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Mills M, Davis A, Lancaster E, Choi B, Martin J, Winston R, Lee J. Longitudinal Analysis of Urban Stormwater Microbiome and Resistome from Watersheds with and without Green Infrastructure using Long-Read Sequencing. WATER RESEARCH 2024; 259:121873. [PMID: 38852387 DOI: 10.1016/j.watres.2024.121873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/14/2024] [Accepted: 06/02/2024] [Indexed: 06/11/2024]
Abstract
Since stormwater conveys a variety of contaminants into water bodies, green infrastructure (GI) is increasingly being adopted as an on-site treatment solution in addition to controlling peak flows. The purpose of this study was to identify differences in microbial water quality of stormwater in watersheds retrofitted with GI vs. those without GI. Considering stormwater is recently recognized as a contributor to the antibiotic resistance (AR) threat, another goal of this study was to characterize changes in the microbiome and collection of AR genes (resistome) of urban stormwater with season, rainfall characteristics, and fecal contamination. MinION long-read sequencing was used to analyze stormwater microbiome and resistome from watersheds with and without GI in Columbus, Ohio, United States, over 18 months. We characterized fecal contamination in stormwater via culturing Escherichia coli and with molecular microbial source tracking (MST) to identify sources of fecal contamination. Overall, season and storm event (rainfall) characteristics had the strongest relationships with changes in the stormwater microbiome and resistome. We found no significant differences in microbial water quality or the microbiome of stormwater in watersheds with and without GI implemented. However, there were differences between the communities of microorganisms hosting antibiotic resistance genes (ARGs) in stormwater from watersheds with and without GI, indicating the potential sensitivity of AR bacteria to treatment. Stormwater was contaminated with high concentrations of human-associated fecal bacterial genes, and the ARG host bacterial community had considerable similarities to human feces/wastewater. We also identified 15 potential pathogens hosting ARGs in these stormwater resistome, including vancomycin-resistant Enterococcus faecium (VRE) and multidrug-resistant Pseudomonas aeruginosa. In summary, urban stormwater is highly contaminated and has a great potential to spread AR and microbial hazards to nearby environments. This study presents the most comprehensive analysis of stormwater microbiome and resistome to date, which is crucial to understanding the potential microbial risk from this matrix. This information can be used to guide future public health policy, stormwater reuse programs, and urban runoff treatment initiatives.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Angela Davis
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Emma Lancaster
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Boseung Choi
- Division of Big Data Science, Korea University, Sejong, Republic of Korea
| | - Jay Martin
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA; Department of Food, Agricultural and Biological Engineering, The Ohio State University, Columbus, OH, USA; Sustainability Institute, The Ohio State University, Columbus, OH, USA
| | - Ryan Winston
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, Columbus, OH, USA; Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA; Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
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2
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Frank EM, Ahlinder J, Jephson T, Persson KM, Lindberg E, Paul CJ. Marine sediments are identified as an environmental reservoir for Escherichia coli: comparing signature-based and novel amplicon sequencing approaches for microbial source tracking. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167865. [PMID: 37863217 DOI: 10.1016/j.scitotenv.2023.167865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.
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Affiliation(s)
- Ellinor M Frank
- Water Resources Engineering, Department of Building and Environmental Technology, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden; Sweden Water Research, Ideon Science Park, Scheelevägen 15, SE-223 70 Lund, Sweden
| | - Jon Ahlinder
- FOI, Swedish Defense Research Agency, Cementvägen 20, SE-906 21 Umeå, Sweden
| | - Therese Jephson
- Sweden Water Research, Ideon Science Park, Scheelevägen 15, SE-223 70 Lund, Sweden
| | - Kenneth M Persson
- Water Resources Engineering, Department of Building and Environmental Technology, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden; Sweden Water Research, Ideon Science Park, Scheelevägen 15, SE-223 70 Lund, Sweden
| | - Elisabet Lindberg
- City of Helsingborg, Department of City Planning, Järnvägsgatan 22, SE-252 25 Helsingborg, Sweden
| | - Catherine J Paul
- Water Resources Engineering, Department of Building and Environmental Technology, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden; Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
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Ren W, Feng Y. Persistence of human- and cattle-associated Bacteroidales and mitochondrial DNA markers in freshwater mesocosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165742. [PMID: 37487899 DOI: 10.1016/j.scitotenv.2023.165742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/05/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
Accurate identification of the origins of non-point source pollution is essential for the effective control of fecal pollution. Host-associated Bacteroidales and mitochondrial DNA (mtDNA) markers have been developed to identify the sources of human and cattle fecal pollution. However, the differences in persistence between these two types of markers under different environmental conditions are still poorly understood. Here, we conducted mesocosm experiments to investigate the influence of indigenous microbiota and nutrients on the decay of Bacteroidales and mtDNA markers associated with humans and cattle. Raw sewage or cattle feces were inoculated into mesocosms containing natural eutrophic water, sterile eutrophic water or artificial freshwater. The Bacteroidales markers HF183 (human) and CowM3 (cattle) and mtDNA markers HcytB (human) and QMIBo (cattle) were quantified using the quantitative polymerase chain reaction (qPCR) assays. All markers but HF183 decreased the fastest in the presence of indigenous microbiota. Nutrients caused a decrease in the persistence of HF183; however, no significant nutrient effects were observed for HcytB, CowM3, and QMIBo. The time to reach one log reduction (T90) for HF183 and HcytB was similar; CowM3 reached T90 earlier than QMIBo in all the treatments but eutrophic water. E. coli persisted longer than both Bacteroidales and mtDNA markers in the mesocosms regardless of inoculum type. Additionally, 16S rRNA gene amplicon sequencing was used to determine the changes in bacterial communities accompanying the marker decay. Analysis using the SourceTracker software showed that bacterial communities in the mesocosms became more dissimilar to those in the corresponding inoculants over time. Our results indicate that environmental factors are important determinants of genetic markers' persistence, but their impact can vary depending on the genetic markers. The cattle Bacteroidales markers may be more suitable for determining recent fecal contamination than cattle mtDNA.
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Affiliation(s)
- Wenjing Ren
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yucheng Feng
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.
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Sherchan S, Shahin S, Alarcon J, Brosky H, Potter C, Dada AC. Microbial source tracking of fecal contamination in stormwater runoff. JOURNAL OF WATER AND HEALTH 2022; 20:1271-1283. [PMID: 36170186 DOI: 10.2166/wh.2022.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Concerns over fecal contamination in stormwater canals have promoted the need for pollution control strategies, including the use of microbial source tracking, to identify fecal contamination in the Greater New Orleans Area. Surface water samples were collected over a 12-month period at five canal locations within Jefferson Parish, Louisiana. Quantitative polymerase chain reaction and the IDEXX method were used to assess the concentrations of coliforms, Escherichia coli (E. coli) and human fecal 183 bacteroides (HF183) in stormwater samples. A 100% positive detection rate of total coliforms and E. coli was observed across all tested sites. Despite the closeness of the five sites, when averaged across all sampling time points, Kruskal-Wallis tests indicated that E. coli was present at significantly different concentrations in these locations (χ2(5) = 19.8, p = 0.0005). HF183 was detected in 62% of the water samples collected during the stormwater sampling. Without further testing for HF183 markers, the conclusion from this study would have been that fecal contamination from an unknown source was always present at varying levels during the study period. Analysis of HF183 markers therefore adds another layer of conclusions to the results deductible from E. coli concentrations. A 100% E. coli detection rate, high E. coli concentrations coupled with low rates of HF183 detection particularly at the Esplanade, Poplar Street, and Bonnabel Boat Launch sites, the sites closest to the lake outlet, throughout the study period, indicate that fecal contamination at these stormwater canal sites comes primarily from non-human sources. However, the Metairie Road and Napoleon Avenue sites, which have the highest HF183 detection rates, on top of chronic pollution by other non-human sources, are also influenced by human fecal pollution, possibly because of human development and faulty infrastructure. This study highlights the advantages of the use of microbial source-tracking methods to complement traditional indicator bacteria.
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Affiliation(s)
- Samendra Sherchan
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA E-mail: ; Department of Biology, Morgan State University, Baltimore, MD 21251, USA
| | - Shalina Shahin
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA E-mail:
| | - Joshua Alarcon
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA E-mail:
| | - Hanna Brosky
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA E-mail:
| | - Collin Potter
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA E-mail:
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Guo Y, Sivakumar M, Jiang G. Decay of four enteric pathogens and implications to wastewater-based epidemiology: Effects of temperature and wastewater dilutions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:152000. [PMID: 34843787 DOI: 10.1016/j.scitotenv.2021.152000] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Measurement of pathogens in raw wastewater from a population within certain sewer catchments can provide quantitative information on public health status within the sampled urban area. This so-called wastewater-based epidemiology (WBE) approach has the potential of becoming a powerful tool to monitor pathogen circulation and support timely intervention during outbreaks. However, many WBE studies failed to account for the pathogen decay during wastewater transportation in back calculating the disease prevalence. Various sewer process factors, including water temperature and infiltration/inflow, can lead to the variation of pathogen decay rates. This paper firstly reviewed the effects of temperature and types of water, i.e., wastewater, freshwater, and saline water, on the decay of four selected enteric pathogens, i.e., Campylobacter, Salmonella, Norovirus, and Adenovirus. To elucidate the importance of the pathogen decay rates (measured by culture and molecular methods) to WBE, a sensitivity analysis was conducted on the back-calculation equation for infection prevalence with decay rates collected from published literature. It was found that WBE back-calculation is more sensitive to decay rates under the condition of high wastewater temperature (i.e., over 25 °C) or if wastewater is diluted by saline water (i.e., sewer infiltration or use of seawater as an alternative source of freshwater constituting around 1/3 household water demand in some cities). Stormwater dilution of domestic wastewater (i.e., sewer inflow might achieve 10 times volumetric dilution) was shown to play a role in increasing the sensitivity of WBE back-calculation to bacterial pathogens, but not viral pathogens. Hence, WBE back-calculation in real sewers should account for in-sewer decay of specific pathogen species under different wastewater temperatures and dilutions. Overall, this review contributes to a better understanding of pathogen decay in wastewater which can lead to improved accuracy of WBE back-calculation.
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Affiliation(s)
- Ying Guo
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia
| | - Muttucumaru Sivakumar
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia.
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Holcomb DA, Knee J, Capone D, Sumner T, Adriano Z, Nalá R, Cumming O, Brown J, Stewart JR. Impacts of an Urban Sanitation Intervention on Fecal Indicators and the Prevalence of Human Fecal Contamination in Mozambique. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11667-11679. [PMID: 34382777 PMCID: PMC8429117 DOI: 10.1021/acs.est.1c01538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fecal source tracking (FST) may be useful to assess pathways of fecal contamination in domestic environments and to estimate the impacts of water, sanitation, and hygiene (WASH) interventions in low-income settings. We measured two nonspecific and two human-associated fecal indicators in water, soil, and surfaces before and after a shared latrine intervention from low-income households in Maputo, Mozambique, participating in the Maputo Sanitation (MapSan) trial. Up to a quarter of households were impacted by human fecal contamination, but trends were unaffected by improvements to shared sanitation facilities. The intervention reduced Escherichia coli gene concentrations in soil but did not impact culturable E. coli or the prevalence of human FST markers in a difference-in-differences analysis. Using a novel Bayesian hierarchical modeling approach to account for human marker diagnostic sensitivity and specificity, we revealed a high amount of uncertainty associated with human FST measurements and intervention effect estimates. The field of microbial source tracking would benefit from adding measures of diagnostic accuracy to better interpret findings, particularly when FST analyses convey insufficient information for robust inference. With improved measures, FST could help identify dominant pathways of human and animal fecal contamination in communities and guide the implementation of effective interventions to safeguard health.
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Affiliation(s)
- David A. Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Drew Capone
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | | | - Rassul Nalá
- Instituto Nacional de Saúde, Ministério da Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
| | - Jill R. Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States of America
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Kerkhof LJ. Is Oxford Nanopore sequencing ready for analyzing complex microbiomes? FEMS Microbiol Ecol 2021; 97:6098400. [PMID: 33444433 PMCID: PMC8068755 DOI: 10.1093/femsec/fiab001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing technology that make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65 to 96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.
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Affiliation(s)
- Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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Tan Q, Li W, Chen X. Identification the source of fecal contamination for geographically unassociated samples with a statistical classification model based on support vector machine. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124821. [PMID: 33340974 DOI: 10.1016/j.jhazmat.2020.124821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
The bacterial diversity and corresponding biological significance revealed by high-throughput sequencing contribute massive information to source tracking of fecal contamination. The performances of classification models on predicting the fecal source of geographical local and foreign samples were examined herein, by applying support vector machine (SVM) algorithm. Random forest (RF) and Adaboost were applied for comparison as well. Discriminatory sequences were selected from Clostridiale, Bacteroidales, or Lactobacillales bacterial groups using extremely randomized trees (ExtraTrees). 1.51-12.64% of the unique sequences in the original library composed the representative markers, and they contributed 70% of the discrepancies between source microbiomes. The overall accuracy of the SVM model and the RF model on local samples was 96.08% and 98.04%, respectively, higher than that of the Adaboost (90.20%). As for the non-local samples, the SVM assigned most of the fecal samples into the correct category while several false-positive judgments occurred in closely related groups. The results in this paper suggested that the SVM was a time-saving and accurate method for fecal source tracking in contaminated water body with the potential capability of executing tasks based on geographically unassociated samples, and underlined the necessity of qPCR analysis for accurate detection of human source pollution.
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Affiliation(s)
- Qiaowen Tan
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Weiying Li
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Xiao Chen
- College of Defence Engineering, The Army Engineering University of PLA, Nanjing 210007, China
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Białasek M, Miłobędzka A. Revealing antimicrobial resistance in stormwater with MinION. CHEMOSPHERE 2020; 258:127392. [PMID: 32947654 PMCID: PMC7297696 DOI: 10.1016/j.chemosphere.2020.127392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 05/17/2020] [Accepted: 06/10/2020] [Indexed: 05/14/2023]
Abstract
Discharge of urban stormwater containing organic matter, heavy metals and sometime human feces, to the natural aquatic reservoirs without any treatment is not only an environmental problem. It can lead to prevalence of antibiotic resistant bacteria in stormwater systems and transmission of antibiotic resistance genes to the environment. We performed antibiotic resistome identification and virus detection in stormwater samples from Stockholm, using publicly available metagenomic sequencing MinION data. A MinION platform offers low-cost, precise environmental metagenomics analysis. 37 groups of antibiotic resistant bacteria (ARB), 11 resistance types with 26 resistance mechanisms - antibiotic resistance genes (ARGs) giving tolerance to the aminoglycoside, beta-lactams, fosmidomycin, MLS, multidrug and vancomycin were identified using ARGpore pipeline. The majority of the identified bacteria species were related to the natural environment such as soil and were not dangerous to human. Alarmingly, human pathogenic bacteria carrying resistance to antibiotics currently used against them (Bordetella resistant to macrolides and multidrug resistant Propionibacterium avidum) were also found in the samples. Most abundant viruses identified belonged to Caudovirales and Herpesvirales and they were not carrying ARGs. Unlike the virome, resistome and ARB were not unique for stormwater sampling points. This results underline the need for extensive monitoring of the microbial community structure in the urban stormwater systems to assess antimicrobial resistance spread.
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Affiliation(s)
- Maciej Białasek
- Department of Cancer Biology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland; Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland.
| | - Aleksandra Miłobędzka
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6, Czech Republic.
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Acharya K, Blackburn A, Mohammed J, Haile AT, Hiruy AM, Werner D. Metagenomic water quality monitoring with a portable laboratory. WATER RESEARCH 2020; 184:116112. [PMID: 32688150 PMCID: PMC7347499 DOI: 10.1016/j.watres.2020.116112] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 05/14/2023]
Abstract
We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units, mini-centrifuges, mini-PCR machines and the memory-stick sized MinION of Oxford Nanopore Technologies, for the library preparation and sequencing of 16S rRNA gene amplicons. Using this portable toolbox on site, we successfully characterized the microbiome of water samples collected from Birtley Sewage Treatment Plant, UK, and its environs. We also demonstrated the applicability of the portable metagenomics toolbox in a low-income country by surveying water samples from the Akaki River around Addis Ababa, Ethiopia. The 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, sequencing library preparation, and sequencing was accomplished within one working day. The metagenomic data became available within 24-72 h, depending on internet speed. Metagenomic analysis clearly distinguished the microbiome of pristine samples from sewage influenced water samples. Metagenomic analysis identified the potential role of two bacterial genera not conventionally monitored, Arcobacter and Aeromonas, as predominant faecal pollution indicators/waterborne hazards. Subsequent quantitative PCR analysis validated the high Arcobacter butzleri abundances observed in the urban influenced Akaki River water samples by portable next generation sequencing with the MinION device. Overall, our field deployable metagenomics toolbox advances the capability of scientists to comprehensively monitor microbiomes anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond.
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Affiliation(s)
- Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Adrian Blackburn
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jemila Mohammed
- International Water Management Institute (IWMI), Addis Ababa, Ethiopia; Addis Ababa Water and Sewerage Authority (AAWSA), Addis Ababa, Ethiopia; Centre for Environmental Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | | | - Andualem Mekonnen Hiruy
- Centre for Environmental Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom.
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Holcomb DA, Stewart JR. Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality. Curr Environ Health Rep 2020; 7:311-324. [PMID: 32542574 PMCID: PMC7458903 DOI: 10.1007/s40572-020-00278-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination. RECENT FINDINGS This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.
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Affiliation(s)
- David A Holcomb
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Dr., Chapel Hill, NC, 27599-7435, USA
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Dr., Chapel Hill, NC, 27599-7431, USA.
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12
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Latorre-Pérez A, Pascual J, Porcar M, Vilanova C. A lab in the field: applications of real-time, in situ metagenomic sequencing. Biol Methods Protoc 2020; 5:bpaa016. [PMID: 33134552 PMCID: PMC7585387 DOI: 10.1093/biomethods/bpaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/18/2023] Open
Abstract
High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.
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Affiliation(s)
| | | | - Manuel Porcar
- Darwin Bioprospecting Excellence SL, Valencia, Spain
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Valencia, Spain
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Li J, Zhu Y, Wu X, Hoffmann MR. Rapid Detection Methods for Bacterial Pathogens in Ambient Waters at the Point of Sample Collection: A Brief Review. Clin Infect Dis 2020; 71:S84-S90. [PMID: 32725238 PMCID: PMC7388722 DOI: 10.1093/cid/ciaa498] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The world is currently facing a serious health burden of waterborne diseases, including diarrhea, gastrointestinal diseases, and systemic illnesses. The control of these infectious diseases ultimately depends on the access to safe drinking water, properly managed sanitation, and hygiene practices. Therefore, ultrasensitive, rapid, and specific monitoring platforms for bacterial pathogens in ambient waters at the point of sample collection are urgently needed. We conducted a literature review on state-of-the-art research of rapid in-field aquatic bacteria detection methods, including cell-based methods, nucleic acid amplification detection methods, and biosensors. The detection performance, the advantages, and the disadvantages of the technologies are critically discussed. We envision that promising monitoring approaches should be automated, real-time, and target-multiplexed, thus allowing comprehensive evaluation of exposure risks attributable to waterborne pathogens and even emerging microbial contaminants such as antibiotic resistance genes, which leads to better protection of public health.
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Affiliation(s)
- Jing Li
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California, USA
| | - Yanzhe Zhu
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California, USA
| | - Xunyi Wu
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California, USA
| | - Michael R Hoffmann
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California, USA
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14
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Quan L, Dong R, Yang W, Chen L, Lang J, Liu J, Song Y, Ma S, Yang J, Wang W, Meng B, Tian G. Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing. Sci Rep 2019; 9:19337. [PMID: 31852945 PMCID: PMC6920169 DOI: 10.1038/s41598-019-55843-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023] Open
Abstract
Human papillomavirus (HPV) is a major pathogen that causes cervical cancer and many other related diseases. HPV infection related cervical microbiome could be an induce factor of cervical cancer. However, it is uncommon to find a single test on the market that can simultaneously provide information on both HPV and the microbiome. Herein, a novel method was developed in this study to simultaneously detect HPV infection and microbiota composition promptly and accurately. It provides a new and simple way to detect vaginal pathogen situation and also provide valuable information for clinical diagnose. This approach combined multiplex PCR, which targeted both HPV16 E6E7 and full-length 16S rRNA, and Nanopore sequencing to generate enough information to understand the vagina condition of patients. One HPV positive liquid-based cytology (LBC) sample was sequenced and analyzed. After comparing with Illumina sequencing, the results from Nanopore showed a similar microbiome composition. An instant sequencing evaluation showed that 15 min sequencing is enough to identify the top 10 most abundant bacteria. Moreover, two HPV integration sites were identified and verified by Sanger sequencing. This approach has many potential applications in pathogen detection and can potentially aid in providing a more rapid clinical diagnosis.
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Affiliation(s)
- Lili Quan
- Department of Gynaecology and Obstetrics, Sanmenxia Central Hospital of Henan University of Science and Technology, Sanmenxia, 472000, Henan, China
| | - Ruyi Dong
- Geneis (Beijing) Co.Ltd, Beijing, 100102, China
| | | | - Lanyou Chen
- Geneis (Beijing) Co.Ltd, Beijing, 100102, China
| | - Jidong Lang
- Geneis (Beijing) Co.Ltd, Beijing, 100102, China
| | - Jia Liu
- Geneis (Beijing) Co.Ltd, Beijing, 100102, China
| | - Yu Song
- Department of Gynaecology and Obstetrics, Sanmenxia Central Hospital of Henan University of Science and Technology, Sanmenxia, 472000, Henan, China
| | - Shuiqing Ma
- Department of Gynaecology and Obstetrics, Peking Union Medical College Hospital, Beijing, 100730, China
| | | | - Weiwei Wang
- Geneis (Beijing) Co.Ltd, Beijing, 100102, China
| | - Bo Meng
- Geneis (Beijing) Co.Ltd, Beijing, 100102, China.
| | - Geng Tian
- Geneis (Beijing) Co.Ltd, Beijing, 100102, China.
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15
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Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Göker M, Murray AE, Lindemann SR, Klenk HP, O'Malley R, Zane M, Cheng JF, Copeland A, Daum C, Singer E, Woyke T. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies. Sci Data 2019; 6:285. [PMID: 31772173 PMCID: PMC6879543 DOI: 10.1038/s41597-019-0287-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/31/2019] [Indexed: 11/17/2022] Open
Abstract
Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2–7.2 Mbp, 40–73% GC content, and 1.5–7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel. Measurement(s) | metagenomic data • sequence_assembly | Technology Type(s) | ONT MinION • Illumina sequencing • PacBio RS II | Factor Type(s) | sequencing platform | Sample Characteristic - Organism | Bacteria | Sample Characteristic - Environment | mock community |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.10260740
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Affiliation(s)
- Volkan Sevim
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Juna Lee
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Robert Egan
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hope Hundley
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Janey Lee
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - R Craig Everroad
- NASA Ames Research Center, Exobiology Branch, Moffett Field, CA, 94035, USA
| | - Angela M Detweiler
- NASA Ames Research Center, Exobiology Branch, Moffett Field, CA, 94035, USA.,Bay Area Environmental Research Institute, Moffett Field, CA, 94035, USA
| | - Brad M Bebout
- NASA Ames Research Center, Exobiology Branch, Moffett Field, CA, 94035, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Nuclear and Chemical Science Division, 7000 East Ave, Livermore, CA, 94550-9234, USA
| | - Markus Göker
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Alison E Murray
- Desert Research Institute, Division of Earth and Ecosystem Sciences, 2215 Raggio Pkwy, Reno, NV, 89512, USA
| | | | - Hans-Peter Klenk
- Newcastle University, School of Natural and Environmental Sciences, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK
| | - Ronan O'Malley
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Matthew Zane
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Alex Copeland
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Christopher Daum
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Esther Singer
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
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16
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A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality. Sci Rep 2019; 9:15726. [PMID: 31673047 PMCID: PMC6823499 DOI: 10.1038/s41598-019-51997-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/10/2019] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.
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17
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Acharya K, Khanal S, Pantha K, Amatya N, Davenport RJ, Werner D. A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality. Sci Rep 2019. [PMID: 31673047 DOI: 10.1038/s41598-01951997-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.
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Affiliation(s)
- Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Santosh Khanal
- Department of Pharmacology, School of Medicine, University of Colorado, Aurora, Colorado, 80045, USA
| | - Kalyan Pantha
- Group for Rural Infrastructure Development, Wise use House, Jwagal, Lalitpur, Nepal
- Faculty of Chemistry, University Duisburg-Essen, Universitätsstr. 5, D-45141, Essen, Germany
| | - Niroj Amatya
- Faculty of Chemistry, University Duisburg-Essen, Universitätsstr. 5, D-45141, Essen, Germany
- Department of Medical Microbiology, Nobel College, Pokhara University, Kathmandu, Nepal
| | - Russell J Davenport
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom.
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18
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Apprill A. On-site sequencing speeds up and re-directs field-based microbiology. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:45-47. [PMID: 30689306 DOI: 10.1111/1758-2229.12732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Amy Apprill
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS #4, Woods Hole, MA, 02543, USA
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19
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Hugerth LW, Andersson AF. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol 2017; 8:1561. [PMID: 28928718 PMCID: PMC5591341 DOI: 10.3389/fmicb.2017.01561] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
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Affiliation(s)
- Luisa W Hugerth
- Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska InstitutetSolna, Sweden.,Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
| | - Anders F Andersson
- Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
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