Enterococcus faecalis

(aka Streptococcus faecalis)

Bacteria
General | Carbohydrate O/F | Substrate utilisation | Enzymes | Metabolites | Antibiotics

Overview

  • Enterococcus faecalis, (aka Streptococcus faecalis), is a Gram-positive, non-spore-forming, facultatively anaerobic, variably-motile, coccus bacterium. It has been detected in at least 29 gut microbiome compilation studies or metastudies. The DNA G+C content is 37-40%. Enterococcus faecalis is often a widespread coloniser of gut. (Schleifer1984; Svec2011Bergey; Terekhov2018; Rossi2016)



  • This organism has been recovered from human faeces, clinical sources (blood, sputum, wound, urine), and animal sources. The risk classification (www.baua.de) for this organism is 2, i.e., risk of individual infection, but low risk of spread. It is an opportunistic pathogen. Is a known gut commensal.
    • QUIRKS
  • Huycke MM, Abrams V, Moore DR. Enterococcus faecalis produces extracellular superoxide and hydrogen peroxide that damages colonic epithelial cell DNA. Carcinogenesis 2002; 23: 529–36. This organism also produces D-lactate, which could be linked to cronic fatigue syndrome (Sheedy2009). Found in human breast milk (Jeurink2013).
    • GENERAL CHARACTERISTICS (Schleifer1984); (Svec2011Bergey);
    Character Response
  • Substrates hydrolysed or digested:
  • aesculin; hippurate;
  • ±
  • Strain-dependent hydrolysis or digestion:
  • gelatin;
  • 🧂
  • Salt tolerance:
  • tolerates 6.5% salt;
  • pH
  • Acidity tolerance:
  • tolerates pH 9.6;
  • H+
  • Acid from carbohydrates usually produced:
  • L-arabinose; fructose; galactose; glucose; mannose; ribose; amygdalin; cellubiose; gentiobiose; lactose; maltose; raffinose; sucrose; trehalose; mannitol; sorbitol; arbutin; N-Ac glucosamine; salicin;
  • ⥅
  • Substrates assimilated or utilised:
  • gluconate; melibiose; arginine; hippurate; serine; citrate; malate; pyruvate;
  • Active enzymes:
  • Ala arylamidase; arginine dihydrolase; esterase C4; esterase lipase C8; β-galactosidase; β-glucosidase; Gly arylamidase; Leu arylamidase; Leu-Gly arylamidase; pyrrolidine arylamidase;
    • SPECIAL FEATURES (Schleifer1984); (Svec2011Bergey);
    Character Response
  • ✗
  • Metabolites not produced:
  • indole;
  • ✓
  • VP test:
  • active
  • ✗
  • Haemolysis:
  • absent
  • ✗
  • Nitrate:
  • not reduced
  • ✗
  • Pigments:
  • not produced
    • RESPONSE TO ANTIBIOTICS (Goldstein2013a); (Citron2012a); (Goldstein2000); (Citron1997);
    Class Active Resistant
  • Penicillins:
  • amoxicillin; amoxicillin-clavulanic acid; ampicillin; ampicillin-sulbactam; imipenem; penicillin G; piperacillin-tazobactam;
  • aztreonam; ertapenem; meropenem; oxacillin;
  • Cephalosporins:
  • cefaclor; cefalexin; cefdinir; cefepime; cefixime; cefoperazone; cefotaxime; cefotetan; cefoxitin; cefpirom; cefpodoxime; cefprozil; ceftazidime; cefuroxime;
  • Macrolides:
  • clarithromycin; fidaxomicin; roxithromycin;
  • quinupristin-dalfopristin; spiramycin;
  • Tetracyclines:
  • tigecycline;
  • minocycline; tetracycline;
  • Quinolines:
  • ciprofloxacin; clinafloxacin; garenoxacin; moxifloxacin; sparfloxacin; trovafloxacin;
  • nalidixic-acid;
  • Aminoglycosides:
  • gentamicin;
  • amikacin; netilmycin; streptomycin;
  • Polypep/ketides:
  • rifampicin;
  • Heterocycles:
  • nitrofurantoin;
  • chloramphenicol; metronidazole;
  • Vancomycins:
  • vancomycin;
  • Miscellaneous antibiotics:
  • daptomycin; linezolid;
  • clindamycin;

  • Linezolid (LZD) has become one of the most important antimicrobial agents for infections caused by gram-positive bacteria, including those caused by Enterococcus species. LZD-resistant (LR) genetic features include mutations in 23S rRNA/ribosomal proteins, a plasmid-borne 23S rRNA methyltransferase gene cfr, and ribosomal protection genes (optrA and poxtA). Recently, a cfr gene variant, cfr(B), was identified in a Tn6218-like transposon (Tn) in a Clostridioides difficile isolate. Complete genome sequencing of KUB3006 revealed that it carried cfr(B) on a chromosomal Tn6218-like element. Surprisingly, this Tn6218-like element was almost (99%) identical to that of C. difficile Ox3196. The LR E. faecalis KUB3006 possesses a notable Tn6218-like-borne cfr(B) and plasmid-borne optrA, and this finding raises further concerns regarding the possible declining effectiveness of LZD treatment in the future. [PMID: 30410481]

  • GutFeeling KnowledgeBase COMMENTS [Website]

    Enterococcus faecalis is a lactic acid-producing gram-positive bacterium that is commonly found in the intestinal tracts of humans and animals and is implicated in several fatal clinical infections, such as bacteremia and infective endocarditis. [PMID: 30410481]

  • Andrewes, FW & TJ Horder (1906). A study of the streptococci pathogenic for man. Lancet 2: 708-713.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Firmicutes Class:  Bacilli Order:  Lactobacillales Family:  Enterococcaceae Genus:  Enterococcus Alt. name:  Streptococcus faecalis Gram stain:  + O2 Relation.:  facultatively anaerobic Spore:  No spore Motility:  vr Morphology:  Coccus Pigment:  neg
    Health:  Unknown
    Source:  human faeces, clinical sources (blood, sputum, wound, urine), and animal sources
    DNA G+C(%):  37-40
    NaCl >6%:  6.5(+)
    pH >8:  9.6(+)
    		Aesculin:  + Urea:  neg Gelatin:  d(neg) Starch:  neg Hippurate:  +
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    Arabinose:  vr D-Arabinose:  neg L-Arabinose:  + Fructose:  + Fucose:  neg D-Fucose:  neg Galactose:  + Glucose:  + Mannose:  + D-Lyxose:  neg Rhamnose:  vr Ribose:  + Sorbose:  neg L-Sorbose:  neg D-Tagatose:  vr Xylose:  neg L-Xylose:  neg Cellubiose:  + Gentiobiose:  + Lactose:  + Maltose:  + Melezitose:  neg Melibiose:  neg Sucrose:  d(+) Trehalose:  + Turanose:  neg Amygdalin:  + Dextrin:  vr Glycogen:  neg Inulin:  neg Starch:  neg Adonitol:  neg D-Arabitol:  neg L-Arabitol:  neg Dulcitol:  neg Erythritol:  neg Glycerol:  vr Inositol:  neg Mannitol:  + Sorbitol:  d(+) Xylitol:  neg Arbutin:  + Gluconate:  vr 2-Ketogluconate:  neg 5-Ketogluconate:  neg Me-α-D-Glc:  neg Me-α-D-Mann:  vr Me-Xyloside:  neg NAc-α-GA:  + Salicin:  +
    SUBSTRATE ASSIMILATION & UTILISATION
    Monosaccharide util/assim Oligosaccharide util/assim Other carboh. util/assim Amino acid util/assim Organic acid util/assim
    Melibiose:  + Gluconate:  + Arg:  + Hippurate:  + Ser:  + Citrate:  + Malate:  + Pyruvate:  +
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Catalase:  vr Urease:  neg α-Fucosidase:  neg α-Galactosidase:  neg β-Galactosidase:  + α-Glucosidase:  neg β-Glucosidase:  + β-Glucuronidase:  neg α-Mannosidase:  neg β-Mannosidase:  vr ArgDH:  + γ-Glu transf.:  neg GluDC:  neg OrnDC:  neg AlanineAA:  + AlaPheProAA:  neg GluGluAA:  neg GlyAA:  + LeuAA:  + LeuGlyAA:  + PyrrolidAA:  + AlkalineP:  neg AcidP:  neg Esterase(C4):  + EstLip(C8):  + Lipase:  neg Lipase(C14):  neg
    METABOLITES - PRODUCTION & USE
    Fuel Usable Metabolites Metabolites Released Special Products Compounds Produced

    		Indole:  neg Pigment:  neg
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    amoxicillin:  S(0.78)
    Augmentin:  S(MIC50): 0.5, MIC90: 1, RNG: (≤0.03->16)
    ampicillin:  S(MIC50): 1, MIC90: 4, RNG: (0.25–4)
    amp-sulb:  S(MIC50): 1, MIC90: 4, RNG: (0.25–4)
    aztreonam:  R(MIC50): >128, MIC90: ≥128, RNG: (≥128->128)
    oxacillin:  R(MIC50): >8, MIC90: >8, RNG: (0.5->8)
    penicillin:  Var(MIC50): 4, MIC90: 16, RNG: (0.12->32)
    penicillin_G:  S(MIC50): 0.25, MIC90: 2, RNG: (≤0.015–2)
    piperacillin:  Var(MIC50): 4, MIC90: 4, RNG: (2-4)
    piper-taz:  S(MIC50): 8, MIC90: 16, RNG: (2–16)
    ertapenem:  R(MIC50): >8, MIC90: >16, RNG: (0.06->16)
    imipenem:  S(MIC50): 1, MIC90: 2, RNG: (0.06->128)
    meropenem:  R(MIC50): 8, MIC90: 16, RNG: (4-16)
    cefaclor:  R(MIC50): 64, MIC90: 64, RNG: (32-64)
    cefalexin:  R(>32/>32)
    cefdinir:  R(MIC50): 4, MIC90: 128, RNG: (0.5->128)
    cefepime:  R(MIC50): 16, MIC90: 32, RNG: (16->64)
    cefixime:  R(MIC50): >32, MIC90: >128, RNG: (4->128)
    cefoperazone:  R(MIC50): 32, MIC90: 32, RNG: (0.5->128)
    cefotaxime:  R(MIC50): >128, MIC90: >128, RNG: (0.25->128)
    cefotetan:  R(MIC50): >128, MIC90: >128, RNG: (4–>128)
    cefoxitin:  R(MIC50): >32, MIC90: >32, RNG: (>32)
    cefpirom:  R(MIC50): 8, MIC90: 32, RNG: (2-128)
    cefpodoxime:  R(MIC50): >32, MIC90: >128, RNG: (1->128)
    cefprozil:  R(8/8)
    ceftazidime:  R(MIC50): >128, MIC90: >128, RNG: (4->128)
    cefuroxime:  R(MIC50): >64, MIC90: >64, RNG: (>64-?)
    amikacin:  R(128)
    gentamicin:  S, vr
    kanamycin:  RNG: (7.5-)
    netilmycin:  R(≥2.5)
    streptomycin:  R(MIC50): >1000, MIC90: >2000, RNG: (≤1000->2000)
    azithromycin:  Var(MIC50): 0.25, MIC90: >32, RNG: (0.06–>32)
    erythromycin:  Var(MIC50): 2, MIC90: 32, RNG: (0.5->32)
    fidaxomicin:  S(MIC50): 2, MIC90: 4, RNG: (0.5–4)
    clarithromycin:  S(1.56)
    pristinamycin:  RNG: (0.125-16)
    quin-dalf:  R(MIC50): 32, MIC90: 32, RNG: (2-128)
    roxithromycin:  S(0.5)
    spiramycin:  R(10)
    linezolid:  S(MIC50): 2, MIC90: 2, RNG: (0.25-64)
    ciprofloxacin:  S(MIC50): 1, MIC90: 1, RNG: (0.5-4)
    clinafloxacin:  S(MIC50): 0.125, MIC90: 0.13, RNG: (0.06-0.25)
    garenoxacin:  S(MIC50): 0.25, MIC90: 2, RNG: (0.12-4)
    gatifloxacin:  Var(MIC50): 0.5, MIC90: 16, RNG: (0.25-16)
    gemifloxacin:  Var(MIC50): 0.12, MIC90: 4, RNG: (0.06-4)
    levofloxacin:  Var(MIC50): 1, MIC90: 32, RNG: (0.25-32)
    moxifloxacin:  S(MIC50): 0.125, MIC90: 0.25, RNG: (0.016-0.5)
    nalidixic-acid:  R(MIC50): >32, MIC90: >32, RNG: (>32-?)
    norfloxacin:  Var
    ofloxacin:  Var(MIC50): 2, MIC90: 64, RNG: (2->128)
    sparfloxacin:  S(MIC50): 0.5, MIC90: 1, RNG: (0.25-1)
    trovafloxacin:  S(MIC50): 0.125, MIC90: 0.5, RNG: (0.015–1)
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    doxycycline:  Var(MIC50): 1, MIC90: 8, RNG: (0.064-32)
    minocycline:  R(MIC50): 16, MIC90: 32, RNG: (0.06-32)
    oxytetracycline:  RNG: (0.78->100)
    tetracycline:  R(MIC50): 32, MIC90: 128, RNG: (0.12->128)
    tigecycline:  S(MIC50): 0.12, MIC90: 0.25, RNG: (0.06-0.25)
    teicoplanin:  Var(MIC50): >0.5, MIC90: >16, RNG: (≤0.12->16)
    vancomycin:  R(MIC50): >16, MIC90: >16, RNG: (0.5–>16)
    rifampicin:  S(MIC50): 2, MIC90: 4, RNG: (0.015->128)
    chloramphenicol:  R(MIC50): >8, MIC90: >16, RNG: (0.25->16)
    metronidazole:  R(MIC50): >512, MIC90: >512, RNG: (>512)
    nitrofurantoin:  Sens
    SXT:  Var(MIC50): ≤0.5, MIC90: 4
    co-trimoxazole:  Var(MIC50): 1, MIC90: >1, RNG: (≤0.5->1)
    clindamycin:  R(MIC50): >16, MIC90: >16, RNG: (2–>16)
    lincomycin:  RNG: (0.39->100)
    daptomycin:  S(MIC50): 1, MIC90: 1, RNG: (0.25-2)

    References

    SPECIFIC REFERENCES FOR ENTEROCOCCUS FAECALIS
  • Schleifer1984 - Transfer of Streptococcus faecalis and Streptococcus faecium to the Genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov.
  • Svec2011Bergey - Bergey's manual of systematic bacteriology. Vol. 3, The Firmicutes. Family Enterococcaceae, Genus I. Enterococcus
  • Terekhov2018 - Ultrahigh-throughput functional profiling of microbiota communities.
  • Rossi2016 - Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota.
  • Bojovic2020 - Gut Microbiota Dysbiosis Associated With Altered Production of Short Chain Fatty Acids in Children With Neurodevelopmental Disorders
  • Gao2020 - Functional Microbiomics Reveals Alterations of the Gut Microbiome and Host Co-Metabolism in Patients With Alcoholic Hepatitis
  • Balamurugan2008 - Real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer
  • Cassir2015 - Clostridium butyricum Strains and Dysbiosis Linked to Necrotizing Enterocolitis in Preterm Neonates
  • Gryp2020 - Isolation and Quantification of Uremic Toxin Precursor-Generating Gut Bacteria in Chronic Kidney Disease Patients
  • Lu2011 - Intestinal microbiota was assessed in cirrhotic patients with hepatitis B virus infection. Intestinal microbiota of HBV cirrhotic patients
  • Manor2016 - Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis
  • Sheedy2009 - Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome
  • Tarallo2019 - Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples
  • Goldstein2013a - Comparative in vitro activities of SMT19969, a new antimicrobial agent, against Clostridium difficile and 350 gram-positive and gram-negative aerobic and anaerobic intestinal flora isolates.
  • Citron2012a - Comparative in vitro activities of LFF571 against Clostridium difficile and 630 other intestinal strains of aerobic and anaerobic bacteria.
  • Goldstein2000 - Comparative in vitro activities of GAR-936 against aerobic and anaerobic animal and human bite wound pathogens.
  • Citron1997 - Comparative in vitro activities of trovafloxacin (CP-99,219) against 221 aerobic and 217 anaerobic bacteria isolated from patients with intra-abdominal infections.
  • Watanabe1981 - Studies on streptococci. I. Distribution of fecal streptococci in man.
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR ENTEROCOCCUS FAECALIS
  • Almeida2019 - A new genomic blueprint of the human gut microbiota.
  • Aujoulat2014 - Temporal dynamics of the very premature infant gut dominant microbiota.
  • Benno1986 - Comparison of the fecal microflora in rural Japanese and urban Canadians.
  • Benno1989 - Comparison of fecal microflora of elderly persons in rural and urban areas of Japan.
  • Byrd2020 - Stability and dynamics of the human gut microbiome and its association with systemic immune traits.
  • Cassir2015 - Clostridium butyricum Strains and Dysbiosis Linked to Necrotizing Enterocolitis in Preterm Neonates
  • Chen2020 - Structural and Functional Characterization of the Gut Microbiota in Elderly Women With Migraine
  • Chen2020a - Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease
  • Chung2019 - Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.
  • Dubinkina2017 - Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease
  • Finegold1977 - Fecal microbial flora in Seventh Day Adventist populations and control subjects.
  • Forster2019 - A human gut bacterial genome and culture collection for improved metagenomic analyses.
  • Hu2019 - The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients
  • Jie2017 - The gut microbiome in atherosclerotic cardiovascular disease
  • Karlsson2013 - Gut metagenome in European women with normal, impaired and diabetic glucose control
  • King2019 - Baseline human gut microbiota profile in healthy people and standard reporting template.
  • Lagier2016 - Culture of previously uncultured members of the human gut microbiota by culturomics.
  • MacFarlane2004 - Chemotaxonomic analysis of bacterial populations colonizing the rectal mucosa in patients with ulcerative colitis.
  • Mangin2004 - Molecular inventory of faecal microflora in patients with Crohn's disease.
  • New2022 - Collective effects of human genomic variation on microbiome function.
  • Pfleiderer2013 - Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample.
  • RajilicStojanovic2014 - The first 1000 cultured species of the human gastrointestinal microbiota.
  • Tyakht2013 - Human gut microbiota community structures in urban and rural populations in Russia.
  • Urban2020 - Altered Fecal Microbiome Years after Traumatic Brain Injury
  • Wang2020a - Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents
  • Woodmansey2004 - Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects.
  • Yang2020 - Species-Level Analysis of Human Gut Microbiota With Metataxonomics.
  • Yang2020a - Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families
  • Zeller2014 - Potential of fecal microbiota for early-stage detection of colorectal cancer
  • Zou2019 - 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.
  • ...............................
    • GENERAL REFERENCES FOR ENTEROCOCCUS FAECALIS
  • Ludwig2009 - Revised road map to the phylum Firmicutes.
  • CCUG - Culture Collection University of Gothenburg - Entire Collection
    • Added: February 08, 2021