data/rag/knowledge_base/Candida/genus.json

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

  "overview": {
    "short": "Candida species are yeast-like fungi commonly found as commensals on human mucosal surfaces but capable of causing opportunistic infections.",
    "clinical_context": "Associated with superficial mucocutaneous infections and invasive candidiasis, particularly in immunocompromised or hospitalized patients."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Yeast",
    "Motility": "Negative",
    "Capsule": "Negative",
    "Spore Formation": "Negative",
    "Haemolysis": "Variable",
    "Haemolysis Type": "Unknown",
    "Media Grown On": [
      "Sabouraud Dextrose Agar",
      "Chromogenic Candida Agar",
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Cream",
      "Smooth",
      "Butyrous"
    ],
    "Oxygen Requirement": "Facultative Anaerobe",
    "Growth Temperature": "25//42",
    "Catalase": "Positive",
    "Oxidase": "Negative",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Negative",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Negative",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Variable",
    "Lipase Test": "Variable",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Negative",
    "Ornitihine Decarboxylase": "Negative",
    "Arginine dihydrolase": "Negative",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Variable",
    "Sucrose Fermentation": "Variable",
    "Maltose Fermentation": "Variable",
    "Mannitol Fermentation": "Variable",
    "Sorbitol Fermentation": "Variable",
    "Xylose Fermentation": "Variable",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Variable",
    "Raffinose Fermentation": "Variable",
    "Trehalose Fermentation": "Variable",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Negative",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "field_notes": {
    "Gram Stain": "Yeast cells often stain Gram-positive but may appear variable.",
    "Shape": "Oval budding yeast; some species form pseudohyphae or true hyphae.",
    "Sugar Fermentation": "Patterns are species-dependent and critical for differentiation."
  },

  "key_differentiators": [
    {
      "field": "Germ Tube Test",
      "expected": "Positive",
      "distinguishes_from": ["Candida glabrata", "Candida tropicalis"],
      "notes": "Rapid screening test for Candida albicans."
    },
    {
      "field": "Chromogenic Agar",
      "expected": "Species-specific colony colour",
      "distinguishes_from": ["Non-Candida yeasts"],
      "notes": "Useful for presumptive species identification."
    }
  ],

  "common_confusions": [
    {
      "genus": "Cryptococcus",
      "reason": "Both are yeasts, but Cryptococcus is urease-positive and encapsulated."
    },
    {
      "genus": "Saccharomyces",
      "reason": "May appear similar on routine culture without speciation."
    }
  ],

  "when_to_question_identification": [
    "Urease positivity suggests Cryptococcus.",
    "Encapsulated yeast with narrow budding argues against Candida.",
    "Poor growth on Sabouraud Agar is atypical."
  ],

  "recommended_next_tests": [
    {
      "test": "Germ tube test",
      "reason": "Rapid differentiation of Candida albicans.",
      "api_kit": "API Candida"
    },
    {
      "test": "Chromogenic Candida Agar",
      "reason": "Presumptive species identification by colony colour."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Gold standard for Candida species identification."
    }
  ],

  "supported_species": [
    "albicans",
    "glabrata",
    "tropicalis"
  ]
}