data/rag/knowledge_base/Cryptococcus/neoformans.json

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

  "overview": {
    "short": "Cryptococcus neoformans is an encapsulated yeast most strongly associated with opportunistic infection and cryptococcal meningoencephalitis.",
    "clinical_context": "Classically affects immunocompromised hosts (especially HIV/AIDS), causing pulmonary disease and CNS infection."
  },

  "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": "25//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"
  },

  "species_markers": [
    {
      "field": "Growth Temperature",
      "value": "25//37",
      "importance": "high",
      "notes": "Consistent growth at 37°C supports pathogenic Cryptococcus species; helps separate from more environmental yeasts."
    },
    {
      "field": "Capsule",
      "value": "Positive",
      "importance": "high",
      "notes": "Strong encapsulation is a key feature in clinical isolates."
    },
    {
      "field": "Urease",
      "value": "Positive",
      "importance": "high",
      "notes": "Urease positivity is expected and supports Cryptococcus identification."
    }
  ],

  "common_confusions": [
    {
      "species": "Cryptococcus gattii",
      "reason": "Closely related; both are encapsulated urease-positive yeasts with overlapping phenotypes."
    },
    {
      "genus": "Candida",
      "reason": "Yeast morphology can confuse early screening, but Candida is typically capsule-negative and urease-negative."
    }
  ],

  "when_to_question_identification": [
    "Capsule not demonstrated argues against Cryptococcus neoformans.",
    "Urease negativity suggests a different yeast genus.",
    "A strong sugar fermentation profile is inconsistent with Cryptococcus."
  ],

  "recommended_next_tests": [
    {
      "test": "India ink preparation",
      "reason": "Demonstrates characteristic capsule.",
      "api_kit": "Not applicable"
    },
    {
      "test": "Cryptococcal antigen (CrAg) test",
      "reason": "Highly useful in clinical context, especially suspected CNS infection.",
      "api_kit": "Not applicable"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Reliable species-level ID between neoformans vs gattii complex.",
      "api_kit": "Not applicable"
    }
  ]
}