Dokument: Short- and long-read based resolution of complete bacterial genomes with applications in outbreak analysis and tracking of resistance genes
| Titel: | Short- and long-read based resolution of complete bacterial genomes with applications in outbreak analysis and tracking of resistance genes | |||||||
| URL für Lesezeichen: | https://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=67387 | |||||||
| URN (NBN): | urn:nbn:de:hbz:061-20241111-140040-6 | |||||||
| Kollektion: | Dissertationen | |||||||
| Sprache: | Englisch | |||||||
| Dokumententyp: | Wissenschaftliche Abschlussarbeiten » Dissertation | |||||||
| Medientyp: | Text | |||||||
| Autor: | Fuchs, Sebastian Alexander [Autor] | |||||||
| Dateien: |
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| Beitragende: | Prof. Dr. Alexander Dilthey [Gutachter] Gunnar Klau [Gutachter] | |||||||
| Dewey Dezimal-Klassifikation: | 500 Naturwissenschaften und Mathematik » 570 Biowissenschaften; Biologie | |||||||
| Beschreibung: | Research in bacterial pathogen genomics has witnessed significant advancements in sequencing
technologies. In the realm of bacterial genomics, our work addresses both bioinformatic challenges, as well as cost and labour constraints, associated with the use of novel long-read sequencing technologies within three different projects. First, introducing Ultraplexing, we present a method that substantially reduces per-sample sequencing costs and hands-on time in Nanopore sequencing for hybrid assembly. Ultraplexing eliminates the need for molecular barcoding bs bioinformatically determining which specific sequenced isolate a long-read belongs to; this is done by comparing each long-read to the kmer spectrum of the sequenced isolates, measured using Illumina data. This method holds promise for large-scale bacterial genome projects that utilize hybrid assembly strategies, enabling considerable savings without compromising assembly quality. These advantages are enabled by the possibility to multiplex at least 100 isolates together, representing roughly fourfold increase of isolates possible at the time of publication, thus also reducing hands-on time in the lab by a factor of four. Second, shifting focus to the hospital associated pathogen Acinetobacter baumannii, we investigate genome plasticity and horizontal gene transfer mechanisms in the context of transmission of colistin resistance elements. Through short- and long-read sequencing and creation of hybrid assemblies, we identify two probable recombination events in the pmrCAB operon, which confers colistin resistance. Our findings highlight the role of homologous recombination and shed light on the possible contribution of mobile genetic elements to this phenomenon in A. baumannii. This study contributes to the understanding of antibiotic resistance dynamics in clinical isolates of A. baumannii, specifically those belonging to International Clone 7. Third, expanding the scope to genomic pathogen surveillance in healthcare facilities, we introduce NanoCore, a user-friendly method developed for Nanopore-based outbreak surveillance and investigation. NanoCore enables the determination and visualization of cgMLST-like sample distances directly from raw Nanopore reads by mapping Nanopore data to a core genome reference, variant-calling and calculating distances from the results, thus offering a fast and flexible solution. Validated on methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE) datasets, NanoCore demonstrates high accuracy, producing results quasi-identical to those of current gold-standard tools with an averagevii difference of 0.75 alleles for MRSA and 0.81 alleles for VRE in Nanopore-only-mode and 3.44 and 1.95 alleles respectively in hybrid-mode (measured in closely related isolates). The computational efficiency, open-source availability, and user-friendly installation via bioconda make NanoCore a valuable tool for effective bacterial pathogen surveillance in healthcare settings. In conclusion, the work presented in this thesis spans the development of methods for hybrid genome assembly, long-read-based genomic surveillance and the investigation of the transmission of antibiotic resistance elements. The presented work demonstrates the potential of combining data generated by different sequencing technologies for bacterial genomics, as well as the potential of bioinformatics methods development for emerging sequencing technologies. | |||||||
| Lizenz: |  Dieses Werk ist lizenziert unter einer Creative Commons Namensnennung 4.0 International Lizenz | |||||||
| Fachbereich / Einrichtung: | Mathematisch- Naturwissenschaftliche Fakultät » WE Informatik | |||||||
| Dokument erstellt am: | 11.11.2024 | |||||||
| Dateien geändert am: | 11.11.2024 | |||||||
| Promotionsantrag am: | 08.05.2024 | |||||||
| Datum der Promotion: | 06.11.2024 |
