Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen genotyping

Abstract

Vibrio parahaemolyticus is an important food-borne human pathogen and presents immunogenic surface polysaccharides, which can be used to distinguish problematic and disease-causing lineages. V. parahaemolyticus is divided in 16 O-serotypes (O-antigen) and 71 K-serotypes (K-antigen). Agglutination tests are still the gold standard for serotyping, but many V. parahaemolyticus isolates are not typable by agglutination. An alternative for agglutination tests is genotyping using whole-genome sequencing data, by which K- and O- genotypes have been curated and identified previously for other clinically relevant organisms with the software tool Kaptive. In this study, V. parahaemolyticus isolates were serotyped and sequenced, and all known and several novel O- and K-loci were identified. We developed Kaptive databases for all O- and K-loci after manual curation of the loci. In our study, we could genotype the O- and K-loci of 98 and 93 % of the genomes, respectively, with a Kaptive confidence score higher than ‘none’. The newly developed Kaptive databases with the identified V. parahaemolyticus O- and K-loci can be used to identify the O- and K-genotypes of V. parahaemolyticus isolates from genome sequences.

Epidemiological and Genomic analysis of Vibrio parahaemolyticus isolated from imported travelers at the port of Shanghai, China (2017-2019)

“…In terms of pathogen risk assessment, virulence genes (tdh, trh) were found in most of isolates in this study. The presence of these two virulence genes in V. parahaemolyticus is commonly used in clinical, surveillance, and research testing as an indicator of pathogenicity [1,12]. The tlh gene, as the unique marker for V. parahaemolyticus identification, revealed in all the 74 isolates obtained from environmental or other sources that were included in our study [31] (Additional file 1).…”

“…WGS of V. parahaemolyticus isolates and comparative genomics analyses have revealed various mutations, chromosomal rearrangements and gene gain or loss events caused by duplication or horizontal gene transfer [10]. Bioinformatics methods such as the VPsero [11] and Kaptive database [12] have been developed to identify gene clusters associated with O-loci (lipopolysaccharide, LPS) and K-loci (capsular polysaccharide, CPS) for serotype determination of V. parahaemolyticus. Clinical isolates of V. parahaemolyticus also contain numerous virulence factors, including the thermostable direct hemolysin (tdh) and the tdh-related hemolysin (trh) [1,13].…”

Bacteriophage–Host Interactions and the Therapeutic Potential of Bacteriophages

“…A bioinformatic tool, Kaptive, was developed to rapidly identify capsule and lipopolysaccharide (K and O) types of K. pneumoniae and A. baumannii [ 215 ]. Recently, Vibrio parahaemolyticus was added to this database [ 216 ]. Rapid capsule-typing tools have several advantages over traditional capsule typing which includes serological reactivity assays or polymerase chain reaction-based sequencing [ 217 ].…”

Therapeutic Potential of Bacteriophage-derived Proteins

“…Bioinformatic tools such as Kaptive was developed to rapidly identify capsule and lipopolysaccharide (K and O) types of K. pneumoniae and A. baumannii [211]. Recently, Vibrio parahaemolyticus was added to this database [212]. Rapid capsule typing tools have several advantages over traditional capsule typing which includes serological reactivity assays or polymerase chain reaction-based sequencing [213].…”