title: Lactococcus garvieae: where is it from? A first approach to explore the evolutionary history of this emerging pathogen.
abstract: The population structure and diversity of Lactococcus garvieae, an emerging pathogen of increasing clinical significance, was determined at both gene and genome level. Selected lactococcal isolates of various origins were analyzed by a multi locus sequence typing (MLST). This gene-based analysis was compared to genomic characteristics, estimated through the complete genome sequences available in database. The MLST identified two branches containing the majority of the strains and two branches bearing one strain each. One strain was particularly differentiated from the other L. garvieae strains, showing a significant genetic distance. The genomic characteristics, correlated to the MLST-based phylogeny, indicated that this "separated strain" appeared first and could be considered the evolutionary intermediate between Lactococcus lactis and L. garvieae main clusters. A preliminary genome analysis of L. garvieae indicated a pan-genome constituted of about 4100 genes, which included 1341 core genes and 2760 genes belonging to the dispensable genome. A total of 1491 Clusters of Orthologous Genes (COGs) were found to be specific to the 11 L. garvieae genomes, with the genome of the "separated strain" showing the highest presence of unique genes.
authors.affiliation: Department of Food, Environmental and Nutritional Sciences (DeFENS) - Division of Food Microbiology and Bioprocesses, Università degli Studi di Milano, Milan, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Ferrario
authors.affiliation: Department of Food, Environmental and Nutritional Sciences (DeFENS) - Division of Food Microbiology and Bioprocesses, Università degli Studi di Milano, Milan, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Ricci
authors.affiliation: Department of Life Sciences, Laboratory of Probiogenomics, Università di Parma, Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Department of Life Sciences, Laboratory of Probiogenomics, Università di Parma, Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Department of Life Sciences, Laboratory of Probiogenomics, Università di Parma, Parma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
authors.affiliation: Department of Food, Environmental and Nutritional Sciences (DeFENS) - Division of Food Microbiology and Bioprocesses, Università degli Studi di Milano, Milan, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Eraclio
authors.affiliation: Department of Food, Environmental and Nutritional Sciences (DeFENS) - Division of Food Microbiology and Bioprocesses, Università degli Studi di Milano, Milan, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Borgo
authors.affiliation: Department of Food, Environmental and Nutritional Sciences (DeFENS) - Division of Food Microbiology and Bioprocesses, Università degli Studi di Milano, Milan, Italy.
authors.forename: Maria Grazia
authors.initials: MG
authors.lastname: Fortina
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D016000:Cluster Analysis; D021821:Communicable Diseases, Emerging / Q000382:microbiology*; D019295:Computational Biology; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D017045:Lactococcus / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D012336:RNA, Ribosomal, 16S