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Fast, Scalable, and Practical: An Alkaline DNA Extraction Pipeline for Emergency Microbiomics Biosurveillance.
Goudoudaki, Stavroula; Milioni, Aphroditi; Kritikou, Stavroula; Velegraki, Aristea; Patrinos, George P; Gioula, Georgia; Manoussopoulos, Yiannis; Kambouris, Manousos E.
  • Goudoudaki S; Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece.
  • Milioni A; National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
  • Kritikou S; National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
  • Velegraki A; National Collection of Pathogenic Fungi, Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
  • Patrinos GP; Department of Pharmacy, University of Patras, Patras, Greece.
  • Gioula G; Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
  • Manoussopoulos Y; Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
  • Kambouris ME; Microbiology Department, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece.
OMICS ; 25(8): 484-494, 2021 08.
Article in English | MEDLINE | ID: covidwho-1307504
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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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA / Microbiological Techniques / Biosurveillance / Public Health Surveillance Type of study: Prognostic study Limits: Animals / Humans Language: English Journal: OMICS Journal subject: Molecular Biology Year: 2021 Document Type: Article Affiliation country: Omi.2021.0090

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Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA / Microbiological Techniques / Biosurveillance / Public Health Surveillance Type of study: Prognostic study Limits: Animals / Humans Language: English Journal: OMICS Journal subject: Molecular Biology Year: 2021 Document Type: Article Affiliation country: Omi.2021.0090