Comparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samples
Abstract Sepsis, a leading cause of mortality, requires rapid and accurate pathogen identification to ensure effective treatment. Current diagnostic methods such as blood cultures are time-consuming, whereas molecular diagnostic techniques represent a promising alternative for faster pathogen detect...
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Nature Portfolio
2025-02-01
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| Online Access: | https://doi.org/10.1038/s41598-025-87225-y |
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| author | Byungjoon Na Junghun Park Sojin Park Eunseon Park Jimin Jang Yu-Hee Kim Jinyeop Lee Hae-Sun Chung |
| author_facet | Byungjoon Na Junghun Park Sojin Park Eunseon Park Jimin Jang Yu-Hee Kim Jinyeop Lee Hae-Sun Chung |
| author_sort | Byungjoon Na |
| collection | DOAJ |
| description | Abstract Sepsis, a leading cause of mortality, requires rapid and accurate pathogen identification to ensure effective treatment. Current diagnostic methods such as blood cultures are time-consuming, whereas molecular diagnostic techniques represent a promising alternative for faster pathogen detection. Therefore, the aim of this study was to evaluate different DNA extraction methods for the improved detection of infectious pathogens in the bloodstream. Specifically, we compared one column-based DNA extraction method (QIAamp DNA Blood Mini Kit) with two magnetic bead-based DNA extraction methods (K-SL DNA Extraction Kit and GraBon™ system). Real-time PCR was performed using specific primers to assess the efficiency of each method. The K-SL DNA Extraction Kit and GraBon™ system exhibited higher accuracy rates of 77.5% (22/40) and 76.5% (21/40), respectively, compared to the QIAamp DNA Blood Mini Kit, which had an accuracy rate 65.0% (12/40) for Escherichia coli detection, whereas the GraBon™ system demonstrated higher accuracy rate of 77.5% (22/40) than the other two methods, which had an accuracy rates of 67.5% (14/40) for Staphylococcus aureus detection. All methods displayed high specificity for negative samples (100%). These findings highlight the superior performance of magnetic bead-based methods, particularly when automated, for extracting bacterial DNA from whole blood samples. Such methods may enable the more rapid and accurate diagnosis of bloodstream infections, potentially improving patient outcomes. |
| format | Article |
| id | doaj-art-2e9de2def0824e41a9214ecaeb34672b |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-2e9de2def0824e41a9214ecaeb34672b2025-02-09T12:34:47ZengNature PortfolioScientific Reports2045-23222025-02-011511610.1038/s41598-025-87225-yComparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samplesByungjoon Na0Junghun Park1Sojin Park2Eunseon Park3Jimin Jang4Yu-Hee Kim5Jinyeop Lee6Hae-Sun Chung7KingoBio, Inc. Research CenterEwha Education & Research Center for Infection, Ewha Womans University Medical CenterKingoBio, Inc. Research CenterKingoBio, Inc. Research CenterKingoBio, Inc. Research CenterEwha Education & Research Center for Infection, Ewha Womans University Medical CenterKingoBio, Inc. Research CenterEwha Education & Research Center for Infection, Ewha Womans University Medical CenterAbstract Sepsis, a leading cause of mortality, requires rapid and accurate pathogen identification to ensure effective treatment. Current diagnostic methods such as blood cultures are time-consuming, whereas molecular diagnostic techniques represent a promising alternative for faster pathogen detection. Therefore, the aim of this study was to evaluate different DNA extraction methods for the improved detection of infectious pathogens in the bloodstream. Specifically, we compared one column-based DNA extraction method (QIAamp DNA Blood Mini Kit) with two magnetic bead-based DNA extraction methods (K-SL DNA Extraction Kit and GraBon™ system). Real-time PCR was performed using specific primers to assess the efficiency of each method. The K-SL DNA Extraction Kit and GraBon™ system exhibited higher accuracy rates of 77.5% (22/40) and 76.5% (21/40), respectively, compared to the QIAamp DNA Blood Mini Kit, which had an accuracy rate 65.0% (12/40) for Escherichia coli detection, whereas the GraBon™ system demonstrated higher accuracy rate of 77.5% (22/40) than the other two methods, which had an accuracy rates of 67.5% (14/40) for Staphylococcus aureus detection. All methods displayed high specificity for negative samples (100%). These findings highlight the superior performance of magnetic bead-based methods, particularly when automated, for extracting bacterial DNA from whole blood samples. Such methods may enable the more rapid and accurate diagnosis of bloodstream infections, potentially improving patient outcomes.https://doi.org/10.1038/s41598-025-87225-ySepsisDNA extractionMolecular diagnostic techniqueMagnetic beadWhole blood |
| spellingShingle | Byungjoon Na Junghun Park Sojin Park Eunseon Park Jimin Jang Yu-Hee Kim Jinyeop Lee Hae-Sun Chung Comparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samples Scientific Reports Sepsis DNA extraction Molecular diagnostic technique Magnetic bead Whole blood |
| title | Comparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samples |
| title_full | Comparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samples |
| title_fullStr | Comparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samples |
| title_full_unstemmed | Comparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samples |
| title_short | Comparison evaluation of bacterial DNA extraction methods for improved molecular diagnostic accuracy of sepsis-causing pathogens in clinical whole blood samples |
| title_sort | comparison evaluation of bacterial dna extraction methods for improved molecular diagnostic accuracy of sepsis causing pathogens in clinical whole blood samples |
| topic | Sepsis DNA extraction Molecular diagnostic technique Magnetic bead Whole blood |
| url | https://doi.org/10.1038/s41598-025-87225-y |
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