Database Authors
Summary The Gram-positive bacterium Enterococcus faecalis is a natural inhabitant of the mammalian gastrointestinal tract and is commonly found in soil, sewage, water, and food, frequently through fecal contamination. It can withstand oxidative stress, desiccation, extremes of temperature and pH, and it has high endogenous resistance to salinity, bile acids, detergents, and antibiotics [Klare01]. It is also an opportunistic pathogen that is becoming increasingly resistant to antimicrobial agents due to acquisition of resistance-conferring mobile genetic elements. Enterococci are resistant to cephalosporins, clindamycin, tetracycline, penicillinase-resistant penicillins such as oxacillin, and vancomycin [Tailor93, Huycke98]. In the past decades Enterococcus faecalis strains have emerged as the second to third most common cause of nosocomial infections, including urinary tract and soft tissue infections, bacteremia, and endocarditis [Murray90].

Enterococcus faecalis was originally isolated in 1906 under the name Streptococcus faecalis [Andrewes06]. In the following years the term Enterococcus was used frequently as a separate generic designation outside the Streptococci. However, a classification scheme proposed in 1937 separated Streptococci into four divisions, one of which was the enterococci [Sherman37]. It was only in 1984, after DNA-DNA and DNA-rRNA hybridizations showed that S. faecalis was distantly related to streptococci, that the organism was transferred to a new genus that was named Enterococcus [Schleifer84].

Enterococcus faecalis V583 was isolated in February 12th 1987 from a blood culture of a patient at the Barnes Hospital, St. Louis, Mo, that had received vancomycin previously. It was the first vancomycin-resistant clinical isolate reported in the United States [Sahm89]. Its genome was fully sequenced in 2003, revealing that over a quarter of the genome consists of mobile and/or exogenously acquired DNA, including seven probable integrated phage regions, 38 insertion elements, multiple conjugative and composite transposons, a pathogenicity island, and integrated plasmid genes [Paulsen03].

Enterococcus faecalis V583 possesses pathways for the utilization of more than 15 different sugars and has 35 PTS-type sugar transporters along with ABC-type and other sugar uptake systems. Even though it lacks a TCA cycle, it is able to respire aerobically when grown in the presence of hemin [Winstedt00, Portela14]. It is auxotrophic for seven amino acids, including L-histidine, L-tryptophan, L-arginine, L-methionine, and the branched-chain amino acids L-isoleucine, L-valine, and L-leucine [Veith15]. The organism is non-motile, and belongs to serotype CPS-C [Sahm89].

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 28.5 and MetaCyc [Caspi18] version 28.1 on 12-Apr-2024.

We thank Professor Jose Lemos and his team (University of Florida) and Professor Kimberly Kline and her team (University of Geneva) for their assistance in identifying recent advancements in E. faecalis research and relevant data collections for this PGDB.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0046683,3293,045211733,218,031NCBI Assembly:GCF_000007785.1
pTEF1867212266,320NCBI Assembly:GCF_000007785.1
pTEF267606157,660NCBI Assembly:GCF_000007785.1
pTEF321181217,963NCBI Assembly:GCF_000007785.1
Total:3,5033,195230783,359,974
Ortholog data available?Yes
Database Contents
Genes3,503
Pathways220
Enzymatic Reactions1,149
Transport Reactions63
Polypeptides3,201
Protein Complexes133
Enzymes704
Transporters287
Compounds1,074
Transcription Units2,486
tRNAs67
Transcriptional Regulation88
Protein Features3,950
GO Terms24,393
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Enterococcaceae
Enterococcus
Enterococcus faecalis
Enterococcus faecalis V583
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603978
NCBI BioProjectPRJNA224116
NCBI-Taxonomy226185
Geographic LocationBarnes Hospital, St. Louis, MO USA
Collection Date1987-02-10
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipcommensal
Pathogenicityhuman
Human Microbiome Body Sitegastrointestinal-tract
Annotation ProviderNCBI RefSeq
Annotation Date2024-03-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.7
Annotation CommentBest-placed reference protein set; GeneMarkS-2+


References

Andrewes06: Andrewes FW, Horder TJ (1906). "A study of the Streptococci pathogenic for man." The Lancet 168(4333);708-713.

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Huycke98: Huycke MM, Sahm DF, Gilmore MS (1998). "Multiple-drug resistant enterococci: the nature of the problem and an agenda for the future." Emerg Infect Dis 4(2);239-49. PMID: 9621194

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Klare01: Klare I, Werner G, Witte W (2001). "Enterococci. Habitats, infections, virulence factors, resistances to antibiotics, transfer of resistance determinants." Contrib Microbiol 8;108-22. PMID: 11764728

Murray90: Murray BE (1990). "The life and times of the Enterococcus." Clin Microbiol Rev 3(1);46-65. PMID: 2404568

Paulsen03: Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM (2003). "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis." Science 299(5615);2071-4. PMID: 12663927

Portela14: Portela CA, Smart KF, Tumanov S, Cook GM, Villas-Boas SG (2014). "Global metabolic response of Enterococcus faecalis to oxygen." J Bacteriol 196(11);2012-22. PMID: 24659768

Sahm89: Sahm DF, Kissinger J, Gilmore MS, Murray PR, Mulder R, Solliday J, Clarke B (1989). "In vitro susceptibility studies of vancomycin-resistant Enterococcus faecalis." Antimicrob Agents Chemother 33(9);1588-91. PMID: 2554802

Schleifer84: Schleifer K H, Kilpper-Balz R (1984). "Transfer of Streptococcus faecalis and Streptococcus faecium to the Genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov." International Journal of Systematic Bacteriology 34(1);31-34.

Sherman37: Sherman JM (1937). "The Streptococci." Bacteriol Rev 1(1);3-97. PMID: 16350049

Tailor93: Tailor SA, Bailey EM, Rybak MJ (1993). "Enterococcus, an emerging pathogen." Ann Pharmacother 27(10);1231-42. PMID: 8251694

Veith15: Veith N, Solheim M, van Grinsven KW, Olivier BG, Levering J, Grosseholz R, Hugenholtz J, Holo H, Nes I, Teusink B, Kummer U (2015). "Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism." Appl Environ Microbiol 81(5);1622-33. PMID: 25527553

Winstedt00: Winstedt L, Frankenberg L, Hederstedt L, von Wachenfeldt C (2000). "Enterococcus faecalis V583 contains a cytochrome bd-type respiratory oxidase." J Bacteriol 182(13);3863-6. PMID: 10851008


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