Comparative Genomics of Lactococcus spp. From Global Aquaculture Outbreaks Reveals Virulence Determinants, Antibiotic Resistance, and Phage Defence Mechanisms

Lactococcosis is a major bacterial disease impacting rainbow trout production in South Africa and Southeast Asia, particularly during summer. In this study, 15 isolates from affected aquaculture facilities were characterised, revealing Lactococcus petauri (n = 12) as the predominant species, rather than the traditionally recognised L. garvieae (n = 3). This indicates a potential shift in the aetiology of lactococcosis with implications for diagnosis and management. Genomic screening identified multiple virulence factors, including adhesins in 14 isolates, capsular polysaccharide biosynthesis genes in 12, and sortase-anchored proteins in all isolates, highlighting strain-specific differences in pathogenic potential. Antimicrobial resistance (AMR) profiling revealed ermB (n = 10) and tetS (n = 11), consistent with resistance to macrolides and tetracyclines commonly applied in aquaculture. Phenotypic susceptibility testing against eight antimicrobial agents showed uniform resistance to nalidixic acid (15/15 isolates), alongside resistance to trimethoprim (12/15), sulfamethoxazole (11/15), and ciprofloxacin and oxacillin (7/15 each). These phenotypic results, while not fully aligned with the ARG profile, reflect aquaculture-relevant antimicrobial exposures and indicate the presence of both intrinsic and acquired resistance mechanisms. Most (13/15) isolates contained 1-3 prophage regions, although none of these harboured any known virulence or AMR genes. However, they did genes encoding phage defence such as AbiD and R-M systems. This information is important when considering the potential development of phage therapy to control piscine disease. Together, these findings advance understanding of the epidemiology, pathogenicity, and resistance dynamics of Lactococcus species in aquaculture and underscore the need for sustainable strategies to mitigate lactococcosis outbreaks.