Global diversity of enterococci and description of 18 previously unknown species

Global diversity of enterococci and description of 18 previously unknown species

Schwartzman, Julia A. (Harvard Medical School; University of Southern California)
Lebreton, Francois (Harvard Medical School; Walter Reed Army Institute of Research)
Salamzade, Rauf (Massachusetts Institute of Technology; University of Wisconsin School of Medicine and Public Health)
Shea, Terrance (Massachusetts Institute of Technology)
Martin, Melissa J. (Harvard Medical School; Walter Reed Army Institute of Research)
Schaufler, Katharina (Harvard Medical School; Greifswald University; Christian-Albrechts-Universität zu Kiel)
Urhan, A. (TU Delft Pattern Recognition and Bioinformatics; Massachusetts Institute of Technology)
Abeel, T.E.P.M.F. (TU Delft Pattern Recognition and Bioinformatics; Massachusetts Institute of Technology)
Camargo, Ilana L.B.C. (Universidade de São Paulo)

2024

Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.

antibiotic resistance
Enterococcus
genomics
global diversity
host microbe interaction

http://resolver.tudelft.nl/uuid:9a1569e1-d573-43e2-93a4-257dfd6cd22f

https://doi.org/10.1073/pnas.2310852121

1091-6490

Proceedings of the National Academy of Sciences of the United States of America, 121 (10)

Institutional Repository

journal article

© 2024 Julia A. Schwartzman, Francois Lebreton, Rauf Salamzade, Terrance Shea, Melissa J. Martin, Katharina Schaufler, A. Urhan, T.E.P.M.F. Abeel, Ilana L.B.C. Camargo, More Authors