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Future diagnosis of sepsis: Exploring the nanopore sequencing on MinION as a potential tool for early sepsis diagnosis
University of Skövde, School of Bioscience.
2024 (English)Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Sepsis is a serious condition characterized by a strong systematic inflammatory reaction that takes place because the immune system is not responding properly to an infection. This study focused on sepsis caused by bacterial infections. The most important factor in the diagnosis of sepsis is time and the current golden standard of blood culturing used can take several days and leaves room for improvement. This study aimed to evaluate the ability of nanopore sequencing of DNA extracted from whole human blood on the MinION device, to evaluate its efficiency and potential as a future tool for early sepsis diagnosis. Furthermore, the study aimed to examine if it is feasible to identify genes that encode antimicrobial resistance in the sequenced DNA. Three different DNA extraction kits were used to extract DNA from whole human blood spiked with microbial DNA. The obtained data from nanopore sequencing was analyzed using EPI2ME, and the FASTQ-files were further analyzed with What’s-In-My-Pot and BV-BRC taxonomic classification and metagenomic read mapping. Two of the DNA extraction kits yielded DNA extractions with higher quality, whereas DNA extractions performed with the third kit led to challenges with purity. The results from nanopore sequencing indicated a difference in reads depending on both the two flow cells as well as the DNA extraction kit used. The DNA from gram-positive bacterial species added to the whole blood was the focus of this project, and using taxonomic classification and metagenomic read mapping all DNA included in the microbial spike was detected, and genes that code for antimicrobial resistance were identified. Differences in the number of detected bacterial species could be seen depending on the algorithm used. However, the time aspect remains an issue. The results indicated that this technique could possibly be used in future studies, but there is a need for optimization.

Place, publisher, year, edition, pages
2024. , p. 24
National Category
Medical Bioscience
Identifiers
URN: urn:nbn:se:his:diva-24307OAI: oai:DiVA.org:his-24307DiVA, id: diva2:1883304
Subject / course
Bioscience
Educational program
Bioscience - Molecular Biodesign
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Examiners
Available from: 2024-07-09 Created: 2024-07-09 Last updated: 2024-07-09Bibliographically approved

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