Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions

• Published in: BMC genomics Vol. 25; no. 1; p. 28
• Main Authors: Choi, Dae Gyu, Baek, Ju Hye, Han, Dong Min, Khan, Shehzad Abid, Jeon, Che Ok
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03.01.2024; BioMed Central; BMC
• Subjects: Adaptive evolution; Amino acids; Analysis; Animals; Anti-Bacterial Agents; Antibiotic resistance; Antibiotics; Bacteria; Bacteriocins; Carbon; Clustering; Drug resistance in microorganisms; Enterococcus; Enterococcus faecium; Enterococcus lactis; Evolution; Evolution & development; Fermentation; Food; Food sources; Gene transfer; Genes; Genomes; Genomics; Horizontal gene transfer; Horizontal transfer; Humans; Inflammatory bowel disease; Lactic acid; Lactic acid bacteria; Metabolism; Nosocomial infections; Pangenome; Phylogenetics; Phylogeny; Strains (organisms); Tetracycline; Tetracyclines; Virulence; Virulence (Microbiology); Adaptive evolution; Enterococcus faecium; Pangenome; Antibiotic resistance; Enterococcus lactis; Horizontal gene transfer
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09945-7

Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.