Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.
Vibrio parahaemolyticusis an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood, with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database forV. parahaemolyticuswas created in 2008, and a large number of clones have been identified, causing severe outbreaks worldwide (sequence type 3 [ST3]), recurrent outbreaks in certain regions (e.g., ST36), or spreading to other regions where they are nonendemic (e.g., ST88 or ST189). The current MLST scheme uses sequences of 7 genes to generate an ST, which results in a powerful tool for inferring the population structure of this pathogen, although with limited resolution, especially compared to pulsed-field gel electrophoresis (PFGE). The application of whole-genome sequencing (WGS) has become routine for trace back investigations, with core genome MLST (cgMLST) 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 amongV. parahaemolyticusstrains using WGS data. We sequenced 92V. parahaemolyticusgenomes and used the genome of strain RIMD 2210633 as a reference (with a total of 4,832 genes) to determine which genes were suitable for establishing aV. parahaemolyticuscgMLST scheme. This analysis resulted in the identification of 2,254 suitable core genes for use in the cgMLST scheme. To evaluate the performance of this scheme, we performed a cgMLST analysis of 92 newly sequenced genomes, plus an additional 142 strains with genomes available at NCBI. cgMLST analysis 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 non-outbreak-related strains within the same ST. The sequences obtained from this work were deposited and are available in the public database (http://pubmlst.org/vparahaemolyticus). The application of this cgMLST scheme to the characterization ofV. parahaemolyticusstrains provided by different laboratories from around the world will reveal the global picture of the epidemiology, spread, and evolution of this pathogen and will become a powerful tool for outbreak investigations, allowing for the unambiguous comparison of strains with global coverage.
Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA narjol.gonzalez-escalona@fda.hhs.gov.
Narjol
0000-0003-4568-0022
N
Gonzalez-Escalona
Department of Zoology, University of Oxford, Oxford, United Kingdom.
Keith A
KA
Jolley
Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA.
Elizabeth
E
Reed
The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom.
Jaime
J
Martinez-Urtaza
D004196:Disease Outbreaks; D016680:Genome, Bacterial; D014943:Global Health; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods*; D058885:Multilocus Sequence Typing / Q000379:methods*; D014735:Vibrio Infections / Q000453:epidemiology* / Q000382:microbiology*; D014736:Vibrio parahaemolyticus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
Vibrio parahaemolyticus; cgMLST; clinical; core genome multilocus sequence typing; phylogenetic analysis; phylogeny; single nucleotide polymorphism (SNP); whole-genome sequencing (WGS)