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Goudoudaki S, Kambouris ME, Manoussopoulou M, Patrinos GP, Velegraki A, Manoussopoulos Y. Fast and Sustainable Thermo-osmotic DNA Extraction Protocol for Trans-spectrum Contingency and Field Use. Bio Protoc 2023; 13:e4796. [PMID: 37719074 PMCID: PMC10501911 DOI: 10.21769/bioprotoc.4796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 09/19/2023] Open
Abstract
In the field of molecular genetics, DNA extraction protocols and kits are sample-specific and proprietary, preventing lateral distribution among similar facilities from different sectors to alleviate supply shortages during a crisis. Expanding upon previous fast extraction protocols such as alkaline- and detergent-based ones, the use of boiling-hot water to rupture cells, virions, and nuclei, as proposed during the COVID-19 pandemic, might alleviate shortages and costs. Different soft, relatively abundant (highly enriched), and uncomplicated (genomically homogenous and with few inhibitors) biosamples are collected in 1.5 mL tubes, mixed with boiling-hot water, and stirred vigorously, so as to have membranes lysed and proteins deactivated; mechanical disruption may be used as well if necessary. Incubation in boiling water bath for 20-30 min follows. Depending on sample type and quantity, which affects the total extraction volume, 2-5 μL are pipetted off for direct PCR and the same volume for two decimal serial dilutions. The latter are intended to optimize the crude extract to a workable DNA/inhibitor concentration balance for direct PCR. Uncomplicated, highly enriched samples such as mycelial growth in fruits and human swab samples can be processed, contrary to complicated samples such as blood and physically unyielding samples such as plant tissue. The extract can be used for immediate PCR in both benchtop and portable thermocyclers, thus allowing nucleic acid amplification tests (NAAT) being performed in resource-limited settings with low cost and waste footprint or during prolonged crises, where supply chain failures may occur. Key features DNA extraction from different sample types using only boiling water and occasional mechanical assistance. Crude extract serially diluted twice, 10- and 100-fold, to bypass purification and quantification steps. Direct PCR for 2-10 μL of crude lysate and dilutions (conditional to sample type and quantity) to enhance probability of workable DNA-inhibitors' concentrations. Lowers the cost and curtails the overall footprint of testing to increase sustainability in field operations and in standard lab environments under supply chain derailment.
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Affiliation(s)
| | | | - Marianna Manoussopoulou
- Plant Protection Division of Patras, ELGO-Demeter,
Patras, Greece
- Department of Agronomics, Food, Natural Resources,
Animals and Environment, University of Padua, Padua, Italy
| | - George P. Patrinos
- Department of Pharmacy, University of Patras, Patras,
Greece
- Department of Genetics and Genomics & Zayed
Center for Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi,
United Arab Emirates
| | - Aristea Velegraki
- Department of Medicine, National and Kapodistrian
University of Athens, Athens, Greece
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Goudoudaki S, Kambouris ME, Siamoglou S, Gioula G, Kantzanou M, Manoussopoulou M, Patrinos GP, Manoussopoulos Y. Can Water-Only DNA Extraction Reduce the Logistical Footprint of Biosurveillance and Planetary Health Diagnostics? Toward a New Method. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:116-126. [PMID: 36809194 DOI: 10.1089/omi.2022.0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The coronavirus disease-2019 (COVID-19) pandemic has raised the stakes for planetary health diagnostics. Because pandemics pose enormous burdens on biosurveillance and diagnostics, reduction of the logistical burdens of pandemics and ecological crises is essential. Moreover, the disruptive effects of catastrophic bioevents impact the supply chains in both highly populated urban centers and rural communities. One "upstream" focus of methodological innovation in biosurveillance is the footprint of Nucleic Acid Amplification Test (NAAT)-based assays. We report in this study a water-only DNA extraction, as an initial step in developing future protocols that may require few expendables, and with low environmental footprints, in terms of wet and solid laboratory waste. In the present work, boiling-hot distilled water was used as the main cell lysis agent for direct polymerase chain reactions (PCRs) on crude extracts. After evaluation (1) in blood and mouth swabs for human biomarker genotyping, and (2) in mouth swabs and plant tissue for generic bacterial or fungal detection, and using different combinations of extraction volume, mechanical assistance, and extract dilution, we found the method to be applicable in low-complexity samples, but not in high-complexity ones such as blood and plant tissue. In conclusion, this study examined the doability of a lean approach for template extraction in the case of NAAT-based diagnostics. Testing our approach with different biosamples, PCR settings, and instruments, including portable ones for COVID-19 or dispersed applications, warrant further research. Minimal resources analysis is a concept and practice, vital and timely for biosurveillance, integrative biology, and planetary health in the 21st century.
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Affiliation(s)
| | - Manousos E Kambouris
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Stavroula Siamoglou
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Georgia Gioula
- Microbiology Department, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Kantzanou
- Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Marianna Manoussopoulou
- ELGO-Demeter, Plant Protection Division of Patras, Patras, Greece.,Department of Agronomics, Food, Natural Resources, Animals and Environment, University of Padua, Padua, Italy
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Genetics and Genomics, and Zayed Center for Health Sciences, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Goudoudaki S, Milioni A, Kritikou S, Velegraki A, Patrinos GP, Gioula G, Manoussopoulos Y, Kambouris ME. Fast, Scalable, and Practical: An Alkaline DNA Extraction Pipeline for Emergency Microbiomics Biosurveillance. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:484-494. [PMID: 34255557 DOI: 10.1089/omi.2021.0090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Pandemics and environmental crises evident from the first two decades of the 21st century call for methods innovation in biosurveillance and early detection of risk signals in planetary ecosystems. In crises conditions, conventional methods in public health, biosecurity, and environmental surveillance do not work well. In addition, the standard laboratory amenities and procedures may become unavailable, irrelevant, or simply not feasible, for example, owing to disruptions in logistics and process supply chains. The COVID-19 pandemic has been a wakeup call in this sense to reintroduce point-of-need diagnostics with an eye to limited resource settings and biosurveillance solutions. We report here a methodology innovation, a fast, scalable, and alkaline DNA extraction pipeline for emergency microbiomics biosurveillance. We believe that the presented methodology is well poised for effective, resilient, and anticipatory responses to future pandemics and ecological crises while contributing to microbiome science and point-of-need diagnostics in nonelective emergency contexts. The alkaline DNA extraction pipeline can usefully expand the throughput in emergencies by deployment or to allow backup in case of instrumentation failure in vital facilities. The need for distributed public health genomics surveillance is increasingly evident in the 21st century. This study makes a contribution to these ends broadly, and for future pandemic preparedness in particular. We call for innovation in biosurveillance methods that remain important existentially on a planet under pressure from unchecked human growth and breach of the boundaries between human and nonhuman animal habitats.
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Affiliation(s)
- Stavroula Goudoudaki
- Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece
| | - Aphroditi Milioni
- National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Stavroula Kritikou
- National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Aristea Velegraki
- National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - George P Patrinos
- Department of Pharmacy, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Georgia Gioula
- Microbiology Department, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Yiannis Manoussopoulos
- Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece
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Kambouris ME, Siamoglou S, Kordou Z, Milioni A, Vassilakis S, Goudoudaki S, Kritikou S, Manoussopoulos Y, Velegraki A, Patrinos GP. Point-of-need molecular processing of biosamples using portable instrumentation to reduce turnaround time. BIOSAFETY AND HEALTH 2020. [DOI: 10.1016/j.bsheal.2020.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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