data/rag/knowledge_base/Citrobacter/genus.json

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

  "overview": {
    "short": "Citrobacter species are Gram-negative, facultatively anaerobic rods within the Enterobacterales, commonly found in the intestinal tract and environment.",
    "clinical_context": "Associated with opportunistic infections including urinary tract, bloodstream, neonatal meningitis, and intra-abdominal infections."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Rods",
    "Motility": "Variable",
    "Capsule": "Variable",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "MacConkey Agar",
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Smooth",
      "Grey",
      "Moist"
    ],
    "Oxygen Requirement": "Facultative Anaerobe",
    "Growth Temperature": "10//45",
    "Catalase": "Positive",
    "Oxidase": "Negative",
    "Indole": "Variable",
    "Urease": "Variable",
    "Citrate": "Positive",
    "Methyl Red": "Positive",
    "VP": "Negative",
    "H2S": "Variable",
    "DNase": "Negative",
    "ONPG": "Positive",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Variable",
    "Esculin Hydrolysis": "Variable",
    "Nitrate Reduction": "Positive",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Variable",
    "Ornithine Decarboxylase": "Variable",
    "Ornitihine Decarboxylase": "Variable",
    "Arginine dihydrolase": "Negative",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Variable",
    "Sucrose Fermentation": "Variable",
    "Maltose Fermentation": "Positive",
    "Mannitol Fermentation": "Variable",
    "Sorbitol Fermentation": "Variable",
    "Xylose Fermentation": "Positive",
    "Rhamnose Fermentation": "Variable",
    "Arabinose Fermentation": "Positive",
    "Raffinose Fermentation": "Variable",
    "Trehalose Fermentation": "Positive",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Variable",
    "TSI Pattern": "A/A",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Peritrichous"
  },

  "field_notes": {
    "Lactose Fermentation": "Often delayed or variable on MacConkey Agar.",
    "H2S": "Some species produce H2S, which may cause confusion with Salmonella.",
    "Indole": "Indole reactions vary by species and are useful at the species level."
  },

  "key_differentiators": [
    {
      "field": "Methyl Red",
      "expected": "Positive",
      "distinguishes_from": ["Enterobacter", "Klebsiella"],
      "notes": "MR positivity helps separate Citrobacter from VP-positive Enterobacterales."
    },
    {
      "field": "H2S",
      "expected": "Variable",
      "distinguishes_from": ["Escherichia"],
      "notes": "Possible H2S production differentiates Citrobacter from E. coli."
    },
    {
      "field": "Lactose Fermentation",
      "expected": "Variable",
      "distinguishes_from": ["Escherichia"],
      "notes": "Delayed or absent lactose fermentation helps exclude E. coli."
    }
  ],

  "common_confusions": [
    {
      "genus": "Salmonella",
      "reason": "Shared H2S production and Enterobacterales profile."
    },
    {
      "genus": "Enterobacter",
      "reason": "Overlapping sugar fermentation and citrate positivity."
    }
  ],

  "when_to_question_identification": [
    "Strong VP positivity suggests Enterobacter or Klebsiella.",
    "Consistent lactose fermentation suggests Escherichia.",
    "Absence of nitrate reduction argues against Citrobacter."
  ],

  "recommended_next_tests": [
    {
      "test": "Indole test",
      "reason": "Critical for species-level differentiation."
    },
    {
      "test": "H2S production assessment",
      "reason": "Helps separate Citrobacter from related genera."
    },
    {
      "test": "API 20E",
      "reason": "Standard biochemical panel for Enterobacterales identification."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Provides rapid and reliable species-level identification."
    }
  ],

  "supported_species": [
    "braakii",
    "freundii",
    "koseri"
  ]
}