Characterization of Lactococcus isolated from diseased yellowtail in Japan using whole-genome sequencing.

Abstract

Lactococcus is the causative agent of lactococcosis in fish; however, its genetic characteristics in yellowtail from Japan have not been fully elucidated. In this study, we used whole-genome sequencing (WGS) to investigate virulence genes, antimicrobial resistance genes, and genetic relationships among 40 Lactococcus isolates from diseased yellowtail in 2021. Serotype II accounted for 82.5% of the isolates, while the remaining 17.5% comprised serotype I. No novel serotype (serotype III) was identified. Compared with serotype III Lactococcus strains isolated from other fish species, virulence gene patterns varied among serotypes, and the nucleotide sequences were distinct from those of serotype III. The isolates showed resistance rates of 87.5% to lincomycin and 12.5% for erythromycin, and no resistance to tetracycline, ampicillin, or florfenicol was detected. All erythromycin-resistant isolates carried the erm(B) gene on a plasmid. The core-genome single-nucleotide polymorphism-based phylogenetic tree showed clear clustering by serotype. Although no novel serotype was found in the yellowtail, isolates from other fish species exhibited distinct gene sequences encoding surface proteins, suggesting caution regarding vaccine efficacy. Because high lincomycin resistance was observed, susceptibility testing is recommended to guide appropriate antimicrobial selection. Overall, the elucidation of the WGS-based characteristics of field isolates of Lactococcus provides useful information for vaccine use and antimicrobial therapy for the prevention and treatment of lactococcosis.