A Virulent Phage Infecting Lactococcus garvieae, with Homology to Lactococcus lactis Phages

Abstract

A new virulent phage belonging to the Siphoviridae family and able to infect Lactococcus garvieae strains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only two L. garvieae strains out of 73 tested. Phage GE1 has a doublestranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacterium Lactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness of L. garvieae phage GE1 to L. lactis phages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58 L. lactis strains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor. Lactococcus garvieae is the etiological agent of lactococcosis, a pathology affecting a variety of fish species that is responsible for significant economic losses in both marine and freshwater aquacultures (1). In addition, L. garvieae has been associated with subclinical intramammary infections in cows (2). More recently, L. garvieae was associated with infections in humans and is now considered an opportunistic and potentially zoonotic pathogen (3, 4). In an effort to find its ecological niches, genetic investigations have revealed its presence, and sometimes dominance, in several habitats: river and sewage waters and raw and processed foods, including milk, meats, and vegetables (5-7).Despite growing attention, genomic characterization of L. garvieae progresses slowly, yet the evolutionary history and global diversity of this emerging pathogen are particularly interesting. The population structure and diversity of L. garvieae strains have been studied using comparative genome analysis, which led to the development of a multilocus sequence type (MLST) scheme to identify specific strains (8). These studies also revealed that L. garvieae is related to Lactococcus lactis, a nonpathogenic bacterium used for the manufacture of several fermented dairy products (9). Divergent genomic lineages were observed, with some ecotypes representing evolutionary intermediates between L. lactis and L. garvieae (8). The presence of insertion sequences (ISs) was also highly variable among L. garvieae strains (10). Analysis of these ISs within individual genomes revealed limited intragenomic sequence diversity, suggesting that many ISs in L. garvieae are evolutionarily young and may have been only recently acquired. Of note, the similarity of most L. garvieae ISs to L. lactis ISs suggests...

Characterization of prophages of Lactococcus garvieae

“…The recent isolation of a lytic phage infecting a strain of L. garvieae with significant similarities to dairy L. lactis phages belonging to the c2 and Q54 groups 14 , raised the question of whether the same was true for temperate L. garvieae phages and prophages. Moreover, since little data is available on MGEs that contribute to the evolution and adaptability of the L. garvieae species, we characterized an inducible temperate phage and analysed several prophages found within the genomes of L. garvieae strains available in public databases.…”

“…Finally, not much is known about phages infecting L. garvieae . To our knowledge, only two virulent phages of L. garvieae have been described and studied at the genomic level 14 , 15 , and more recently, a temperate L. garvieae phage induced from a strain isolated from a marine fish in Japan was characterized 16 .…”

Comparative Genomic Analyses of Lactococcus garvieae Isolated from Bovine Mastitis in China

“…Both tetS and tetM were associated with conjugative transposon-associated genes in isolates from healthy fish intestines ( 64 ). Most of the ISs in L. garvieae had substantial homology to Lactococcus lactis elements, implying movement of ISs between these 2 species that are phylogenetically closely related ( 65 , 66 ). That these 9 AMR genes were reported only in humans does not support the assertion that AMR genes are transferred to humans from fish or dairy products.…”

Comparative genomic analyses of Lactococcus garvieae isolated from bovine mastitis in China

“…Both tetS and tetM were associated with conjugative transposon-associated gene in isolates from healthy fish intestines ( 63 ). Most of the IS in L. garvieae had substantial homology to Lactococcus lactis elements, implying movement of IS between these 2 species that are phylogenetically closely related ( 64, 65 ). That these 9 AMR genes were only reported in humans does not support the assertion that AMR genes are transferred to humans from fish or dairy products.…”