Citrobacter amalonaticus

(aka Levinea amalonatica)

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

Overview

  • Citrobacter amalonaticus, (aka Levinea amalonatica), is a Gram-negative, non-spore-forming, facultatively anaerobic, motile, rod-shaped bacterium. It has been detected in at least 4 gut microbiome compilation studies or metastudies. The DNA G+C content is 51-52%. Citrobacter amalonaticus is probably a rare gut coloniser. (Farmer1985; Brenner1999; Young1971; Friederiksen2005Bergey)



  • This organism has been recovered from human faeces, clinical sources (ear, urine- CCUG), animals and soil. 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.
    • GENERAL CHARACTERISTICS (Farmer1985); (Brenner1999); (Young1971); (Friederiksen2005Bergey);
    Character Response
  • Substrates hydrolysed or digested:
  • arginine; urea;
  • H+
  • Acid from carbohydrates usually produced:
  • arabinose; L-arabinose; glucose; mannose; rhamnose; xylose; amygdalin; cellubiose; maltose; mucate; trehalose; mannitol; sorbitol; 5-ketogluconate;
  • ±
  • Strain-dependent acid from carbs:
  • lactose; glycerol;
  • ⥅
  • Substrates assimilated or utilised:
  • L-arabinose; cellubiose; ethanolamine; fructose; fucose; galactose; gluconate; gentiobiose; glucose; glycerol; lactose; maltose; maltotriose; mannitol; mannose; rhamnose; ribose; sorbitol; sorbose; trehalose; alanine; D-alanine; aspartate; glutamate; proline; acetate; aconitate; benzoate; citrate; fumarate; DL-glycerate; 3-hydroxybenzoate; 4-hydroxybenzoate; 2-ketogluconate; DL-lactate; malate; L-malate; mucate; propionate; L-tartrate; meso-tartrate; methyl-β-glucoside; glutamine; tricarballylate;
  • ±
  • Strain-dependent substrate utilisation:
  • δ-aminovalerate; caprate; 3-hydroxybutyrate; 2-ketoglutarate; methyl-β-galactoside;
  • Active enzymes:
  • arginine dihydrolase; catalase; β-galactosidase; β-glucosidase; ornithine decarboxylase; urease;
    • SPECIAL FEATURES (Farmer1985); (Brenner1999); (Young1971); (Friederiksen2005Bergey);
    Character Response
  • ✓
  • Metabolites produced:
  • indole;
  • ✗
  • Metabolites not produced:
  • H₂S;
  • ✓
  • Methyl red test:
  • active
  • ✗
  • VP test:
  • not active
  • ✓
  • ONPG test:
  • active
  • KCN growth:
  • growth observed
  • ✓
  • NO3➔NO2:
  • reduced
  • ✗
  • Pigments:
  • not produced
    • RESPONSE TO ANTIBIOTICS (Friederiksen2005Bergey); (Citron1997);
    Class Active Resistant
  • Penicillins:
  • amoxicillin-clavulanic acid; ertapenem; imipenem; piperacillin-tazobactam;
  • ampicillin; aztreonam; ticarcillin;
  • Cephalosporins:
  • cefepime; cefixime; cefotetan;
  • cefpodoxime; ceftazidime;
  • Macrolides:
  • erythromycin;
  • Tetracyclines:
  • tetracycline;
  • Quinolines:
  • ciprofloxacin; gatifloxacin; levofloxacin; nalidixic-acid; ofloxacin; trovafloxacin;
  • Aminoglycosides:
  • gentamicin;
  • Heterocycles:
  • chloramphenicol; fosfomycin; nitrofurantoin; trimethoprim;
  • fusidic-acid;
  • Vancomycins:
  • vancomycin;
  • Miscellaneous antibiotics:
  • polymyxin B;
  • clindamycin; lincomycin;

  • Brenner, D. J., Grimont, P. A., Steigerwalt, A. G., Fanning, G. R., Ageron, E., & Riddle, C. F. (1993). Classification of citrobacteria by DNA hybridization: designation of Citrobacter farmeri sp. nov., Citrobacter youngae sp. nov., Citrobacter braakii sp. nov., Citrobacter werkmanii sp. nov., Citrobacter sedlakii sp. nov., and three unnamed Citrobacter genomospecies. International Journal of Systematic Bacteriology, 43(4), 645–658.

    • Details

    GENERAL
    Lineage Physiology General Growth Tolerances Hydrol./digest./degr.
    Phylum:  Proteobacteria Class:  Gammaproteobacteria Order:  Enterobacterales Family:  Enterobacteriaceae Genus:  Citrobacter Alt. name:  Levinea amalonatica Gram stain:  neg O2 Relation.:  facultatively anaerobic Spore:  No spore Motility:  Swimming Morphology:  Rod Pigment:  neg
    Health:  Unknown
    Source:  human faeces, clinical sources (ear, urine- CCUG), animals and soil
    DNA G+C(%):  51-52
    		Urea:  + Gelatin:  neg Arginine:  d(+) Alginate:  neg DNA:  neg
    CARBOHYDRATE ACID FORMATION
    Monosaccharide O/F Oligosaccharide O/F Polysaccharide O/F Polyol O/F Other O/F
    Arabinose:  + L-Arabinose:  + Glucose:  + Mannose:  + Rhamnose:  + Xylose:  + Cellubiose:  + Lactose:  d Maltose:  + Melibiose:  neg Sucrose:  neg Trehalose:  + Amygdalin:  + Adonitol:  neg D-Arabitol:  neg L-Arabitol:  neg Dulcitol:  neg Erythritol:  neg Glycerol:  d Inositol:  neg Mannitol:  + Sorbitol:  + 5-Ketogluconate:  + Me-α-D-Glc:  neg Salicin:  neg
    SUBSTRATE ASSIMILATION & UTILISATION
    Monosaccharide util/assim Oligosaccharide util/assim Other carboh. util/assim Amino acid util/assim Organic acid util/assim
    L-Arabinose:  + Fructose:  + Fucose:  + Galactose:  + Glucose:  + D-Lyxose:  neg Mannose:  + Rhamnose:  + Ribose:  + Sorbose:  d(+) D-Tagatose:  neg Xylose:  neg Cellubiose:  + Gentiobiose:  + Lactose:  d(+) Maltose:  + Maltotriose:  + Melezitose:  neg Melibiose:  neg Raffinose:  neg Sucrose:  neg D-Turanose:  neg Trehalose:  + Adonitol:  neg D-Arabitol:  neg L-Arabitol:  neg Dulcitol:  neg Erythritol:  neg Aesculin:  neg Ethanolamine:  d(+) Gluconate:  + Glycerol:  + Inositol:  neg Mannitol:  + Me-α-D-Glc:  neg Sorbitol:  + Xylitol:  neg Ala:  + D-Ala:  + 4-Aminobutyrate:  neg 5-Aminovalerate:  d Asp:  + Betaine:  neg Glu:  + Histamine:  neg His:  neg Pro:  d(+) Trigonelline:  neg Tryptamine:  neg Trp:  neg Tyr:  neg Acetate:  + Aconitate:  cis(+) trans(neg) Benzoate:  d(+) Caprate:  d(neg) Caprylate:  neg Citrate:  + Fumarate:  + Glutarate:  neg DL-Glycerate:  + 3-Hydroxybutyrate:  d(neg) 3-Hydroxybenzoate:  + 4-Hydroxybenzoate:  + Itaconate:  neg 2-Ketogluconate:  + 5-Ketogluconate:  neg DL-Lactate:  + Malate:  + L-Malate:  + Malonate:  neg Mucate:  + Phenylacetate:  neg Phenylpropionate:  neg Propionate:  d(+) Quinate:  neg D-Tartrate:  neg L-Tartrate:  d(+)
    ENZYME ACTIVITY
    Enzymes: General Enzymes: Carbohydrate Enzymes: Protein Enzymes: Arylamidases Enzymes: Esters/fats
    Oxidase:  neg Catalase:  + Urease:  + Ac-β-glcamnd:  neg α-Galactosidase:  neg β-Galactosidase:  + α-Glucosidase:  neg β-Glucosidase:  + β-Glucuronidase:  neg ArgDH:  + LysDC:  neg OrnDC:  + Phe deaminase:  neg DNAse:  neg Lipase:  neg
    METABOLITES - PRODUCTION & USE
    Fuel Usable Metabolites Metabolites Released Special Products Compounds Produced

    		H2S:  neg Indole:  + Pigment:  neg
    ANTIBIOTICS ℞
    Penicillins & Penems (μg/mL) Cephalosporins (μg/mL) Aminoglycosides (μg/mL) Macrolides (μg/mL) Quinolones (μg/mL)
    Augmentin:  S(MIC50): 8, MIC90: 16, RNG: (4–16)
    ampicillin:  Res
    aztreonam:  Var(MIC50): >0.12, MIC90: >16, R(>64)
    piper-taz:  S(MIC50): 0.5, MIC90: 8, RNG: (0.5–64)
    ticarcillin:  Res
    ertapenem:  S(MIC50): 0.008, MIC90: 0.25, RNG: (0.008-4)
    imipenem:  S(MIC50): 0.25, MIC90: 1, RNG: (0.5->8)
    cefaclor:  Var(MIC50): 2, MIC90: 32
    cefdinir:  RNG: (8.5)
    cefepime:  S(MIC50): 0.12, MIC90: 0.5, R(31.3)
    cefixime:  S(0.5/1)
    cefotaxime:  Var(MIC50): 8), MIC90: Var(8
    cefotetan:  S(MIC50): 0.5, MIC90: 0.5, RNG: (0.5)
    cefoxitin:  Var(MIC50): 2, MIC90: 64, RNG: (1–64)
    cefpodoxime:  R(16)
    ceftazidime:  R(MIC50): >2, MIC90: >16, RNG: (2->16)
    amikacin:  Var(MIC50): 0.25-32), MIC90: Var(0.25-32
    gentamicin:  S(MIC50): 0.5, MIC90: 0.5, RNG: (0.5)
    erythromycin:  Res
    ciprofloxacin:  S(MIC50): 0.03, MIC90: 1, RNG: (0.008->16)
    gatifloxacin:  S(MIC50): 0.03, MIC90: 1, RNG: (0.03->4)
    levofloxacin:  S(MIC50): 0.015, MIC90: 0.015, RNG: (0.015–0.03)
    nalidixic-acid:  Sens
    ofloxacin:  S(MIC50): 0.06, MIC90: 0.06, RNG: (0.015–0.125)
    trovafloxacin:  S(MIC50): 0.015, MIC90: 0.03, RNG: (0.015–0.125)
    Tetracyclines (μg/mL) Vancomycin Class (μg/mL) Polypep/ketides (μg/mL) Heterocycles (μg/mL) Other (μg/mL)
    tetracycline:  Sens
    vancomycin:  Res
    chloramphenicol:  Sens
    fosfomycin:  Sens
    nitrofurantoin:  Sens
    trimethoprim:  Sens
    clindamycin:  Res
    lincomycin:  Res
    polymyxin_B:  Sens
    fusidic-acid:  Res

    References

    SPECIFIC REFERENCES FOR CITROBACTER AMALONATICUS
  • Farmer1985 - Biochemical identification of new species and biogroups of Enterobacteriaceae isolated from clinical specimens.
  • Brenner1999 - Biochemical identification of Citrobacter species defined by DNA hybridization and description of Citrobacter gillenii sp. nov. (formerly Citrobacter genomospecies 10) and Citrobacter murliniae sp. nov. (formerly Citrobacter genomospecies 11).
  • Young1971 - Levinea, a New Genus of the Family Enterobacteriaceae.
  • Friederiksen2005Bergey - Bergey's manual of systematic bacteriology. Vol. 2, The Gammaproteobacteria Part B. Family Enterobacteriaceae, Genus X. Citrobacter
  • Citron1997 - Comparative in vitro activities of trovafloxacin (CP-99,219) against 221 aerobic and 217 anaerobic bacteria isolated from patients with intra-abdominal infections.
  • ...............................
    • GUT MICROBIOME COMPILATIONS AND METASTUDIES FOR CITROBACTER AMALONATICUS
  • Byrd2020 - Stability and dynamics of the human gut microbiome and its association with systemic immune traits.
  • De2020 - Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter.
  • Lagier2016 - Culture of previously uncultured members of the human gut microbiota by culturomics.
  • RajilicStojanovic2014 - The first 1000 cultured species of the human gastrointestinal microbiota.
  • ...............................
    • GENERAL REFERENCES FOR CITROBACTER AMALONATICUS
  • CCUG - Culture Collection University of Gothenburg - Entire Collection
    • Added: April 08, 2021