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SHR Neuro Krebs Kardio Lipid Stoffw Microb

Wagner, GE; Dabernig-Heinz, J; Lipp, M; Cabal, A; Simantzik, J; Kohl, M; Scheiber, M; Lichtenegger, S; Ehricht, R; Leitner, E; Ruppitsch, W; Steinmetz, I.
Real-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance.
J Clin Microbiol. 2023; 61(4):e0163122 Doi: 10.1128/jcm.01631-22 [OPEN ACCESS]
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Führende Autor*innen der Med Uni Graz
Steinmetz Ivo
Wagner-Lichtenegger Gabriel
Co-Autor*innen der Med Uni Graz
Dabernig-Heinz Johanna
Leitner-Meyer Eva
Lipp Michaela
Wagner-Lichtenegger Sabine
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Abstract:
Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.
Find related publications in this database (using NLM MeSH Indexing)
Humans - administration & dosage
Multilocus Sequence Typing - methods
Genome, Bacterial - genetics
Nanopore Sequencing - administration & dosage
Molecular Epidemiology - methods
Phylogeny - administration & dosage
Nanopores - administration & dosage
Bacteria - genetics
Bacterial Typing Techniques - methods

Find related publications in this database (Keywords)
Bordetella pertussis
bacterial typing
molecular surveillance
next-generation sequencing
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