VPsero: Rapid Serotyping of Vibrio parahaemolyticus Using Serogroup-Specific Genes Based on Whole-Genome Sequencing Data

Abstract

Vibrio parahaemolyticus has emerged as a significant enteropathogen in human and marine habitats worldwide, notably in regions where aquaculture products constitute a major nutritional source. It is a growing cause of diseases including gastroenteritis, wound infections, and septicemia. Serotyping assays use commercially available antisera to identify V. parahaemolyticus strains, but this approach is limited by high costs, complicated procedures, cross-immunoreactivity, and often subjective interpretation. By leveraging high-throughput sequencing technologies, we developed an in silico method based on comparison of gene clusters for lipopolysaccharide (LPSgc) and capsular polysaccharide (CPSgc) by firstly using the unique-gene strategy. The algorithm, VPsero, which exploits serogroup-specific genes as markers, covers 43 K and all 12 O serogroups in serotyping assays. VPsero is capable of predicting serotypes from assembled draft genomes, outputting LPSgc/CPSgc sequences, and recognizing possible novel serogroups or populations. Our tool displays high specificity and sensitivity in prediction toward V. parahaemolyticus strains, with an average sensitivity in serogroup prediction of 0.910 for O and 0.961 for K serogroups and a corresponding average specificity of 0.990 for O and 0.998 for K serogroups.

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

“…Of the total set of 831 selected genomes from Genbank (n=775) and in-house sequenced genomes (n=56), 436 genomes had a known O-serotype and 294 genomes had a known K-serotype, whereas the PATRIC genomes had all unknown O- and K-loci serotypes. The O- and K-loci of the genomes with the known serotypes were all serotyped by the newly developed Kaptive databases and VPSero (14). Furthermore, performance of the Kaptive databases was tested and compared with VPSero by using the VPSero sequence data collection, deposited into CNGB Sequence Archive project CNP0000343 described by Bian et al (14).…”

“…The O- and K-loci of the genomes with the known serotypes were all serotyped by the newly developed Kaptive databases and VPSero (14). Furthermore, performance of the Kaptive databases was tested and compared with VPSero by using the VPSero sequence data collection, deposited into CNGB Sequence Archive project CNP0000343 described by Bian et al (14).…”

“…The genomic regions associated with the somatic synthesis locus (O-locus) and capsule synthesis locus (K-locus) for V. parahaemolyticus are generally found on the same genomic location (2,12,13), which makes it possible to locate and extract the O- and K-loci nucleotide sequences from whole genome sequencing data of V. parahaemolyticus strains. Recently, the algorithm VPsero was developed, which identified serogroup-specific genes as markers in silico , but only marker genes for 12 O- and 43 K-serotypes were covered (14).…”

Characterization of the Novel Phage vB_VpaP_FE11 and Its Potential Role in Controlling Vibrio parahaemolyticus Biofilms

“…V. parahaemolyticus has been classified to 13 types based on its LPS O antigens [19]. Phage host range was determined using 133 V. parahaemolyticus strains that represent the different O types.…”

Development of a Molecular Serotyping Scheme for Morganella morganii

“…An O-antigenic scheme of M. morganii was established in the 1970s to 1990s ( Vörös and Senior, 1990 ); however, the relevant antisera and the strains used for those studies are not currently available. The approach of traditional serotyping is limited by its high cost, high time and labor requirements, complicated procedures, cross-reactivity and subjective interpretation ( Sumrall et al, 2020 ; Bian et al, 2021 ; Chaiden et al, 2021 ). To address these issues, many DNA-based serotyping methods on variant platforms targeting specific genes involved in the synthesis of surface polysaccharide antigens have been developed ( Li et al, 2018 , 2020 ; Zürn et al, 2020 ; Ouattara et al, 2021 ).…”