000K utf8 0100 1943776059 1100 $c2025 1500 eng 2050 urn:nbn:de:gbv:27-dbt-68377-7 2051 10.22032/dbt.68377 3000 Krautwurst, Sebastian 4000 Tackling global pathogen threats with nanopore sequencing data [Krautwurst, Sebastian] 4060 105 Seiten 4209 Infectious diseases caused by bacteria and viruses are a large burden on human health and the healthcare systems of the world. Of particular interest are the so-called emerging infectious diseases, which are those that have an increased incidence in the last 20 years and have a potential to further amplify in the future, such as influenza, Ebola, cholera and COVID-19. For bacterial pathogens exists the constant threat of antibiotic resistance: as antibiotics use and misuse rise worldwide, more resistant strains emerge and render the antibiotics less effective over time. For infectious viruses there is a need for deeper understanding of replication mechanisms and how they play a role in mutation and recombination of viral genomes. I investigated the potential of long-read sequencing with nanopores to tackle these challenges. For the first time, we employed direct RNA nanopore sequencing to examine the viral RNA transcripts produced in cells infected with large-genome RNA viruses. I recovered genome copies and mRNA transcripts at full length in single contiguous reads, as well as a large variety of uncharacterized subgenomic RNAs. Direct RNA sequencing allowed me to detect RNA methylation patterns on the viral mRNAs. My collaborators and I devised an easy-to-use, fully reproducible and highly parallelizable bioinformatic analysis pipeline (poreCov) for nanopore amplicon sequencing data that is used for genomic surveillance during pathogen outbreaks. Additionally, I implemented CholerAegon, a Nextflow pipeline for automatic genome assembly and prediction of antibiotic resistance profiles of bacterial samples. It harnesses the advantages of short and long reads for accurate assembly, and utilizes the curated resistance database CARD to predict resistance genes or SNPs on the assembled genomes. With my bioinformatic analyses and programs, I demonstrate that nanopore sequencing data is an important tool for the study of viral and bacterial pathogens. 4950 https://doi.org/10.22032/dbt.68377$xR$3Volltext$534 4950 https://nbn-resolving.org/urn:nbn:de:gbv:27-dbt-68377-7$xR$3Volltext$534 4961 http://uri.gbv.de/document/gvk:ppn:1943776059 5051 004 5051 570 5550 Bakterien 5550 Bioinformatik 5550 Genomik 5550 Infektionskrankheit 5550 Viren