Genomic characterization and pathogenicity analysis of the probiotic Vagococcus lutrae strain VL-18 causing severe skin lesions in warm-blooded animals

Abstract

Vagococcus sp. has been recently used in aquaculture as a probiotic for gilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax). However, the safety of this probiotic species remains largely unclear. In this study, V. lutrae strain VL-18, which caused a systematic skin lesion in a sea lion, was isolated from an aquarium in Dalian, China. Infection tests were performed to confirm its potential toxicity for European sea bass and mice. A chicken embryo chorioallantoic membrane (CAM) assay was conducted to validate the pathogenesis of this strain in chicken embryos. We further determined the complete genome of strain VL-18 by the PacBio RSII sequencing platform to understand its genetic basis as a potential pathogen. The results showed that V. lutrae strain VL-18 did not cause any noticeable tissue damage to European sea bass. However, intracutaneous injection of 1.8 × 108 CFU ml−1 V. lutrae strain VL-18, the LD50 value, caused severe skin lesions in mice. In addition, no mortality was observed for the mice after oral injection of strain VL-18, indicating that V. lutrae might infect mice via direct contact instead of oral administration. The chicken embryo CAM assay with 5 × 107 CFU ml−1 strain VL-18 caused 93.3% mortality of chicken embryos. Comparative genomic analysis of Vagococcus sp. revealed that the majority of Vagococcus sp. strains harboured multiple virulence factors, such as cytolysin, haemolysin, and serine protease, which resulted in potential pathogenesis in warm-blooded animals. This study confirmed that V. lutrae is an emerging zoonotic pathogen in warm-blooded animals. Therefore, the use of Vagococcus strains as probiotics should be immediately stopped. This is the first complete genome of Vagococcus lutrae. This study enhanced our understanding of the pathogenesis of a probiotic agent and underscored the safety assessment of probiotic strains, which are essential for the sustainable development of the aquaculture industry.