Bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis : bioinformatic analysis using a tailored genomics framework

• Type: Article in International Scientific Journal
• Date: 2024

Authors

Tedim, AP (Author) Other; Almeida-Santos, AC (Author) Other; Lanza, VF (Author) Other; Novais, Carla (Author) FFUP; Coque, TM (Author) Other; Freitas, AR (Author) Other; Peixe, L (Author) Other

Journal

Title: Applied and Environmental Microbiology

ISSN: 0099-2240

Publisher: American Society for Microbiology

Indexing

ISI Web of Knowledge - 0 Citations

Scopus - 0 Citations

Other information

Authenticus ID: P-017-649

DOI: 10.1128/aem.01376-24

Abstract (EN): <jats:title>ABSTRACT</jats:title> <jats:sec> <jats:title/> <jats:p> Multidrug-resistant <jats:italic>Enterococcus faecium</jats:italic> strains represent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins to <jats:italic>E. faecium</jats:italic> ¿s adaptability remains poorly explored. <jats:italic>E. faecium</jats:italic> , within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filtered <jats:italic>E. faecium</jats:italic> and <jats:italic>Enterococcus lactis</jats:italic> (former <jats:italic>E. faecium</jats:italic> clade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged between <jats:italic>E. faecium</jats:italic> and <jats:italic>E. lactis</jats:italic> , highlighting species-specific adaptations. <jats:italic>E. faecium</jats:italic> strains from hospitalized patients were significantly enriched in bacteriocins as enterocin A and bacteriocins 43 (or T8), AS5, and AS11. These bacteriocin genes were strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18 <jats:italic>rep</jats:italic> 2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Such bacteriocin arsenal likely enhances the adaptability and competitive fitness of <jats:italic>E. faecium</jats:italic> in the nosocomial environment. By combining a novel tailored database, whole-genome sequencing, and epidemiological data, our work elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins in <jats:italic>E. faecium</jats:italic> and provides a framework for elucidating bacteriocin landscapes in other organisms. Characterizing species- and strain-level differences in bacteriocin profiles may reveal determinants of ecological adaptation, and translating these discoveries could further inform strategies to exploit bacteriocins against high-risk clones. </jats:p> </jats:sec> <jats:sec> <jats:title>IMPORTANCE</jats:title> <jats:p>This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution in the adaptation to different environments. It underscores the importance of placing increased emphasis on genetic platforms carrying bacteriocins as well as on cryptic plasmids that often exclusively harbor bacteriocins since bacteriocin production can significantly contribute to plasmid maintenance, potentially facilitating their stable transmission across generations. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unraveling the therapeutic and biotechnological potential of bacteriocins.</jats:p> </jats:sec>

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 15