Analysis of clinical research samples by nanopore sequencing with Q20+ chemistry reveals inaccurate classifications within the genus Serratia

The identification of human pathogens is crucial for clinical diagnostics, and false assignment of species can interfere with treatment and harm the patient. We analysed human clinical research samples that had been assigned as the pathogen Serratia marcescens by standard clinical methods with nanopore sequencing and found we could assign some to the distinct species Serratia bockelmannii as they displayed a significant distance to all genomes of known Serratia species on the nucleotide level, which indicated that they belonged to a novel species. Other samples in the NCBI database were shown to cluster with our proposed novel species or formed their own clusters, indicating the presence of additional novel species according to a classification with the type strain genome server (TYGS) that could not be discriminated between based on 16S sequences alone. Thus, we propose that whole-genome sequencing with Oxford Nanopore Q20+ chemistry is a superior way for fast and reliable species identification compared to 16S amplicon sequencing for example.