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Van Ngoc H, Quyen TL, Vinayaka AC, Bang DD, Wolff A. Point-of-care system for rapid real-time detection of SARS-CoV-2 virus based on commercially available Arduino platforms. Front Bioeng Biotechnol 2022; 10:917573. [PMID: 35992344 PMCID: PMC9385952 DOI: 10.3389/fbioe.2022.917573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID-19 pandemic emphasized the importance of rapid, portable, and on-site testing technologies necessary for resource-limited settings for effective testing and screening to reduce spreading of the infection. Realizing this, we developed a fluorescence-based point-of-care (fPOC) detection system with real-time reverse transcriptase loop-mediated isothermal amplification for rapid and quantitative detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The system is built based on the Arduino platform compatible with commercially available open-source hardware–software and off-the-shelf electronic components. The fPOC system comprises of three main components: 1) an instrument with integrated heaters, 2) optical detection components, and 3) an injection-molded polymeric cartridge. The system was tested and experimentally proved to be able to use for fast detection of the SARS-CoV-2 virus in real-time in less than 30 min. Preliminary results of testing the performance of the fPOC revealed that the fPOC could detect the SARS-CoV-2 virus at a limit of detection (LOD50%) at two to three copies/microliter (15.36 copies/reaction), which was comparable to reactions run on a standard commercial thermocycler. The performance of the fPOC was evaluated with 12 SARS-CoV-2 clinical throat swab samples that included seven positive and five negative samples, as confirmed by reverse transcription–polymerase chain reaction. The fPOC showed 100% agreement with the commercial thermocycler. This simple design of the fPOC system demonstrates the potential to greatly enhance the practical applicability to develop a totally integrated point-of-care system for rapid on-site screening of the SARS-CoV-2 virus in the management of the pandemic.
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Affiliation(s)
- Huynh Van Ngoc
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
- *Correspondence: Huynh Van Ngoc, ; Anders Wolff,
| | - Than Linh Quyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Anders Wolff
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
- *Correspondence: Huynh Van Ngoc, ; Anders Wolff,
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Quyen TL, Vinayaka AC, Golabi M, Ngoc HV, Bang DD, Wolff A. Elimination of Carryover Contamination in Real-Time Reverse Transcriptase Loop-Mediated Isothermal Amplification for Rapid Detection of the SARS-CoV-2 Virus in Point-of-Care Testing. Front Cell Infect Microbiol 2022; 12:856553. [PMID: 35521217 PMCID: PMC9065284 DOI: 10.3389/fcimb.2022.856553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is being used as a robust rapid diagnostic tool to prevent the transmission of infectious diseases. However, carryover contamination of LAMP-amplified products originating from previous tests has been a problem in LAMP-based bio-analytical assays. In this study, we developed a Cod-uracil-DNA-glycosylase real-time reverse transcriptase LAMP assay (Cod-UNG-rRT-LAMP) for the elimination of carryover contamination and the rapid detection of SARS-CoV-2 in point-of-care (POC) testing. Using the Cod-UNG-rRT-LAMP assay, the SARS-CoV-2 virus could be detected as low as 2 copies/µl (8 copies/reaction) within 45 min of amplification and 2.63 ± 0.17 pg (equivalent to 2.296 × 109 copies) of contaminants per reaction could be eliminated. Analysis of clinical SARS-CoV-2 samples using the Cod-UNG-rRT-LAMP assay showed an excellent agreement with a relative accuracy of 98.2%, sensitivity of 97.1%, and specificity of 95.2% in comparison to rRT-PCR. The results obtained in this study clearly demonstrate the feasibility of the use of the Cod-UNG-rRT-LAMP assay for applications toward the POC diagnosis of SARS-CoV-2 and on-site testing of other pathogens.
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Affiliation(s)
- Than Linh Quyen
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Huynh Van Ngoc
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Anders Wolff
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
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Feist SM, Lance RF. Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions. NEOBIOTA 2021. [DOI: 10.3897/neobiota.66.60751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.
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Chen Y, Mei Y, Zhao X, Jiang X. Reagents-Loaded, Automated Assay that Integrates Recombinase-Aided Amplification and Cas12a Nucleic Acid Detection for a Point-of-Care Test. Anal Chem 2020; 92:14846-14852. [DOI: 10.1021/acs.analchem.0c03883] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yong Chen
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Yixin Mei
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Xiaohui Zhao
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Xingyu Jiang
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
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Nguyen T, Chidambara VA, Andreasen SZ, Golabi M, Huynh VN, Linh QT, Bang DD, Wolff A. Point-of-care devices for pathogen detections: The three most important factors to realise towards commercialization. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Quyen TL, Nordentoft S, Vinayaka AC, Ngo TA, Engelsmenn P, Sun Y, Madsen M, Bang DD, Wolff A. A Sensitive, Specific and Simple Loop Mediated Isothermal Amplification Method for Rapid Detection of Campylobacter spp. in Broiler Production. Front Microbiol 2019; 10:2443. [PMID: 31708907 PMCID: PMC6821646 DOI: 10.3389/fmicb.2019.02443] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Campylobacteriosis is one of the most common foodborne diseases worldwide. Two Campylobacter species - C. jejuni and C. coli in poultry and poultry products are considered to be the main source of human campylobacteriosis. Therefore, studying Campylobacter status in poultry flocks is needed to prevent transmission of disease and reduce human risk, health cost, and economic losses. In this study, we adapted and used a Loop-Mediated Isothermal Amplification (LAMP) assay for specific, sensitive, simple and cost-effective rapid detection of C. jejuni and C. coli in the poultry production chain. Amplified LAMP products were detected using a small, low-cost portable commercial blue LED transilluminator and a direct visual detection strategy was demonstrated. By using optimized conditions for amplification a limit of detection (LOD) of 50 CFU/ml was achieved for testing of C. jejuni and C. coli in spiked chicken feces without enrichment. The method took 60-70 min from receiving the samples to the final results (including 30 min for amplification). The optimized LAMP showed a relative accuracy of 98.4%, a specificity of 97.9%, and a sensitivity of 100% in comparison to real-time PCR method. Cohen's kappa index also showed an excellent agreement (0.94) between the two methods. The results showed that the method is specific, sensitive and is suitable to develop for rapid detection of Campylobacter spp. at poultry production.
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Affiliation(s)
- Than Linh Quyen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Steen Nordentoft
- National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | | | - Tien Anh Ngo
- National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Pia Engelsmenn
- National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Yi Sun
- Department of Health Technology, Technical University of Denmark (DTU-Health Tech), Lyngby, Denmark
| | - Mogens Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Dang Duong Bang
- National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Anders Wolff
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
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Quyen TL, Ngo TA, Bang DD, Madsen M, Wolff A. Classification of Multiple DNA Dyes Based on Inhibition Effects on Real-Time Loop-Mediated Isothermal Amplification (LAMP): Prospect for Point of Care Setting. Front Microbiol 2019; 10:2234. [PMID: 31681184 PMCID: PMC6803449 DOI: 10.3389/fmicb.2019.02234] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
LAMP has received great interest and is widely utilized in life sciences for nucleic acid analysis. To monitor a real-time LAMP assay, a fluorescence DNA dye is an indispensable component and therefore the selection of a suitable dye for real-time LAMP is a need. To aid this selection, we investigated the inhibition effects of twenty-three DNA dyes on real-time LAMP. Threshold time (Tt) values of each real-time LAMP were determined and used as an indicator of the inhibition effect. Based on the inhibition effects, the dyes were classified into four groups: (1) non-inhibition effect, (2) medium inhibition effect, (3) high inhibition effect, and (4) very high inhibition effect. The signal to noise ratio (SNR) and the limit of detection (LOD) of the dyes in groups 1, 2, and 3 were further investigated, and possible inhibition mechanisms of the DNA dyes on the real-time LAMP are suggested and discussed. Furthermore, a comparison of SYTO 9 in different LAMP reactions and different systems is presented. Of the 23 dyes tested, SYTO 9, SYTO 82, SYTO 16, SYTO 13, and Miami Yellow were the best dyes with no inhibitory effect, low LOD and high SNR in the real-time LAMP reactions. The present classification of the dyes will simplify the selection of fluorescence dye for real-time LAMP assays in point of care setting.
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Affiliation(s)
- Than Linh Quyen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Tien Anh Ngo
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Mogens Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Anders Wolff
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
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Huang X, Lin X, Urmann K, Li L, Xie X, Jiang S, Hoffmann MR. Smartphone-Based in-Gel Loop-Mediated Isothermal Amplification (gLAMP) System Enables Rapid Coliphage MS2 Quantification in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6399-6407. [PMID: 29738236 PMCID: PMC5990930 DOI: 10.1021/acs.est.8b00241] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/12/2018] [Accepted: 05/08/2018] [Indexed: 05/03/2023]
Abstract
Model coliphages (e.g., ΦX174, MS2, and PRD1) have been widely used as surrogates to study the fate and transport of pathogenic viruses in the environment and during wastewater treatment. Two groups of coliphages (F-specific and somatic) are being explored as indicators of viral fecal pollution in ambient water. However, the detection and quantification of coliphages still largely rely on time-consuming culture-based plaque assays. In this study, we developed an in-gel loop-mediated isothermal amplification (gLAMP) system enabling coliphage MS2 quantification within 30 min using standard laboratory devices. Viral particles (MS2) were immobilized with LAMP reagents in polyethylene glycol hydrogel, and then viral RNAs were amplified through a LAMP reaction. Due to the restriction effect of the hydrogel matrix, one viral particle would only produce one amplicon dot. Therefore, the sample virus concentrations can be determined based on the number of fluorescent amplicon dots using a smartphone for imaging. The method was validated by using artificially spiked and naturally contaminated water samples. gLAMP results were shown to correlate well with plaque assay counts ( R2 = 0.984, p < 0.05) and achieved similar sensitivity to quantitative reverse-transcription polymerase chain reaction (RT-qPCR; 1 plaque-forming unit per reaction). Moreover, gLAMP demonstrated a high level of tolerance against inhibitors naturally present in wastewater, in which RT-qPCR was completely inhibited. Besides MS2, gLAMP can also be used for the quantification of other microbial targets (e.g., Escherichia coli and Salmonella). Considering its simplicity, sensitivity, rapidity, and versatility, gLAMP holds great potential for microbial water-quality analysis, especially in resource-limited settings.
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Affiliation(s)
- Xiao Huang
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xingyu Lin
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Katharina Urmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Lijie Li
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xing Xie
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sunny Jiang
- Department
of Civil and Environmental Engineering, Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Michael R. Hoffmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
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Trebitz AS, Hoffman JC, Darling JA, Pilgrim EM, Kelly JR, Brown EA, Chadderton WL, Egan SP, Grey EK, Hashsham SA, Klymus KE, Mahon AR, Ram JL, Schultz MT, Stepien CA, Schardt JC. Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 202:299-310. [PMID: 28738203 PMCID: PMC5927374 DOI: 10.1016/j.jenvman.2017.07.045] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/13/2017] [Accepted: 07/16/2017] [Indexed: 05/19/2023]
Abstract
Following decades of ecologic and economic impacts from a growing list of nonindigenous and invasive species, government and management entities are committing to systematic early- detection monitoring (EDM). This has reinvigorated investment in the science underpinning such monitoring, as well as the need to convey that science in practical terms to those tasked with EDM implementation. Using the context of nonindigenous species in the North American Great Lakes, this article summarizes the current scientific tools and knowledge - including limitations, research needs, and likely future developments - relevant to various aspects of planning and conducting comprehensive EDM. We begin with the scope of the effort, contrasting target-species with broad-spectrum monitoring, reviewing information to support prioritization based on species and locations, and exploring the challenge of moving beyond individual surveys towards a coordinated monitoring network. Next, we discuss survey design, including effort to expend and its allocation over space and time. A section on sample collection and analysis overviews the merits of collecting actual organisms versus shed DNA, reviews the capabilities and limitations of identification by morphology, DNA target markers, or DNA barcoding, and examines best practices for sample handling and data verification. We end with a section addressing the analysis of monitoring data, including methods to evaluate survey performance and characterize and communicate uncertainty. Although the body of science supporting EDM implementation is already substantial, research and information needs (many already actively being addressed) include: better data to support risk assessments that guide choice of taxa and locations to monitor; improved understanding of spatiotemporal scales for sample collection; further development of DNA target markers, reference barcodes, genomic workflows, and synergies between DNA-based and morphology-based taxonomy; and tools and information management systems for better evaluating and communicating survey outcomes and uncertainty.
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Affiliation(s)
- Anett S Trebitz
- U.S. Environmental Protection Agency, National Health and Environmental Effects Laboratory, Duluth, MN, 55804, USA.
| | - Joel C Hoffman
- U.S. Environmental Protection Agency, National Health and Environmental Effects Laboratory, Duluth, MN, 55804, USA.
| | - John A Darling
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, Durham, NC, 27713, USA.
| | - Erik M Pilgrim
- U.S. Environmental Protection Agency, National Exposure Research Laboratory, Cincinnati, OH, 45268, USA.
| | - John R Kelly
- U.S. Environmental Protection Agency, National Health and Environmental Effects Laboratory, Duluth, MN, 55804, USA.
| | - Emily A Brown
- Université du Québec à Montréal, Montreal, Québec, H2L 2C4, Canada.
| | - W Lindsay Chadderton
- The Nature Conservancy, c/o Environmental Change Initiative, South Bend, IN, 46617, USA.
| | - Scott P Egan
- Rice University, BioSciences Department, Houston, TX, 77005, USA.
| | - Erin K Grey
- Governors State University, Division of Chemistry and Biological Sciences, University Park, IL, 60484, USA.
| | - Syed A Hashsham
- Engineering Research Center, Michigan State University, East Lansing, MI, 48823, USA.
| | - Katy E Klymus
- University of Toledo, Great Lakes Genetics/Genomics Laboratory, Department of Environmental Sciences, Toledo, OH, 43606, USA.
| | - Andrew R Mahon
- Central Michigan University, Department of Biology, Institute for Great Lakes Research, Mount Pleasant, MI, 48859, USA.
| | - Jeffrey L Ram
- Wayne State University, Department of Physiology, Detroit, MI, 48201, USA.
| | - Martin T Schultz
- U.S. Army Corps of Engineers, Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, 39180, USA.
| | - Carol A Stepien
- National Oceanic and Atmospheric Administration, Pacific Marine Environmental Lab, Seattle, WA, 98115, USA.
| | - James C Schardt
- U.S. Environmental Protection Agency, Great Lakes National Program Office, Chicago, IL, 60604, USA.
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Williams MR, Stedtfeld RD, Engle C, Salach P, Fakher U, Stedtfeld T, Dreelin E, Stevenson RJ, Latimore J, Hashsham SA. Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp. PLoS One 2017; 12:e0186462. [PMID: 29036210 PMCID: PMC5643059 DOI: 10.1371/journal.pone.0186462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/02/2017] [Indexed: 02/01/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) of aquatic invasive species environmental DNA (AIS eDNA) was used for rapid, sensitive, and specific detection of Dreissena sp. relevant to the Great Lakes (USA) basin. The method was validated for two uses including i) direct amplification of eDNA using a hand filtration system and ii) confirmation of the results after DNA extraction using a conventional thermal cycler run at isothermal temperatures. Direct amplification eliminated the need for DNA extraction and purification and allowed detection of target invasive species in grab or concentrated surface water samples, containing both free DNA as well as larger cells and particulates, such as veligers, eggs, or seeds. The direct amplification method validation was conducted using Dreissena polymorpha and Dreissena bugensis and uses up to 1 L grab water samples for high target abundance (e.g., greater than 10 veligers (larval mussels) per L for Dreissena sp.) or 20 L samples concentrated through 35 μm nylon screens for low target abundance, at less than 10 veligers per liter water. Surface water concentrate samples were collected over a period of three years, mostly from inland lakes in Michigan with the help of a network of volunteers. Field samples collected from 318 surface water locations included i) filtered concentrate for direct amplification validation and ii) 1 L grab water sample for eDNA extraction and confirmation. Though the extraction-based protocol was more sensitive (resulting in more positive detections than direct amplification), direct amplification could be used for rapid screening, allowing for quicker action times. For samples collected between May and August, results of eDNA direct amplification were consistent with known presence/absence of selected invasive species. A cross-platform smartphone application was also developed to disseminate the analyzed results to volunteers. Field tests of the direct amplification protocol using a portable device (Gene-Z) showed the method could be used in the field to obtain results within one hr (from sample to result). Overall, the direct amplification has the potential to simplify the eDNA-based monitoring of multiple aquatic invasive species. Additional studies are warranted to establish quantitative correlation between eDNA copy number, veliger, biomass or organismal abundance in the field.
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Affiliation(s)
- Maggie R. Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert D. Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Cathrine Engle
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Paul Salach
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Umama Fakher
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Tiffany Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Erin Dreelin
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
- Center for Water Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - R. Jan Stevenson
- Center for Water Sciences, Michigan State University, East Lansing, Michigan, United States of America
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jo Latimore
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
| | - Syed A. Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples. J Microbiol Methods 2017; 143:44-49. [PMID: 29031631 DOI: 10.1016/j.mimet.2017.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 01/26/2023]
Abstract
The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation). Despite having a detection limit less than the threshold recommended for effective remediation, the application of the assay was limited because of the semi-quantitative nature of the data. Moreover, the assay was prone to false positives due to the aerosolization of amplicons. In this study, deoxyuridine triphosphate (dUTP) and uracil DNA glycosylase (UNG) were incorporated into the assay to reduce the probability of false positives. Optimization experiments revealed a UNG concentration of 0.2units per reaction was adequate for degrading trace levels of AUGC based contamination (~1.4×104 gene copies/reaction) without significant changes to the detection limit (~100 gene copies/reaction). Additionally, the optimized assay was used with the most probable number (MPN) method to quantify RDase genes (vcrA and tceA) in multiple groundwater samples from a chlorinated solvent contaminated site. Using this approach, gene concentrations were significantly correlated to concentrations obtained using traditional methods (qPCR and DNA templates). Although the assay underestimated RDase genes concentrations, a strong correlation (R2=0.78 and 0.94) was observed between the two data sets. The regression equations obtained will be valuable to determine gene copies in groundwater using the newly developed, low cost and time saving method.
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Affiliation(s)
- Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Paul B Hatzinger
- APTIM Federal Services, 17 Princess Road, Lawrenceville, NJ 08648, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
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Williams MR, Stedtfeld RD, Stedtfeld TM, Tiedje JM, Hashsham SA. Quantification of microRNAs directly from body fluids using a base-stacking isothermal amplification method in a point-of-care device. Biomed Microdevices 2017; 19:45. [PMID: 28536858 PMCID: PMC5896010 DOI: 10.1007/s10544-017-0191-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MicroRNAs have been proposed to be a class of biomarkers of disease as expression levels are significantly altered in various tissues and body fluids when compared to healthy controls. As such, the detection and quantification of microRNAs is imperative. While many methods have been established for quantification of microRNAs, they typically rely on time consuming handling such as RNA extraction, purification, or ligation. Here we describe a novel method for quantification of microRNAs using direct amplification in body fluids without upstream sample preparation. Tested with a point-of-care device (termed Gene-Z), the presence of microRNA promotes base-stacking hybridization, and subsequent amplification between two universal strands. The base-stacking approach, which was achieved in <60 min, provided a sensitivity of 1.4 fmol per reaction. Tested in various percentages of whole blood, plasma, and faeces, precision (coefficient of variation = 2.6%) was maintained and comparable to amplification in pristine samples. Overall, the developed method represents a significant step towards rapid, one-step detection of microRNAs.
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Affiliation(s)
- Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA.
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13
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Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 198:213-220. [PMID: 28460328 PMCID: PMC5513725 DOI: 10.1016/j.jenvman.2017.04.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 05/05/2023]
Abstract
Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R2 = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Hassen Waseem
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | | | - Xueping Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Trevor Shook
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Amanda Logan
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Ally Graham
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Jong-Chan Chae
- Division of Biotechnology, Chonbuk National University, Iksan, 54596, Republic of Korea
| | - Woo-Jun Sul
- Department of Systems Biotechnology, Chung Ang University, Anseong, 17546, Republic of Korea
| | - Jacob VanHouten
- Science Division, Delta College, University Center, MI, 48710, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Gerben J Zylstra
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Brad L Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI, 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA.
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14
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Williams MR, Stedtfeld RD, Waseem H, Stedtfeld T, Upham B, Khalife W, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA. Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:1229-1241. [PMID: 29657581 PMCID: PMC5898395 DOI: 10.1039/c6ay03405e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.
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Affiliation(s)
- M R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - R D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - H Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - T Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - B Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - W Khalife
- Department of Microbiology, Sparrow Laboratories, Sparrow Health System, Lansing, MI 48912, USA
| | - B Etchebarne
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - M Hughes
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - J M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - S A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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15
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Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater. Appl Microbiol Biotechnol 2017; 101:4827-4835. [PMID: 28238079 DOI: 10.1007/s00253-017-8203-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 10/20/2022]
Abstract
TaqMan probe-based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes is a widely accepted molecular biological tool (MBT) for determining the abundance of Dehalococcoides sp. in groundwater samples from chlorinated solvent-contaminated sites. However, there are significant costs associated with this MBT. In this study, we describe an approach that requires only low-cost laboratory equipment (a bench top centrifuge and a water bath) and requires less time and resources compared to qPCR. The method involves the concentration of biomass from groundwater, without DNA extraction, and loop-mediated isothermal amplification (LAMP) of the cell templates. The amplification products are detected by a simple visual color change (orange/green). The detection limits of the assay were determined using groundwater from a contaminated site. In addition, the assay was tested with groundwater from three additional contaminated sites. The final approach to detect RDase genes, without DNA extraction or a thermal cycler, was successful to 1.8 × 105 gene copies per L for vcrA and 1.3 × 105 gene copies per L for tceA. Both values are below the threshold recommended for effective in situ dechlorination.
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Affiliation(s)
- Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA
| | - Paul B Hatzinger
- CB&I Federal Services, 17 Princess Road, Lawrenceville, NJ, 08648, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA.,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA.
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16
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Nicolini AM, McCracken KE, Yoon JY. Future developments in biosensors for field-ready Zika virus diagnostics. J Biol Eng 2017; 11:7. [PMID: 28127399 PMCID: PMC5260080 DOI: 10.1186/s13036-016-0046-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/27/2016] [Indexed: 12/11/2022] Open
Abstract
Since early reports of the recent Zika virus outbreak in May 2015, much has been learned and discussed regarding Zika virus infection and transmission. However, many opportunities still remain for translating these findings into field-ready sensors and diagnostics. In this brief review, we discuss current diagnostic methods, consider the prospects of translating other flavivirus biosensors directly to Zika virus sensing, and look toward the future developments needed for high-sensitivity and high-specificity biosensors to come.
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Affiliation(s)
- Ariana M. Nicolini
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721 USA
| | - Katherine E. McCracken
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
| | - Jeong-Yeol Yoon
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721 USA
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
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17
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Stedtfeld RD, Stedtfeld TM, Samhan F, Kanitkar YH, Hatzinger PB, Cupples AM, Hashsham SA. Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater. J Microbiol Methods 2016; 131:61-67. [PMID: 27720723 DOI: 10.1016/j.mimet.2016.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022]
Abstract
Nucleic acid amplification of biomarkers is increasingly used to monitor microbial activity and assess remedial performance in contaminated aquifers. Previous studies described the use of filtration, elution, and direct isothermal amplification (i.e. no DNA extraction and purification) as a field-able means to quantify Dehalococcoides spp. in groundwater. This study expands previous work with direct loop mediated isothermal amplification (LAMP) for the detection and quantification of Dehalobacter spp. in groundwater. Experiments tested amplification of DNA with and without crude lysis and varying concentrations of humic acid. Three separate field-able methods of biomass concentration with eight aquifer samples were also tested, comparing direct LAMP with traditional DNA extraction and quantitative PCR (qPCR). A new technique was developed where filters were amplified directly within disposable Gene-Z chips. The direct filter amplification (DFA) method eliminated an elution step and provided a detection limit of 102Dehalobacter cells per 100mL. LAMP with crudely lysed Dehalobacter had a negligible effect on threshold time and sensitivity compared to lysed samples. The LAMP assay was more resilient than traditional qPCR to humic acid in sample, amplifying with up to 100mg per L of humic acid per reaction compared to 1mg per L for qPCR. Of the tested field-able concentrations methods, DFA had the lowest coefficient of variation among Dehalobacter spiked groundwater samples and lowest threshold time indicating high capture efficiency and low inhibition. While demonstrated with Dehalobacter, the DFA method can potentially be used for a number of applications requiring field-able, rapid (<60min) and highly sensitive quantification of microorganisms in environmental water samples.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Farag Samhan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Water Pollution Control, National Research Centre, 33 El-Bohouth, P.O. 12622, Ad-Doqi, Giza, Egypt
| | - Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | | | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
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18
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Wilson FP, Liu X, Mattes TE, Cupples AM. Nocardioides, Sediminibacterium, Aquabacterium, Variovorax, and Pseudomonas linked to carbon uptake during aerobic vinyl chloride biodegradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19062-19070. [PMID: 27343076 DOI: 10.1007/s11356-016-7099-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
Vinyl chloride (VC) is a frequent groundwater contaminant and a known human carcinogen. Bioremediation is a potential cleanup strategy for contaminated sites; however, little is known about the bacteria responsible for aerobic VC degradation in mixed microbial communities. In attempts to address this knowledge gap, the microorganisms able to assimilate labeled carbon ((13)C) from VC within a mixed culture capable of rapid VC degradation (120 μmol in 7 days) were identified using stable isotope probing (SIP). For this, at two time points during VC degradation (days 3 and 7), DNA was extracted from replicate cultures initially supplied with labeled or unlabeled VC. The extracted DNA was ultracentrifuged, fractioned, and the fractions of greater buoyant density (heavy fractions, 1.758 to 1.780 g mL(-1)) were subject to high-throughput sequencing. Following this, specific primers were designed for the most abundant phylotypes in the heavy fractions. Then, quantitative PCR (qPCR) was used across the buoyant density gradient to confirm label uptake by these phylotypes. From qPCR and/or sequencing data, five phylotypes were found to be dominant in the heavy fractions, including Nocardioides (∼40 %), Sediminibacterium (∼25 %), Aquabacterium (∼17 %), Variovorax (∼6 %), and Pseudomonas (∼1 %). The abundance of two functional genes (etnC and etnE) associated with VC degradation was also investigated in the SIP fractions. Peak shifts of etnC and etnE gene abundance toward heavier fractions were observed, indicating uptake of (13)C into the microorganisms harboring these genes. Analysis of the total microbial community indicated a significant dominance of Nocardioides over the other label-enriched phylotypes. Overall, the data indicate Nocardioides is primarily responsible for VC degradation in this mixed culture, with the other putative VC degraders generating a small growth benefit from VC degradation. The specific primers designed toward the putative VC degraders may be of use for investigating VC degradation potential at contaminated sites.
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Affiliation(s)
- Fernanda Paes Wilson
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, 48824, MI, USA
| | - Xikun Liu
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, 52242, IA, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, 52242, IA, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, 48824, MI, USA.
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19
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Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites. Appl Microbiol Biotechnol 2016; 100:7297-309. [DOI: 10.1007/s00253-016-7559-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/07/2016] [Accepted: 04/14/2016] [Indexed: 11/30/2022]
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20
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS NANO 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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21
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Kanitkar YH, Stedtfeld RD, Steffan RJ, Hashsham SA, Cupples AM. Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9. Appl Environ Microbiol 2016; 82:1799-1806. [PMID: 26746711 PMCID: PMC4784023 DOI: 10.1128/aem.03660-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/27/2015] [Indexed: 12/23/2022] Open
Abstract
Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures.
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Affiliation(s)
- Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Robert J Steffan
- Biotechnology Development and Applications Group, CB&I Federal Services, LLC, Lawrenceville, New Jersey, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan, USA
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22
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Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. J Microbiol Methods 2015; 119:223-7. [PMID: 26554941 DOI: 10.1016/j.mimet.2015.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/04/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used for point-of-care nucleic acid based diagnostics. LAMP can be monitored in real-time by measuring the increase in fluorescence of DNA binding dyes. However, there is little information comparing the effect of various fluorescent dyes on signal to noise ratio (SNR) or threshold time (Tt). This information is critical for implementation with field deployable diagnostic tools that require small, low power consumption, robust, and inexpensive optical components with reagent saving low volume reactions. In this study, SNR and Tt during real-time LAMP was evaluated with eleven fluorescent dyes. Of all dyes tested, SYTO-82, SYTO-84, and SYTOX Orange resulted in the shortest Tt, and SYTO-81 had the widest range of working concentrations. The optimized protocol detected 10 genome copies of Mycobacterium tuberculosis in less than 10 min, 10 copies of Giardia intestinalis in ~20 min, and 10 copies of Staphylococcus aureus or Salmonella enterica in less than 15 min. Results demonstrate that reaction efficiency depends on both dye type and concentration and the selected polymerase. The optimized protocol was evaluated in the Gene-Z™ device, a hand-held battery operated platform characterized via simple and low cost optics, and a multiple assay microfluidic chip with micron volume reaction wells. Compared to the more conventional intercalating dye (SYBR Green), reliable amplification was only observed in the Gene-Z™ when using higher concentrations of SYTO-81.
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