Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors

Core-genome multi-locus sequence typing (cgMLST) is a well-established and standardized method for genomics-based cluster detection and phylogenomic analysis of bacteria. The reduced error rate of Oxford Nanopore Technologies (ONT) R10 sequencing has prompted many laboratories to explore incorporating this technology into their activities. However, conflicting reports exist on the performance of ONT R10 sequencing for cgMLST analysis. This study evaluates the suitability of ONT R10 data for cgMLST allele calling and cluster detection for bacterial outbreak investigation. ONT and Illumina sequencing data were generated for 24 Neisseria meningitidis and 24 Salmonella enterica isolates. For ONT, both the rapid barcoding kit (RBK) and the rapid PCR barcoding kit (RPB) were used.

Authors:
Bert Bogaerts1,*, Margo Maex2,*, Florian Commans2, Nathalie Goeders1,2, An Van den Bossche2, Sigrid C. J. De Keersmaecker1, Nancy H. C. Roosens1, Pieter-Jan Ceyssens2, Wesley Mattheus2,*, Kevin Vanneste1,*

1 Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium

2 Bacterial Diseases, Sciensano, Brussels, Belgium

* Shared first and last author contributions