data/rag/knowledge_base/Enterococcus/faecalis.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Enterococcus",
  "species": "faecalis",

  "overview": {
    "short": "Enterococcus faecalis is a Gram-positive, facultatively anaerobic coccus and the most commonly isolated Enterococcus species in human infections.",
    "clinical_context": "Frequently associated with urinary tract infections, endocarditis, wound infections, and intra-abdominal infections."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Cocci",
    "Motility": "Negative",
    "Capsule": "Variable",
    "Spore Formation": "Negative",
    "Haemolysis": "Variable",
    "Haemolysis Type": "Variable",
    "Media Grown On": [
      "Blood Agar",
      "Bile Esculin Agar"
    ],
    "Colony Morphology": [
      "Small",
      "Grey",
      "Smooth"
    ],
    "Oxygen Requirement": "Facultative Anaerobe",
    "Growth Temperature": "10//45",
    "Catalase": "Negative",
    "Oxidase": "Negative",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Positive",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Positive",
    "Esculin Hydrolysis": "Positive",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Positive",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Negative",
    "Ornitihine Decarboxylase": "Negative",
    "Arginine dihydrolase": "Positive",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Positive",
    "Sucrose Fermentation": "Positive",
    "Maltose Fermentation": "Positive",
    "Mannitol Fermentation": "Positive",
    "Sorbitol Fermentation": "Variable",
    "Xylose Fermentation": "Negative",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Negative",
    "Raffinose Fermentation": "Variable",
    "Trehalose Fermentation": "Positive",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Negative",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "species_markers": [
    {
      "field": "Arginine dihydrolase",
      "value": "Positive",
      "importance": "high",
      "notes": "Helps distinguish E. faecalis from E. faecium."
    },
    {
      "field": "Gelatin Hydrolysis",
      "value": "Positive",
      "importance": "medium",
      "notes": "More commonly positive in E. faecalis than other Enterococcus species."
    }
  ],

  "common_confusions": [
    {
      "species": "Enterococcus faecium",
      "reason": "Closely related species with overlapping biochemical profiles."
    }
  ],

  "when_to_question_identification": [
    "Arginine dihydrolase negativity suggests E. faecium.",
    "Atypical sugar fermentation patterns warrant confirmation.",
    "Identification based solely on hemolysis pattern."
  ],

  "recommended_next_tests": [
    {
      "test": "Arginine dihydrolase",
      "reason": "Key discriminator from E. faecium.",
      "api_kit": "API Strep"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Accurate species-level identification.",
      "api_kit": "Not applicable"
    }
  ]
}