GENOMIC COMPARISON OF Vibrio STRAINS RESPONSIBLE FOR AHPND/EMS OF SHRIMPS

In 2013 V. parahaemolyticus was characterized for the first time as an important shrimp pathogen and causative agent of the acute hepatopancreatic necrosis disease (AHPND), most commonly known as early mortality syndrome (EMS) (Tran et al. 2013; Soto-Rodriguez et al. 2015). A plasmid had been identified as the main responsible element that produces a potent delta-endotoxin (Lee et al., 2015). Whole genome sequencing was done to V. parahaemolyticus strains from China (Yang et al. 2014), Thailand (Kondo et al. 2014; Yang et al. 2014), Vietnam (Tang & Lightner 2014), and Mexico (Gomez-Gil et al. 2014) with the aim to identify all the pathogenicity mechanism involved.

Bioinformatic genomic comparisons were done with six sequenced Mexican isolates and related V. parahaemolyticus strains publicly available in GenBank for a total of 22 genomes. Genome of the highly pathogenic isolate M0904 was used as a reference genome for further genomics comparisons.

The multilocus sequence analysis (MLSA) concatenated tree (11,961 bp, Fig. 1) of seven housekeeping genes clearly showed that most of the isolates are independent strains although some could not be differentiated at this level and thus considered MLSA clones because they have similarly values equal or above 99.9 %.

Apart from the common two chromosomes found in all vibrios, extra chromosomal elements found in these strains were: 1) a 73.3 Kbp IncP type plasmid (pVp-AP, 45.0% GC), 2) a 73.0 Kbp IncP plasmid (pVp-AP2, 45.6% GC), and 3) a 37.0 Kbp 45.4% GC circular tailed phage. Several inserted sequences were also detected in the chromosomes of M0904.

All major pathogenicity mechanisms were detected in strain M0904, classified according to the Virulence Factor of Pathogenic Bacteria database (VFPB). In chromosome I, up to 55 mechanisms were located, and in chromosome II 45 mechanisms were detected. V. parahaemolyticus pathogenic strains show diverse proteomic similarity values ranging from as low as 49.4% to 98.8%. Strains isolated from Asia have more similar proteomes (74.5 - 98.9 %) than Mexican strains (53.6 - 86.5 %). The core genome of all V. parahaemolyticus strains is composed of 3,284 genes, 24.3 % of the total pangenome. The core genome of only the pathogenic strains has 3,558 genes.