Optical DNA Mapping as a Tool for Determination of EHEC Serotypes
Typ
Examensarbete för masterexamen
Master's Thesis
Master's Thesis
Program
Biotechnology (MPBIO), MSc
Publicerad
2024
Författare
Mårtensson , Hanna
Modellbyggare
Tidskriftstitel
ISSN
Volymtitel
Utgivare
Sammanfattning
Enterohemorrhagic Escerichia coli (EHEC) is a pathogenic subgroup of E. coli, responsible for causing severe diarrheal disease though food-borne outbreaks. Infection can further progress to Hemolytic Uremic Syndrome (HUS), a critical condition associated with renal failure and potential fatality. In epidemiological surveillance of EHEC infection, it is of interest to determine the serotype of the EHEC strain, as the risk of severe disease is linked to a few serotypes. Currently, this process involves extensive hands-on involvement while also being time-consuming, suggesting the need to explore alternative methods to identify EHEC serotypes.
In this project, Optical DNA Mapping was employed for bacterial typing. DNA from seven different EHEC samples was labeled through competitive binding and then stretched in nanochannels. Using fluorescence microscopy, the DNA molecules were imaged which due to the labeling resulted in unique fluorescence intensity profiles along the molecules corresponding to the DNA sequence. These intensity profiles
were then matched trough reference-based alignment to a reference database in order to identify the bacterial strain associated with the DNA.
The method demonstrated a 100% true positive rate identification at the species level. At the strain level, a majority of matches corresponded to the correct serotype. The results also indicated the potential to assign the matches to strain groups with high taxonomic resolution. In conclusion, the findings provide a positive indication of the possibility in using ODM for determining of EHEC serotypes.
Beskrivning
Ämne/nyckelord
DNA , Optical DNA Mapping , Competitive binding , Nanofluidics , Fluorescence , Enterohemorrhagic Escherichia coli , Serotype