Core genome multilocus sequence typing scheme for global epidemiology of Vibrio parahaemolyticus strains

Vibrio parahaemolyticus is an important human foodborne pathogen worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 1998 and a large number of clones have been identified causing... [ view full abstract ]

Vibrio parahaemolyticus is an important human foodborne pathogen worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 1998 and a large number of clones have been identified causing severe outbreaks worldwide (ST3), recurrent outbreaks in certain regions (e.g., ST36) or spreading to other regions where they are non-endemic (e.g., ST88). Application of whole genome sequencing has become a routine for tracing infections over outbreaks with core genome MLST analysis as one of the most straightforward ways to explore complex genomic data in an epidemiological context. Therefore, there is a need to generate a new, portable, standardized, and more advanced system that provides higher resolution and discriminatory power among V. parahaemolyticus strains using WGS data. To establish this cgMLST scheme, we sequenced 92 V. parahaemolyticus genomes and used the genome of strain RIMD 2210633 as reference to determine which genes were suitable for the stablishing of the V. parahaemolyticus cgMLST scheme. This analysis resulted in the identification of 2254 suitable core genes for use in the cgMLST scheme. To evaluate the performance of this scheme, we performed a cgMLST analysis of the 92 new sequenced genomes plus an additional 142 strains with genomes available at NCBI. The cgMLST scheme was able to distinguish related and unrelated strains including those with the same ST, clearly showing its enhanced resolution over conventional MLST analysis. It also distinguished outbreak-related from unrelated strains within the same ST.