{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Clostridioides",
  "species": "difficile",

  "overview": {
    "short": "Clostridioides difficile is a Gram-positive, anaerobic, spore-forming rod and a leading cause of antibiotic-associated diarrhoea and pseudomembranous colitis.",
    "clinical_context": "Classically associated with recent antibiotic exposure, healthcare settings, and detection of toxin production."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Rods",
    "Motility": "Positive",
    "Capsule": "Negative",
    "Spore Formation": "Positive",
    "Haemolysis": "Variable",
    "Haemolysis Type": "Variable",
    "Media Grown On": [
      "Blood Agar",
      "CCFA Agar"
    ],
    "Colony Morphology": [
      "Irregular",
      "Flat",
      "Grey"
    ],
    "Oxygen Requirement": "Anaerobic",
    "Growth Temperature": "25//42",
    "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": "Variable",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "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": "Negative",
    "Sorbitol Fermentation": "Negative",
    "Xylose Fermentation": "Variable",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Variable",
    "Raffinose Fermentation": "Negative",
    "Trehalose Fermentation": "Variable",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Variable",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Variable"
  },

  "species_markers": [
    {
      "field": "Motility",
      "value": "Positive",
      "importance": "medium",
      "notes": "Motility supports C. difficile in context, but is not exclusive among anaerobic rods."
    },
    {
      "field": "Indole",
      "value": "Negative",
      "importance": "medium",
      "notes": "Indole negativity helps distinguish from certain other clostridial anaerobes."
    },
    {
      "field": "Media Grown On",
      "value": "CCFA Agar",
      "importance": "high",
      "notes": "Growth on selective media supports isolation/confirmation in appropriate clinical context."
    }
  ],

  "common_confusions": [
    {
      "species": "Clostridioides mangenotii",
      "reason": "Same genus and broad anaerobic spore-forming profile; requires higher-resolution confirmation."
    },
    {
      "genus": "Clostridium",
      "reason": "Many species are anaerobic spore-forming rods with overlapping biochemical reactions."
    }
  ],

  "when_to_question_identification": [
    "Lack of anaerobic growth suggests an aerobe/facultative organism rather than Clostridioides.",
    "Non-spore-forming phenotype argues strongly against C. difficile.",
    "If clinical context is not gastrointestinal/antibiotic-associated, consider alternative anaerobes."
  ],

  "recommended_next_tests": [
    {
      "test": "Toxin A/B detection (EIA) or GDH + toxin algorithm",
      "reason": "Toxin detection is central to clinically relevant identification of toxigenic C. difficile.",
      "api_kit_example": "C. difficile GDH + toxin A/B rapid immunoassay kits (varies by lab supplier)."
    },
    {
      "test": "NAAT (PCR) for toxin genes (e.g., tcdB)",
      "reason": "High sensitivity confirmation for toxigenic strains when algorithm indicates.",
      "api_kit_example": "C. difficile toxin gene NAAT/PCR assay kits (platform-dependent)."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Reliable organism identification; toxin status still requires toxin/NAAT testing."
    }
  ]
}