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van der Waals MJ, van Bel N, van Charante F, van Rijn J, van der Veen A, van der Wielen PWJJ. Alternative for HPC22 after repairs in the drinking water distribution system. WATER RESEARCH 2024; 265:122264. [PMID: 39173355 DOI: 10.1016/j.watres.2024.122264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/08/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
There is a risk of contamination by (pathogenic) microorganisms from the outside environment into the drinking water during maintenance or pipe breaches in the drinking water distribution system (DWDS) and, consequently, the drinking water distributed to consumers may result in possible detrimental effects on public health. Traditional time-consuming microbiological testing is, therefore, performed to confirm drinking water is not microbially contaminated. This is done by culturing methods of the faecal indicators Escherichia coli, intestinal enterococci and the technical parameters coliform bacteria and heterotrophic plate counts at 22 °C (HPC22). In this study, fast methods (adenosine triphosphate (ATP), flow cytometry, enzyme activity and qPCR) were compared as an alternative for HPC22. Using dilution series and field samples, ATP (ATPtotal-lab and ATPcell-mob) and enzymatic activity (ALP-2) methods proved to be the more reliable and sensitive than flow cytometry and qPCR methods for detecting microbiological contaminations in drinking water. Significant (p < 0.05) and relatively strong correlations (R2 = 0.61-0.76) were obtained between HPC22 and both ATP methods, enzyme activity and qPCR parameters, but relations with flow cytometry were weak (R2 = 0.24 - 0.52). The samples taken after repairs or a calamity from the DWDS showed in general limited variation in the HPC22 count and were in most cases below the guidance level of 1,000 CFU/mL. We recommend that the best performing alternative methods, i.e. ATPtotal-lab and ATPcell-mob and ALP-2, should be included next to HPC22 in additional field studies to further test and compare these methods to be able to decide which fast method can replace HPC22 analysis after maintenance work in the DWDS.
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Affiliation(s)
| | - Nikki van Bel
- KWR Water Research Institute, Groningenhaven 7, Nieuwegein, 3433 PE, the Netherlands.
| | - Frits van Charante
- KWR Water Research Institute, Groningenhaven 7, Nieuwegein, 3433 PE, the Netherlands
| | - Jeroen van Rijn
- KWR Water Research Institute, Groningenhaven 7, Nieuwegein, 3433 PE, the Netherlands
| | - Anita van der Veen
- KWR Water Research Institute, Groningenhaven 7, Nieuwegein, 3433 PE, the Netherlands
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2
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Abkar L, Moghaddam HS, Fowler SJ. Microbial ecology of drinking water from source to tap. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168077. [PMID: 37914126 DOI: 10.1016/j.scitotenv.2023.168077] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.
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Affiliation(s)
- Leili Abkar
- Civil Engineering Department, University of British Columbia, Canada.
| | | | - S Jane Fowler
- Department of Biological Sciences, Simon Fraser University, Canada.
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3
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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4
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Chen WT, Chien CC, Ho WS, Ou JH, Chen SC, Kao CM. Effects of treatment processes on AOC removal and changes of bacterial diversity in a water treatment plant. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 311:114853. [PMID: 35276566 DOI: 10.1016/j.jenvman.2022.114853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
The effectiveness of different treatment processes on assimilable organic carbon (AOC) removal and bacterial diversity variations was evaluated in a water treatment plant. The van der Kooij technique was applied for AOC analysis and responses of bacterial communities were characterized by the metagenomics assay. Results show that the AOC concentrations were about 93, 148, 43, 51, 37, and 38 μg acetate-C/L in effluents of raw water basin, preozonation, rapid sand filtration (RSF), ozonation, biofiltration [biological activated carbon (BAC) filtration], and chlorination (clear water), respectively. Increased AOC concentrations were observed after preozonation, ozonation, and chlorination units due to the production of biodegradable organic matters after the oxidation processes. Results indicate that the oxidation processes were the main causes of AOC formation, which resulted in significant increases in AOC concentrations (18-59% increment). The AOC removal efficiencies were 47, 28, and 60% in the RSF, biofiltration, and the whole system, respectively. RSF and biofiltration were responsible for the AOC treatment and both processes played key roles in AOC removal. Thus, both RSF and biofiltration processes would contribute to AOC treatment after oxidation. Sediments from the raw water basin and filter samples from RSF and BAC units were collected and analyzed for bacterial communities. Results from scanning electron microscope analysis indicate that bacterial colonization was observed in filter materials. This indicates that the surfaces of the filter materials were beneficial to bacterial growth and AOC removal via the adsorption and biodegradation mechanisms. Next generation sequencing analyses demonstrate that water treatment processes resulted in the changes of bacterial diversity and community profiles in filters of RSF and BAC. According to the findings of bacterial composition and interactions, the dominant bacterial phyla were Proteobacteria (41% in RSF and 56% in BAC) followed by Planctomycetes and Acidobacteria in RSF and BAC systems, which might affect the AOC biodegradation efficiency. Results would be useful in developing AOC treatment and management processes in water treatment plants.
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Affiliation(s)
- W T Chen
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - C C Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Chung-Li City, Taoyuan, Taiwan
| | - W S Ho
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - J H Ou
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - S C Chen
- Department of Life Sciences, National Central University, Taoyuan, Taiwan.
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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5
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McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
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6
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Jing Z, Lu Z, Mao T, Cao W, Wang W, Ke Y, Zhao Z, Wang X, Sun W. Microbial composition and diversity of drinking water: A full scale spatial-temporal investigation of a city in northern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 776:145986. [PMID: 33640542 DOI: 10.1016/j.scitotenv.2021.145986] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
The microbiological water quality of drinking water distribution systems (DWDSs) is of primary importance for public health. The detachment of biofilm attached on the pipe wall attribution to water source switch and the occurrence of potentially pathogenic chlorine-resistant bacteria (CRB) under chlorine disinfection get lots of attention. Studies examining microbial communities after the water source switch, particularly in low-salinity water, have been scant. The UV‑chlorine combined disinfection applied in one of the investigated drinking water plants provided insight into the control of CRBs. We applied high-throughput sequencing of the 16S rRNA gene to characterize the bacterial communities of the DWDS in northern China over 1 year. A network comprising four different DWDSs was sampled at 48 sites every season (temperate continental monsoon climate), and the impact of key spatial-temporal and physicochemical parameters was investigated. Overall, the entire bacterial community was not significantly different among the four DWDSs (spatial parameter) but varied with seasons (temporal parameter). The switch in water sources might increase the relative abundance of potentially opportunistic pathogens in DWDSs. UV‑chlorine combined disinfection can decrease community diversity and is likely to control the growth of potential opportunistic pathogens in DWDSs.
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Affiliation(s)
- Zibo Jing
- School of Environment, Tsinghua University, Beijing 100084, China; Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zedong Lu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ted Mao
- Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China; MW Technologies, Inc., London, Ontario, Canada
| | - Wenfeng Cao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Weibo Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yanchu Ke
- School of Environment, Tsinghua University, Beijing 100084, China; State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhinan Zhao
- School of Environment, Tsinghua University, Beijing 100084, China; Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China.
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7
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Zhang C, Qin K, Struewing I, Buse H, Santo Domingo J, Lytle D, Lu J. The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water. Front Microbiol 2021; 12:625324. [PMID: 33967975 PMCID: PMC8102780 DOI: 10.3389/fmicb.2021.625324] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial drinking water quality in premise plumbing systems (PPSs) strongly affects public health. Bacterial community structure is the essential aspect of microbial water quality. Studies have elucidated the microbial community structure in cold tap water, while the microbial community structures in hot tap and shower water are poorly understood. We sampled cold tap, hot tap, and shower water from a simulated PPS monthly for 16 consecutive months and assessed the bacterial community structures in those samples via high-throughput sequencing of bacterial 16S rRNA genes. The total relative abundance of the top five most abundant phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes) was greater than 90% among the 24 identified phyla. The most abundant families were Burkholderiaceae, Sphingomonadaceae, unclassified Alphaproteobacteria, unclassified Corynebacteriales, and Mycobacteriaceae. A multiple linear regression suggests that the bacterial community diversity increased with water temperature and the age of the simulated PPS, decreased with total chlorine residual concentration, and had a limited seasonal variation. The bacterial community in hot tap water had significantly lower Shannon and Inverse Simpson diversity indices (p < 0.05) and thus a much lower diversity than those in cold tap and shower water. The paradoxical results (i.e., diversity increased with water temperature, but hot tap water bacterial community was less diverse) were presumably because (1) other environmental factors made hot tap water bacterial community less diverse, (2) the diversity of bacterial communities in all types of water samples increased with water temperature, and (3) the first draw samples of hot tap water could have a comparable or even lower temperature than shower water samples and the second draw samples of cold tap water. In both a three-dimensional Non-metric multidimensional scaling ordination plot and a phylogenetic dendrogram, the samples of cold tap and shower water cluster and are separate from hot tap water samples (p < 0.05). In summary, the bacterial community in hot tap water in the simulated PPS had a distinct structure from and a much lower diversity than those in cold tap and shower water.
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Affiliation(s)
- Chiqian Zhang
- Pegasus Technical Services, Inc., Cincinnati, OH, United States
| | - Ke Qin
- Oak Ridge Institute for Science and Education Participation Program, Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, United States
| | - Ian Struewing
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, United States
| | - Helen Buse
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, United States
| | - Jorge Santo Domingo
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, United States
| | - Darren Lytle
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, United States
| | - Jingrang Lu
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, United States
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8
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Bonadonna L, Briancesco R, La Rosa G. Innovative analytical methods for monitoring microbiological and virological water quality. Microchem J 2019. [DOI: 10.1016/j.microc.2019.104160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Neu L, Proctor CR, Walser JC, Hammes F. Small-Scale Heterogeneity in Drinking Water Biofilms. Front Microbiol 2019; 10:2446. [PMID: 31736893 PMCID: PMC6828615 DOI: 10.3389/fmicb.2019.02446] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
Biofilm heterogeneity has been characterized on various scales for both natural and engineered ecosystems. This heterogeneity has been attributed to spatial differences in environmental factors. Understanding their impact on localized biofilm heterogeneity in building plumbing systems is important for both management and representative sampling strategies. We assessed heterogeneity within the confined engineered ecosystem of a shower hose by high-resolution sampling (200 individual biofilm sections per hose) on varying scales (μm to m). We postulated that a biofilm grown on a single material under uniform conditions should be homogeneous in its structure, bacterial numbers, and community composition. A biofilm grown for 12 months under controlled laboratory conditions, showed homogeneity on large-scale. However, some small-scale heterogeneity was clearly observed. For example, biofilm thickness of cm-sections varied up to 4-fold, total cell concentrations (TCC) 3-fold, and relative abundance of dominant taxa up to 5-fold. A biofilm grown under real (i.e., uncontrolled) use conditions developed considerably more heterogeneity in all variables which was attributed to more discontinuity in environmental conditions. Interestingly, biofilm communities from both hoses showed comparably low diversity, with <400 taxa each, and only three taxa accounting for 57%, respectively, 73% of the community. This low diversity was attributed to a strong selective pressure, originating in migrating carbon from the flexible hoses as major carbon source. High-resolution sampling strategy enabled detailed analysis of spatial heterogeneity within an individual drinking water biofilm. This study gives insight into biofilm structure and community composition on cm-to m-scale and is useful for decision-making on sampling strategies in biofilm research and monitoring.
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Affiliation(s)
- Lisa Neu
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Caitlin R. Proctor
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Schools of Civil, Environmental and Ecological, Materials, and Biomedical Engineering, Purdue University, West Lafayette, IN, United States
| | | | - Frederik Hammes
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
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Aryal N, Deng D, Jha MK, Ofori-Boadu A. Monitoring, sampling, and automated analysis. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2019; 91:1288-1293. [PMID: 31509322 DOI: 10.1002/wer.1224] [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: 05/20/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
A review of the literature published in 2018 on topics related to monitoring, sampling, and automated analysis is presented. The review includes current developments in monitoring, sampling, and analysis of water, wastewater, and groundwater. This review includes the following sections: brief introduction; sample preparation and extraction techniques; real-time, high-frequency, and/or in situ monitoring (microbiological, inorganic, organic, metals, and others); passive monitoring; and the biosensors. In the end, the authors have discussed future of the topic. PRACTITIONER POINTS: Advances in monitoring, sampling and automated analysis of water and wastewater are summarized. Real-time, high-frequency, and in-situ monitoring and analysis of pollutants are summarized. Topics include sample preparation and extraction and passive monitoring, and biosensors for pollutants.
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Affiliation(s)
- Niroj Aryal
- Department of Natural Resources and Environmental Design, North Carolina A&T State University, Greensboro, North Carolina
| | - Dongyang Deng
- Department of Built Environment, North Carolina A&T State University, Greensboro, North Carolina
| | - Manoj K Jha
- Department of Civil, Architectural and Environmental Engineering, North Carolina A&T State University, Greensboro, North Carolina
| | - Andrea Ofori-Boadu
- Department of Built Environment, North Carolina A&T State University, Greensboro, North Carolina
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11
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Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory. Eur J Clin Microbiol Infect Dis 2019; 38:1059-1070. [PMID: 30834996 PMCID: PMC6520317 DOI: 10.1007/s10096-019-03520-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022]
Abstract
Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of (‘difficult-to-culture’) microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform (‘MYcrobiota’) is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.
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