data/rag/knowledge_base/Enterococcus/genus.json

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

  "overview": {
    "short": "Enterococcus species are Gram-positive, facultatively anaerobic cocci that are part of normal gastrointestinal flora but frequently cause opportunistic infections.",
    "clinical_context": "Common causes of urinary tract infections, bacteremia, endocarditis, and intra-abdominal infections, particularly in healthcare settings."
  },

  "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": "Variable",
    "Esculin Hydrolysis": "Positive",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Positive",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Negative",
    "Ornitihine Decarboxylase": "Negative",
    "Arginine dihydrolase": "Variable",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Variable",
    "Sucrose Fermentation": "Variable",
    "Maltose Fermentation": "Positive",
    "Mannitol Fermentation": "Variable",
    "Sorbitol Fermentation": "Variable",
    "Xylose Fermentation": "Negative",
    "Rhamnose Fermentation": "Variable",
    "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"
  },

  "field_notes": {
    "NaCl Tolerant (>=6%)": "A defining feature of Enterococcus and a key genus-level discriminator.",
    "Esculin Hydrolysis": "Bile esculin positivity is characteristic and diagnostically important.",
    "Catalase": "Typically negative; weak pseudocatalase reactions may occur."
  },

  "key_differentiators": [
    {
      "field": "NaCl Tolerant (>=6%)",
      "expected": "Positive",
      "distinguishes_from": ["Streptococcus"],
      "notes": "Growth in high salt differentiates Enterococcus from most streptococci."
    },
    {
      "field": "Esculin Hydrolysis",
      "expected": "Positive",
      "distinguishes_from": ["Streptococcus"],
      "notes": "Bile esculin positivity supports Enterococcus identification."
    }
  ],

  "common_confusions": [
    {
      "genus": "Streptococcus",
      "reason": "Shared Gram-positive coccal morphology and overlapping hemolysis patterns."
    },
    {
      "genus": "Aerococcus",
      "reason": "Coccal morphology and variable hemolysis may overlap in routine culture."
    }
  ],

  "when_to_question_identification": [
    "NaCl intolerance argues against Enterococcus.",
    "Strong catalase positivity suggests Staphylococcus.",
    "Bile esculin negativity is inconsistent."
  ],

  "recommended_next_tests": [
    {
      "test": "PYR test",
      "reason": "Rapid confirmation of Enterococcus genus.",
      "api_kit": "API Strep"
    },
    {
      "test": "Bile esculin test",
      "reason": "Supports genus-level identification.",
      "api_kit": "API Strep"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Reliable species-level identification.",
      "api_kit": "Not applicable"
    }
  ],

  "supported_species": [
    "faecalis",
    "faecium",
    "gallinarum"
  ]
}