20.500.12556/RUL-189307 Ugotavljanje plazmidnega prenosa genov za karbapenemaze pri izbranih vrstah enterobakterij s sekvenciranjem celotnega genoma Detection of plasmid-mediated carbapenemase gene transfer in selected Enterobacteriaceae species using whole genome sequencing V raziskavi smo analizirali dobro opredeljene seve enterobakterij, ki izločajo karbapenemaze (CPE) različnih vrst, osamljene pri posameznih bolnikih. S sekvenciranjem celotnega genoma smo natančneje opredelili plazmidno kodirane karbapenemaze. Sekvenciranje smo izvedli s platformama za sekvenciranje s kratkimi odčitki (Illumina, Združene države Amerike) in z dolgimi odčitki (Oxford Nanopore Technologies, Združeno kraljestvo). Z bioinformacijskimi orodji smo opredelili morebitne plazmidne prenose med različnimi vrstami CPE ter primerjali uporabnost obeh platform za določanje plazmidnih prenosov. Pri izolatih enterobakterij Escherichia coli, Citrobacter spp., Klebsiella pneumoniae in K. quasipneumoniae smo dokazali prisotnost plazmidov z geni za karbapenemaze blaOXA-48, blaOXA-181 in blaVIM-1. Sekvenciranje z dolgimi odčitki se je izkazalo kot zanesljivejše za dokazovanje plazmidov, saj smo z njim pridobili sklenjene krožne plazmide iz enega kontiga. Pri sekvenciranju s kratkimi odčitki so se v nekaj primerih pokazale težave z nezmožnostjo določitve lokacije gena za karbapenemaze ter razdrobljenostjo sekvenc, kar je vodilo v napačno sestavljanje plazmidov. Pri bolnikih, kjer smo imeli na voljo dovolj kakovostne podatke za preučevanje plazmidnih prenosov, smo na podlagi podatkov sekvenciranja z dolgimi odčitki ugotovili, da je najverjetneje prišlo do horizontalnega prenosa plazmidov z geni za karbapenemaze med različnimi vrstami enterobakterij. Prenosa nismo dokazali pri dveh izolatih dveh različnih bolnikov. In our research, we analyzed well-defined strains of Enterobacteriaceae with carbapenemases (CPE) from various species, isolated from individual patients. We used whole-genome sequencing to further characterize plasmid-encoded carbapenemases. Sequencing was performed using short-read platforms (Illumina, United States) and long-read platforms (Oxford Nanopore Technologies, United Kingdom). We applied bioinformatics tools to identify possible plasmid transfers between different CPE species and compared the suitability of both platforms for determining plasmid transfers. We demonstrated the presence of plasmids with carbapenemase genes blaOXA-48, blaOXA-181 and blaVIM-1 in Enterobacteriaceae isolates, including Escherichia coli, Citrobacter spp., Klebsiella pneumoniae and K. quasipneumoniae. Long-read sequencing proved more reliable for plasmid detection, as it enabled the assembly of complete circular plasmids in a single contig. In some cases, short-read sequencing had difficulty determinig the location of the carbapenemase gene and resulted in sequence fragmentation, leading to incorrect plasmid assembly. In patients, from whom we had sufficient quality data to study plasmid transfers, we found, based on long-read sequencing data, that horizontal transfer of plasmids with carbapenemase genes between different species of Enterobacteriaceae most likely occurred. No transmission was observed in the case of two isolates obtained from two different patients. enterobakterije karbapenemaze plazmidni prenosi sekvenciranje celotnega genoma Illumina Nanopore bioinformacijska analiza Enterobacteriaceae carbapenemases plasmid transfers whole genome sequencing Illumina Nanopore bioinformatic analysis true false false [K. Šink] Slovenski jezik Angleški jezik Magistrsko delo/naloga 2026-10-03 07:15:12 2026-10-03 07:15:33 2026-10-07 03:51:56 0000-00-00 00:00:00 2026 0 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 579.61:575.112 298212 293694979 59821.pdf 59821.pdf 1 B704C4F1961D6CD0F0F4BA1AF2844ECF 52140d81e4d6213a786086db7b50148a170cc8d5209c47f62aab0c489346c811 55f786af-bee9-11f1-8bc5-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=249778 Biotehniška fakulteta 0 0 0