Lactococcus garvieae is one of the deadliest, emerging zoonotic bacterial pathogen, causes fatal haemorrhagic septicaemia in a wide range of cultured fish species and animals, worldwide. Here, we report the whole genome sequence (WGS) of L. garvieae type strain RTCLI04, isolated from farmed rainbow trout, Oncorhynchus mykiss in India showing clinical signs of “warm water lactococcosis”. The genome of L. garvieae RTCLI04 is a single circular chromosome of 2,054,885 base pairs (bp), which encodes 1,993 proteins and has G+C content of 39%.
The WGS analysis revealed the presence of 51 genes for tRNAs (including 2 pseudogenes), 6 genes for rRNAs (4 genes for 5s rRNA; 1 gene for 16s rRNA and 1 gene for 23s rRNA), 5 virulent domains and 28 different genetic pathways. Comparative analysis of L. garvieae RTCLI04 genome with two existing reference genomes, L. garvieae ATCC 49156 (avirulent strain) and L. garvieae Lg2 (virulent strain) revealed that pangenome consisted of 2,239 protein-coding genes in which 1,850 (83%) genes is core gene, 389 genes (17%) is dispensable gene and 19 genes were unique to our strain. Similar to L. garvieae ATCC 49156, L. garvieae RTCLI04 of current study lacks genomic island of 16.5 Kb capsule gene cluster. In addition, 39 virulence associated genes (VAGs) including hly1,-2,-3; PavA, PsaA; eno; LPxTG containing surface proteins 1, 2, 3 and 4; pgm, sod and 29 antimicrobial resistant genes (ARGs) including mefE (clindamycin), srmB (lincomycin), dfrA26 (trimethoprim), gyrB (nalidixic acid), arr-3 (rifampin), otrB (tetracycline), aac(6)-Ic (tobramycin), IrgB (penicillin), mecA (oxacillin), vanRB (vancomycin) and mfpA (fluoroquinolone) were also present in the genome of L. garvieae RTCLI04. Our study provides new insight into understanding the virulence mechanism, AMR and development of therapeutic measures against L. garvieae disease outbreak in aquaculture.