data/rag/knowledge_base/Cryptococcus/genus.json

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

  "overview": {
    "short": "Cryptococcus species are encapsulated, yeast-form fungi primarily affecting immunocompromised hosts.",
    "clinical_context": "Most commonly associated with pulmonary infections and meningoencephalitis, especially in HIV/AIDS and other immunosuppressed patients."
  },

  "expected_fields": {
    "Gram Stain": "Variable",
    "Shape": "Yeast",
    "Motility": "Negative",
    "Capsule": "Positive",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Sabouraud Dextrose Agar",
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Mucoid",
      "Cream",
      "Smooth"
    ],
    "Oxygen Requirement": "Aerobe",
    "Growth Temperature": "20//37",
    "Catalase": "Positive",
    "Oxidase": "Negative",
    "Indole": "Negative",
    "Urease": "Positive",
    "Citrate": "Negative",
    "Methyl Red": "Unknown",
    "VP": "Unknown",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Negative",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Negative",
    "Ornitihine Decarboxylase": "Negative",
    "Arginine dihydrolase": "Negative",
    "Glucose Fermentation": "Negative",
    "Lactose Fermentation": "Negative",
    "Sucrose Fermentation": "Negative",
    "Maltose Fermentation": "Negative",
    "Mannitol Fermentation": "Negative",
    "Sorbitol Fermentation": "Negative",
    "Xylose Fermentation": "Negative",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Negative",
    "Raffinose Fermentation": "Negative",
    "Trehalose Fermentation": "Negative",
    "Inositol Fermentation": "Positive",
    "Gas Production": "Negative",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "field_notes": {
    "Capsule": "Prominent polysaccharide capsule is a defining feature and key virulence factor.",
    "Urease": "Urease positivity is consistent across clinically relevant Cryptococcus species.",
    "Inositol Fermentation": "Positive reaction is characteristic and aids differentiation from other yeasts."
  },

  "key_differentiators": [
    {
      "field": "Capsule",
      "expected": "Positive",
      "distinguishes_from": ["Candida"],
      "notes": "Encapsulation separates Cryptococcus from most Candida species."
    },
    {
      "field": "Urease",
      "expected": "Positive",
      "distinguishes_from": ["Candida"],
      "notes": "Urease activity is a key screening test for Cryptococcus."
    },
    {
      "field": "Inositol Fermentation",
      "expected": "Positive",
      "distinguishes_from": ["Candida"],
      "notes": "Inositol utilization supports Cryptococcus identification."
    }
  ],

  "common_confusions": [
    {
      "genus": "Candida",
      "reason": "Both are yeast-form fungi, but Candida lacks a capsule and is urease negative."
    },
    {
      "genus": "Rhodotorula",
      "reason": "Some species share urease positivity but differ in pigmentation and capsule presence."
    }
  ],

  "when_to_question_identification": [
    "Absence of capsule argues against Cryptococcus.",
    "Urease negativity suggests alternative yeast genera.",
    "Strong carbohydrate fermentation profile is inconsistent with Cryptococcus."
  ],

  "recommended_next_tests": [
    {
      "test": "India ink preparation",
      "reason": "Demonstrates the characteristic polysaccharide capsule.",
      "api_kit": "Not applicable"
    },
    {
      "test": "Urease test",
      "reason": "Rapid screening test for Cryptococcus.",
      "api_kit": "Christensen Urea Agar"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Accurate species-level identification.",
      "api_kit": "Not applicable"
    }
  ],

  "supported_species": [
    "neoformans",
    "gattii",
    "laurentii"
  ]
}