Conditionally essential genes for survival during starvation in Enterococcus faecium E745

• Published in: BMC genomics Vol. 21; no. 1; p. 568
• Main Authors: de Maat, Vincent, Arredondo-Alonso, Sergio, Willems, Rob J L, van Schaik, Willem
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18-08-2020; BioMed Central; BMC
• Subjects: Bacteria; Cellular stress response; Complementation; Deletion mutant; Deoxyribonucleic acid; DNA; DNA repair; Enterococcus; Enterococcus faecium; Enterococcus faecium - genetics; Functional genomics; Gene deletion; Genes; Genes, Essential; Genetic aspects; Genomes; Genomics; Gram-Positive Bacterial Infections; Homeostasis; Hospitals; Humans; Infections; Metabolism; Mutants; Nosocomial infection; Nutrients; Pathogens; Physiological aspects; Population; Species diversity; Starvation; Stress response; Survival; Tn-seq; Universal stress protein; Netherlands; Enterococcus faecium; Starvation; Stress response; Functional genomics; Tn-seq
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-06984-2

The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among patients in hospitals. There is currently a lack of data on the mechanisms that are responsible for the ability of E. faecium to survive in the absence of nutrients.
We performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20 °C. A total of 24 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS was usp (locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant in usp, we were able to confirm that usp significantly contributes to survival in PBS and this defect was restored by in trans complementation. The usp gene is present in 99% of a set of 1644 E. faecium genomes that collectively span the diversity of the species.
We postulate that usp is a key determinant for the remarkable environmental robustness of E. faecium. Further mechanistic studies into usp and other genes identified in this study may shed further light on the mechanisms by which E. faecium can survive in the absence of nutrients for prolonged periods of time.