Comparative genome analysis of Lactococcus garvieae using a suppression subtractive hybridization library: discovery of novel DNA signatures

• Published in: FEMS microbiology letters 2011-12, Vol.325 (1), p.77-84
• Main Authors: Kim, Wonyong, Park, Hee Kuk, Thanh, Hien Dang, Lee, Bo-Young, Shin, Jong Wook, Shin, Hyoung-Shik
• Format: Article
• Language: English
• Subjects: Animals; Bacterial Proteins - genetics; Bacteriological Techniques - methods; Bacteriology; Biological and medical sciences; Cloning; Comparative Genomic Hybridization - methods; Deoxyribonucleic acid; DNA; DNA Primers - genetics; DNA, Bacterial - genetics; Fishes; Fundamental and applied biological sciences. Psychology; Genes, Bacterial; genome; Genome, Bacterial; Genomes; Humans; Hybridization; Lactococcus; Lactococcus - genetics; Lactococcus garvieae; Lactococcus lactis; Microbiology; Miscellaneous; Nucleotides; Phylogeny; Polymerase Chain Reaction - methods; Primers; rRNA 16S; Sensitivity and Specificity; Species; SSH; Virulence Factors - genetics
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2011.02414.x

Abstract Lactococcus garvieae, the pathogenic species in the genus Lactococcus, is recognized as an emerging pathogen in fish, animals, and humans. Despite the widespread distribution and emerging clinical significance of L. garvieae, little is known about the genomic content of this microorganism. Suppression subtractive hybridization was performed to identify the genomic differences between L. garvieae and Lactococcus lactis ssp. lactis, its closest phylogenetic neighbor, and the type species of the genus Lactococcus. Twenty-seven clones were specific to L. garvieae and were highly different from Lactococcus lactis in their nucleotide and protein sequences. Lactococcus garvieae primer sets were subsequently designed for two of these clones corresponding to a pyrH gene and a novel DNA signature for application in the specific detection of L. garvieae. The primer specificities were evaluated relative to three previously described 16S rRNA gene–targeted methods using 32 Lactococcus and closely related strains. Both newly designed primer sets were highly specific to L. garvieae and performed better than did the existing primers. Our findings may be useful for developing more stable and accurate tools for the discrimination of L. garvieae from other closely related species.