentages of BST markers, the environment cannot be accurately characterized unless a correction method is used. The correction method, which requires the solution to a linear system, reduces the mean error in estimating the proportions of host contamination to below 3%. The effectiveness of the method depends on accurate knowledge of the occurrence and prevalence of markers in the various hosts; this may be a challenging task, especially if these values vary across populations in space and time. In addition, the correction method does not compensate for environments with low-density or unmixed contamination. In conclusion, our simulations highlight several fundamental challenges that may prevent absolute quantification of fecal input using discrete marker BST.
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Affiliation(s)
- Mark D Leach
- School of Electrical Engineering and Computer Science, Center for Integrated Biotechnology, Washington State University, Pullman, Washington 99164, USA
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37
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Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. Appl Environ Microbiol 2007; 74:745-52. [PMID: 18065617 DOI: 10.1128/aem.01843-07] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described bovine feces-specific genetic markers and a method for the enumeration of these markers using a Markov chain Monte Carlo approach. Both assays exhibited a range of quantification from 25 to 2 x 10(6) copies of target DNA, with a coefficient of variation of <2.1%. One of these assays can be multiplexed with an internal amplification control to simultaneously detect the bovine-specific genetic target and presence of amplification inhibitors. The assays detected only cattle fecal specimens when tested against 204 fecal DNA extracts from 16 different animal species and also demonstrated a broad distribution among individual bovine samples (98 to 100%) collected from five geographically distinct locations. The abundance of each bovine-specific genetic marker was measured in 48 individual samples and compared to quantitative PCR-enumerated quantities of rRNA gene sequences representing total Bacteroidetes, Bacteroides thetaiotaomicron, and enterococci in the same specimens. Acceptable assay performance combined with the prevalence of DNA targets across different cattle populations provides experimental evidence that these quantitative assays will be useful in monitoring bovine fecal pollution in ambient waters.
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Lau SCK, Liu WT. Recent advances in molecular techniques for the detection of phylogenetic markers and functional genes in microbial communities. FEMS Microbiol Lett 2007; 275:183-90. [PMID: 17651392 DOI: 10.1111/j.1574-6968.2007.00853.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The detection and analysis of nucleic acids extracted from microbial communities are the ultimate ways to determine the diversity and functional capability of microbial communities in the environments. However, it remains a challenge to use molecular techniques for unequivocal determination and quantification of microbial species composition and functional activities. Considerable efforts have been made to enhance the capability of molecular techniques. Here an update of the recent developments in molecular techniques for environmental microbiology is provided.
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Affiliation(s)
- Stanley C K Lau
- Division of Environmental Science and Engineering, National University of Singapore, Singapore, Singapore
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Field KG, Samadpour M. Fecal source tracking, the indicator paradigm, and managing water quality. WATER RESEARCH 2007; 41:3517-38. [PMID: 17643471 DOI: 10.1016/j.watres.2007.06.056] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Revised: 05/18/2007] [Accepted: 06/18/2007] [Indexed: 05/03/2023]
Abstract
Fecal source tracking is used because standard methods of measuring fecal contamination in water by enumerating fecal indicator bacteria (FIB) do not identify the sources of the contamination. This paper presents a critical review of source tracking with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), when methods are applicable, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper discusses the broader question of whether fecal source tracking and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many fecal source-tracking methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the "real" answer is not known, so their comparative performance and accuracy cannot be assessed. For source tracking to be quantitative, stability of ratios between host-specific markers in the environment must be established. In addition, research is needed on the correlation between host-specific markers and pathogens, and survival of markers after waste treatments. As a result of the exclusive emphasis on FIB in legislation, monitoring has concentrated on FIB and lost sight of pathogens. A more rational approach to regulating water quality would start with available epidemiological data to identify pathogens of concern in a particular water body, and then use targeted pathogen monitoring coupled with targeted fecal source tracking to control them. Baseline monitoring of indicators would become just one tool among many.
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Affiliation(s)
- Katharine G Field
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
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40
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Santo Domingo JW, Bambic DG, Edge TA, Wuertz S. Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution. WATER RESEARCH 2007; 41:3539-52. [PMID: 17632210 DOI: 10.1016/j.watres.2007.06.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 05/26/2007] [Accepted: 06/01/2007] [Indexed: 05/07/2023]
Abstract
Advances in microbial source tracking (MST) have largely been driven by the need to comply with water quality standards based on traditional indicator bacteria. Recently, a number of culture-independent, and library-independent methods based on polymerase chain reaction (PCR) have been gaining popularity among source trackers. However, only a limited number of these methods have been successfully used in field applications, primarily due to the fact that many of them are still being developed. In this critical outlook, we examine different viewpoints associated with the practical use of MST to identify critical research gaps, propose a priority-based timeline to address them, and outline emerging technologies that will likely impact the future of source tracking. We propose that it is necessary to consider each of these aspects in order to advance towards a unifying framework in source identification, so that fecal pollution monitoring can be reliably used for comprehensive environmental microbial monitoring, to develop risk assessment models, and to implement and validate adequate management practices.
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Affiliation(s)
- Jorge W Santo Domingo
- US Environmental Protection Agency, NRMRL/WSWRD/MCCB, 26 W. Martin Luther King Dr., MS 387, Cincinnati, OH 45268, USA.
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