MLST Article Abstract

Background: Accurate strain identification is essential when working with bacteria. For many species, Multilocus Sequence Typing (MLST) is considered the "gold standard" of typing, but is traditionally performed in an expensive and time-consuming manner. As the costs of Whole Genome Sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and can with advantage be used for the typing.
Methods: We developed a web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or pre-assembled genomes. Updates from the MLST databases are downloaded monthly and the best matching MLST alleles of the specified MLST scheme is found using a BLAST-based ranking method. The Sequence Type (ST) is determined by the combination of identified alleles.
Results: The method was tested on pre-assembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test-set of short sequence reads from 29 isolates for which the ST had been determined by traditional measures.
Conclusions: The presented method enables investigators to determine the ST based on WGS data. The method is publically available at www.cbs.dtu.dk/services/MLST.