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Evaluation of DNA extraction methods for reliable quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa [Elektronski vir]Bogožalec Košir, Alexandra ...Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the ... yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.Source: Biosensors. - ISSN 2079-6374 (Vol. 13, iss. 4, art. 463, Apr. 2023, str. [1]-15)Type of material - e-article ; adult, seriousPublish date - 2023Language - englishCOBISS.SI-ID - 149291011
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Author | Bogožalec Košir, Alexandra ... |
Title | Evaluation of DNA extraction methods for reliable quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa [Elektronski vir] |
Publication date | 2023-04-06 |
COBISS.SI-ID | 149291011 |
Publication version in repository | Publisher's version |
Publication licence | Creative Commons Attribution 4.0 International |
Embargo | Immediate publication for public |
Project(s) from which the publication was funded
Title | Acronym | Project ID | Funder |
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Biotehnologija in sistemska biologija rastlin | P4-0165-2022 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
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Meroslovje za sledenje bolnišničnih okužb respiratornega trakta, ki jih povzročajo Gram-negativne bakterije | Z2-1860-2019 |
Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije |
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Links to authors' personal bibliographies | Links to information on researchers in the SICRIS system |
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Bogožalec Košir, Alexandra | 37410 |
Lužnik, Dane | 34498 |
Tomič, Viktorija | 22806 |
Milavec, Mojca, 1972- | 19119 |
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