Presenter: Mara Lohde (CaSe Group, Institute for Infection Medicine and Hospital Hygiene, Jena University Hospital)
Location: Centre for Applied Research (ZAF), Philosophenweg 7, 07743 Jena (and online as a hybrid event).
Language: Englisch
Long-read sequencing technologies like Oxford Nanopore Technologies (ONT) and PacBio enable the reliable assembly of plasmids and genomes. But how does ONT perform nowadays for bacterial outbreak investigations where accuracy matters the most? When investigating a three-year-long Klebsiella pneumoniae outbreak using the latest ONT chemistry, we uncovered methylation-induced errors that led to false exclusions of outbreak-related strains in cgMLST and phylogenetic analyses. These errors extend to other species, which we further confirmed by another large multicenter study. However, new advancements in the scientific community and our solutions can tackle these methylation-induced errors when carefully applying additional bioinformatic measures.