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Tuo J, Shen Y, Jia S, Liu S, Zhang Q, Wang D, He X, Liu P, Zhang XX. HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment. WATER RESEARCH 2024; 260:121927. [PMID: 38941866 DOI: 10.1016/j.watres.2024.121927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/30/2024]
Abstract
Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.
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Affiliation(s)
- Jinhua Tuo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengnan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Qifeng Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Depeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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Thomas MC, Waugh G, Vanwonterghem I, Webster NS, Rinke C, Fisher R, Luter HM, Negri AP. Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166658. [PMID: 37659522 DOI: 10.1016/j.scitotenv.2023.166658] [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: 07/11/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Understanding the rapid responses of marine microbiomes to environmental disturbances is paramount for supporting early assessments of harm to high-value ecosystems, such as coral reefs. Yet, management guidelines aimed at protecting aquatic life from environmental pollution remain exclusively defined for organisms at higher trophic levels. In this study, 16S rRNA gene amplicon sequencing was applied in conjunction with propidium monoazide for cell-viability assessment as a sensitive tool to determine taxon- and community-level changes in a seawater microbial community under copper (Cu) exposure. Bayesian model averaging was used to establish concentration-response relationships to evaluate the effects of copper on microbial composition, diversity, and richness for the purpose of estimating microbiome Hazard Concentration (mHCx) values. Predicted mHC5 values at which a 5 % change in microbial composition, diversity, and richness occurred were 1.05, 0.72, and 0.38 μg Cu L-1, respectively. Threshold indicator taxa analysis was applied across the copper concentrations to identify taxon-specific change points for decreasing taxa. These change points were then used to generate a Prokaryotic Sensitivity Distribution (PSD), from which mHCxdec values were derived for copper, suitable for the protection of 99, 95, 90, and 80 % of the marine microbiome. The mHC5dec guideline value of 0.61 μg Cu L-1, protective of 95 % of the marine microbial community, was lower than the equivalent Australian water quality guideline value based on eukaryotic organisms at higher trophic levels. This suggests that marine microbial communities might be more vulnerable, highlighting potential insufficiencies in their protection against copper pollution. The mHCx values proposed here provide approaches to quantitatively assess the effects of contaminants on microbial communities towards the inclusion of prokaryotes in future water quality guidelines.
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Affiliation(s)
- Marie C Thomas
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia.
| | - Gretel Waugh
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia; Australian Institute of Marine Science, Townsville, QLD 4810, Australia; Australian Antarctic Division, Hobart, TAS 7050, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rebecca Fisher
- Australian Institute of Marine Science Crawley, Crawley, WA, Australia
| | - Heidi M Luter
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia; AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, QLD 4811, Australia
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Guo J, Fan F, Wang W, Wan M, Li Y. Development of PMA-qPCR assay to accurately and reproducible quantify viable bacteria of Paenibacillus polymyxa. Lett Appl Microbiol 2023; 76:ovad127. [PMID: 37952090 DOI: 10.1093/lambio/ovad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Paenibacillus polymyxa is an important biocontrol bacterium. The combination of propidium monoazide (PMA) and quantitative polymerase chain reactionq (qPCR) has proven effective in quantifying live bacteria from various microorganisms. The objective was to create a PMA-qPCR assay to precisely and consistently measure the number of living bacteria of biocontrol P. polymyxa. The primers were designed for the spo0A gene of P. polymyxa HY96-2. The optimal conditions for treating the target strain with PMA were a PMA concentration of 15 μg/mL, an incubation time of 5 min, and an exposure time of 10 min. The PMA-qPCR method had a limit of quantification (LOQ) of 1.0 × 103 CFU/mL for measuring the amount of viable P. polymyxa bacteria. The PMA-qPCR method is more sensitive than the qPCR method in detecting viable bacteria in the mixtures of viable and dead bacteria. The accuracy and reproducibility of quantifying viable P. polymyxa bacteria using the PMA-qPCR method were higher compared to the plate count method.
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Affiliation(s)
- Jiacai Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Fei Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weiliang Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Minxi Wan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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Yang Y, Deng Y, Shi X, Liu L, Yin X, Zhao W, Li S, Yang C, Zhang T. QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification. WATER RESEARCH 2023; 235:119858. [PMID: 36931186 DOI: 10.1016/j.watres.2023.119858] [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: 11/04/2022] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
The majority of the current regulatory practices for routine monitoring of beach water quality rely on the culture-based enumeration of faecal indicator bacteria (FIB) to develop criteria for promoting the general public's health. To address the limitations of culture methods and the arguable reliability of FIB in indicating health risks, we developed a Nanopore metagenomic sequencing-based viable cell absolute quantification workflow to rapidly and accurately estimate a broad range of microbes in beach waters by a combination of propidium monoazide (PMA) and cellular spike-ins. Using the simple synthetic bacterial communities mixed with viable and heat-killed cells, we observed near-complete relic DNA removal by PMA with minimal disturbance to the composition of viable cells, demonstrating the feasibility of PMA treatment in profiling viable cells by Nanopore sequencing. On a simple mock community comprised of 15 prokaryotic species, our results showed high accordance between the expected and estimated concentrations, suggesting the accuracy of our method in absolute quantification. We then further assessed the accuracy of our method for counting viable Escherichia coli and Vibrio spp. in beach waters by comparing to culture-based method, which were also in high agreement. Furthermore, we demonstrated that 1 Gb sequences obtained within 2 h would be sufficient to quantify a species having a concentration of ≥ 10 cells/mL in beach waters. Using our viability-resolved quantification workflow to assess the microbial risk of the beach water, we conducted (1) screening-level quantitative microbial risk assessment (QMRA) to investigate human illness risk and site-specific risk patterns that might guide risk management efforts and (2) metagenomics-based resistome risk assessment to evaluate another layer of risk caused by difficult illness treatment due to antimicrobial resistance (AMR). In summary, our metagenomic workflow for the rapid absolute quantification of viable bacteria demonstrated its great potential in paving new avenues toward holistic microbial risk assessment.
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Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Wanwan Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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A Model System for Sensitive Detection of Viable E. coli Bacteria Combining Direct Viability PCR and a Novel Microarray-Based Detection Approach. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We established an innovative approach that included direct, viability, and nested PCR for rapid and reliable identification of the fecal indicator organism Escherichia coli (E. coli). Direct PCR enabled successful amplification of the target uidA gene, omitting a prior DNA isolation or purification step. Furthermore, we applied viability PCR (v-PCR) to ensure the detection of only relevant viable bacterial cells. The principle involves the binding of propidium monoazide (PMA), a selective nucleic acid intercalating dye, to accessible DNA of heat killed bacteria cells and, consequently, allows viable and heat killed E. coli cells to be discriminated. To ensure high sensitivity, direct v-PCR was followed by a nested PCR step. The resulting amplicons were analyzed by a rapid 30 min microarray-based DNA hybridization assay for species-specific DNA detection of E. coli. A positive signal was indicated by enzymatically generated silver nanoparticle deposits, which served as robust endpoint signals allowing an immediate visual readout. The presented novel protocol allows the detection of 1 × 101 viable E. coli cells per PCR run.
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Spiking a Silty-Sand Reference Soil with Bacterial DNA: Limits and Pitfalls in the Discrimination of Live and Dead Cells When Applying Ethidium Monoazide (EMA) Treatment. Curr Microbiol 2019; 76:1425-1434. [PMID: 31552450 PMCID: PMC6817739 DOI: 10.1007/s00284-019-01772-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 10/28/2022]
Abstract
In the present study, EMA (ethidium monoazide) treatment was applied to a silty-sand reference soil prior to DNA extraction to enable a differentiation between dead and living cells. For this purpose, a reference soil was spiked with Listeria monocytogenes cells or cell equivalents, respectively. With the purpose of evaluating optimum treatment conditions, different EMA concentrations have been tested. However, the results remained largely inconclusive. Furthermore, varied dark incubation periods allowing EMA to penetrate dead cells did not allow the selective removal of DNA from membrane-compromised cells in downstream analyses. In contrast to undiluted soil, an effect of EMA treatment during DNA extraction could be observed when using a 1:10 dilution of the reference soil; however, the effect has not been sufficiently selective to act on heat-treated cells only. Although the application of EMA to soil requires further evaluation, the procedure harbors future potential for improving DNA-based approaches in microbial ecology studies.
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Ali M, Wang Z, Salam KW, Hari AR, Pronk M, van Loosdrecht MCM, Saikaly PE. Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8291-8301. [PMID: 31194515 DOI: 10.1021/acs.est.8b07303] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In aerobic granular sludge (AGS) systems, different-sized microbial aggregates having different solids retention time (SRT) coexist in the same reactor compartment and are subjected to the same influent wastewater. Thus, the AGS system provides a unique ecosystem to study the importance of local (species sorting) and regional (immigration) processes in bacterial community assembly. The microbial communities of different-sized aggregates (flocs <0.2 mm, small granules (0.2-1.0 mm) and large granules >1.0 mm), influent wastewater, excess sludge and effluent of a full-scale AGS plant were characterized over a steady-state operation period of 6 months. Amplicon sequencing was integrated with mass balance to determine the SRT and net growth rate of operational taxonomic units (OTUs). We found strong evidence of species sorting as opposed to immigration, which was significantly higher at short SRT (i.e., flocs and small granules) than that at long SRT (large granules). Rare OTUs in wastewater belonging to putative functional groups responsible for nitrogen and phosphorus removal were progressively enriched with an increase in microbial aggregates size. In contrast, fecal- and sewage infrastructure-derived microbes progressively decreased in relative abundance with increase in microbial aggregate size. These findings highlight the importance of AGS as a unique model ecosystem to study fundamental microbial ecology concepts.
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Affiliation(s)
- Muhammad Ali
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center , King Abdullah University of Science and Technology , Thuwal 23955-6900 , Saudi Arabia
| | - Zhongwei Wang
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center , King Abdullah University of Science and Technology , Thuwal 23955-6900 , Saudi Arabia
| | - Khaled W Salam
- Department of Civil and Environmental Engineering , University of Washington , Seattle 98195 , United States
| | - Ananda Rao Hari
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center , King Abdullah University of Science and Technology , Thuwal 23955-6900 , Saudi Arabia
| | - Mario Pronk
- Department of Biotechnology , Delft University of Technology , Delft 2629 HZ , The Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology , Delft University of Technology , Delft 2629 HZ , The Netherlands
| | - Pascal E Saikaly
- Biological and Environmental Science and Engineering Division, Water Desalination and Reuse Center , King Abdullah University of Science and Technology , Thuwal 23955-6900 , Saudi Arabia
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Niu B, Hong B, Zhang Z, Mu L, Malakar PK, Liu H, Pan Y, Zhao Y. A Novel qPCR Method for Simultaneous Detection and Quantification of Viable Pathogenic and Non-pathogenic Vibrio parahaemolyticus ( tlh+ , tdh+ , and ureR + ). Front Microbiol 2018; 9:1747. [PMID: 30116230 PMCID: PMC6083054 DOI: 10.3389/fmicb.2018.01747] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
Pathogenic and non-pathogenic Vibrio parahaemolyticus strains were simultaneously detected and quantified using a novel viable multiplex real-time PCR (novel qPCR). We used a new PCR primer and probe, ureR, as a surrogate for detection of the toxin trh gene as the primer was better at identifying variant V. parahaemolyticus trh strains. The specificity of all primers and probes used in this study were validated on three standard strains of V. parahaemolyticus, 42 clinical strains, 12 wild strains, 4 strains of Vibrio spp., and 4 strains of other bacteria. Then, propidium monoazide (PMA) was applied to inhibit DNA of dead cell, and the results of PMA optimized treatments were 15 μM concentration, 5 min incubation periods, 15 min light exposure periods and 30 RPM rotational speed, which resulted in time and cost savings. Pathogenic and non-pathogenic strains were quantified using a two-reaction tube method where the tlh, tdh, and ureR genes were amplified. Additionally, standard curves with a 7-log dynamic range were generated for quantifying viable V. parahaemolyticus and the amplification efficiencies were 108.68, 105.17, and 115.61% for tlh+, tdh+, and ureR+. This novel qPCR accurately monitored V. parahaemolyticus contamination rates in shrimps (Penaeus vannamei) and clams (Ruditapes philippinarum) sampled from retail stores located in a major district in Shanghai. In conclusion, our assay can prioritize the detection and quantification of viable pathogenic V. parahaemolyticus and can prove to be a more effective tool for reducing infection risks from consumption of seafood in Shanghai.
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Affiliation(s)
- Ben Niu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Bin Hong
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Lili Mu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pradeep K Malakar
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China.,Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
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Huang Z, Zheng J, Shi C, Chen Q. Flow cytometry-based method facilitates optimization of PMA treatment condition for PMA-qPCR method. Mol Cell Probes 2018; 40:37-39. [PMID: 29792916 DOI: 10.1016/j.mcp.2018.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/10/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
Coupling propidium monoazide (PMA) with quantitative PCR (PMA-qPCR) has been successfully applied to specific detection and quantification of viable cells in various samples. The optimal PMA treatment condition is usually determined through qPCR. However, it is a tedious, time consuming and costly process including DNA extraction and qPCR. To overcome this problem, a flow cytometry-based (FCM-based) method was first proposed in this study to replace qPCR for screening of the optimal PMA treatment condition for Helicobacter pylori, since the pure culture treated with PMA was actually a single cell suspension with fluorescent dye. Results showed that the optimal PMA treatment condition (30 μM of PMA and 8 min of exposure time) determined by the novel method was the same as that determined by the qPCR-based method, which demonstrate the feasibility of this approach. In addition, with the comparison of the qPCR-based method, the FCM-based method allows screening of the optimal PMA treatment condition become much more simple, rapid and economical.
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Affiliation(s)
- Zhiqing Huang
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Jianwei Zheng
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Chunmei Shi
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Qiang Chen
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China; Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian Province 350004, China.
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10
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Lee S, Bae S. Evaluating the newly developed dye, DyeTox13 Green C-2 Azide, and comparing it with existing EMA and PMA for the differentiation of viable and nonviable bacteria. J Microbiol Methods 2018; 148:33-39. [DOI: 10.1016/j.mimet.2018.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/10/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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11
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Pinheiro ET, Neves VD, Reis CC, Longo PL, Mayer MPA. Evaluation of the Propidium Monoazide-quantitative Polymerase Chain Reaction Method for the Detection of Viable Enterococcus faecalis. J Endod 2016; 42:1089-92. [PMID: 27179593 DOI: 10.1016/j.joen.2016.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/17/2016] [Accepted: 04/03/2016] [Indexed: 11/26/2022]
Abstract
INTRODUCTION One limitation of DNA-based molecular assays is their inability to distinguish between live and dead cells. A sample treatment with propidium monoazide (PMA) before DNA amplification has been proposed to overcome this problem. The aim of this in vitro study was to test different concentrations of PMA coupled with quantitative polymerase chain reaction (qPCR) for the detection of viable Enterococcus faecalis. METHODS Viable or heat-killed suspensions of E. faecalis (10⁶ colony-forming units/mL) were treated with PMA at 10, 50, and 100 μg/mL before DNA extraction. qPCR was performed using primers complementary for E. faecalis 16S ribosomal RNA sequence. PMA was also tested on bacteria suspensions containing different proportions of viable and dead cells. Bacterial suspensions without PMA treatment were used as positive controls. RESULTS The treatment of heat-killed suspensions with PMA at different concentrations significantly reduced the DNA amplification when compared with the group without treatment (P < .0001), indicating that DNA from dead cells was not used as templates. The greatest reduction in qPCR amplification of dead cell DNA was found when 100 μg/mL PMA was used (P < .005). In mixtures containing live/dead cells, PMA allowed selective detection of viable cells. CONCLUSIONS PMA was effective in inhibiting qPCR amplification from the DNA of dead cells, enabling in vitro detection and quantification of viable cells of E. faecalis.
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Affiliation(s)
- Ericka T Pinheiro
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil.
| | - Viviane D Neves
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Caroline C Reis
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Priscila L Longo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Márcia P A Mayer
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Li H, Xin H, Li SFY. Multiplex PMA-qPCR Assay with Internal Amplification Control for Simultaneous Detection of Viable Legionella pneumophila, Salmonella typhimurium, and Staphylococcus aureus in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:14249-56. [PMID: 26512952 DOI: 10.1021/acs.est.5b03583] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pathogenic microorganisms are responsible for many infectious diseases, and pathogen monitoring is important and necessary for water quality control. This study for the first time explored a multiplex quantitative real-time PCR (qPCR) technique combined with propidium monoazide (PMA) to simultaneously detect viable Legionella pneumophila, Salmonella typhimurium, and Staphylococcus aureus in one reaction from water samples. Sodium lauroyl sarcosinate (sarkosyl) was applied to enhance the dead bacterial permeability of PMA. The sensitivity of the multiplex PMA-qPCR assay achieved two colony-forming units (CFU) per reaction for L. pneumophila and three CFU per reaction for S. typhimurium and S. aureus. No PCR products were amplified from all nontarget control samples. Significantly, with comparable specificity and sensitivity, this newly invented multiplex PMA-qPCR assay took a much shorter time than did conventional culture assays when testing water samples with spiked bacteria and simulated environmental water treatment. The viable multiplex PMA-qPCR assay was further successfully applied to pathogen detection from rivers, canals, and tap water samples after simple water pretreatment.
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Affiliation(s)
- Haiyan Li
- Department of Chemistry, Faculty of Science, National University of Singapore , 3 Science Drive 3, Singapore 117543
| | - Hongyi Xin
- Bioinformatics Institute, Agency for Science, Technology and Research , 30 Biopolis Street, Singapore 138671
| | - Sam Fong Yau Li
- Department of Chemistry, Faculty of Science, National University of Singapore , 3 Science Drive 3, Singapore 117543
- NUS Environmental Research Institute, National University of Singapore , 5A Engineering Drive 1, Singapore 117411
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Quantifying viable Vibrio parahaemolyticus and Listeria monocytogenes simultaneously in raw shrimp. Appl Microbiol Biotechnol 2015; 99:6451-62. [DOI: 10.1007/s00253-015-6715-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 05/16/2015] [Accepted: 05/21/2015] [Indexed: 02/06/2023]
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Zhang S, Ye C, Lin H, Lv L, Yu X. UV disinfection induces a VBNC state in Escherichia coli and Pseudomonas aeruginosa. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1721-1728. [PMID: 25584685 DOI: 10.1021/es505211e] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The occurrence of a viable but nonculturable (VBNC) state in bacteria may dramatically underestimate the health risks associated with drinking water. Therefore, the potential for UV treatment to induce a VBNC state in Escherichia coli and Pseudomonas aeruginosa was investigated. UV disinfection effectively reduced the culturability of E. coli and P. aeruginosa, with the destruction of nucleic acids demonstrated using gadA long gene fragment qPCR amplification. Following UV radiation, copy numbers for the high transcriptional levels of the 16S rRNA gene varied insignificantly in both strains, confirming results from plate counting assays indicating that VBNC states were induced in both strains. Furthermore, the virulence genes gadA and oprL remained highly expressed, suggesting that the VBNC bacteria still displayed pathogenicity. Propidium monoazide qPCR indicated that cell membranes remained intact even at a UV dose of 300 mJ/cm(2). The RT-qPCR results after UV and chlorine treatments in E. coli were significantly different (8.41 and 5.59 log units, respectively), further confirming the induction of VBNC bacteria induced by UV radiation. Finally, resuscitation was achieved, with E. coli showing greater resuscitation ability than P. aeruginosa. These results systematically revealed the potential health risks of UV disinfection and strongly suggest a combined disinfection strategy.
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Affiliation(s)
- Shenghua Zhang
- Institute of Urban Environment, Chinese Academy of Science , Xiamen, 361021, P. R. China
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