data/rag/knowledge_base/Comamonas/genus.json

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

  "overview": {
    "short": "Comamonas species are Gram-negative, aerobic, non-fermentative rods commonly found in soil and water, occasionally implicated in opportunistic human infections.",
    "clinical_context": "Rarely isolated in clinical microbiology but reported in bloodstream, intra-abdominal, and wound infections, often in immunocompromised hosts."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Rods",
    "Motility": "Positive",
    "Capsule": "Negative",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Blood Agar",
      "Nutrient Agar"
    ],
    "Colony Morphology": [
      "Smooth",
      "Grey",
      "Non-pigmented"
    ],
    "Oxygen Requirement": "Aerobic",
    "Growth Temperature": "15//42",
    "Catalase": "Positive",
    "Oxidase": "Positive",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Variable",
    "Methyl Red": "Negative",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Variable",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Variable",
    "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": "Negative",
    "Gas Production": "Negative",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Polar"
  },

  "field_notes": {
    "Oxidase": "Oxidase positivity supports differentiation from Enterobacterales.",
    "Glucose Fermentation": "Non-fermentative metabolism is genus-defining.",
    "Motility": "Motile by polar flagella."
  },

  "key_differentiators": [
    {
      "field": "Oxidase",
      "expected": "Positive",
      "distinguishes_from": ["Enterobacter", "Escherichia"],
      "notes": "Separates Comamonas from oxidase-negative Gram-negative rods."
    },
    {
      "field": "Glucose Fermentation",
      "expected": "Negative",
      "distinguishes_from": ["Aeromonas", "Vibrio"],
      "notes": "Non-fermentative profile excludes common oxidase-positive fermenters."
    },
    {
      "field": "Oxygen Requirement",
      "expected": "Aerobic",
      "distinguishes_from": ["Bacteroides", "Clostridium"],
      "notes": "Strict aerobic growth pattern."
    }
  ],

  "common_confusions": [
    {
      "genus": "Alcaligenes",
      "reason": "Shared oxidase positivity and non-fermentative metabolism."
    },
    {
      "genus": "Achromobacter",
      "reason": "Environmental origin and overlapping biochemical reactions."
    }
  ],

  "when_to_question_identification": [
    "Glucose fermentation suggests Aeromonas or Vibrio.",
    "Oxidase negativity is inconsistent with Comamonas.",
    "Anaerobic growth argues against identification."
  ],

  "recommended_next_tests": [
    {
      "test": "Oxidative-fermentative (OF) glucose test",
      "reason": "Confirms non-fermentative metabolism.",
      "api_kit": "API 20NE"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Accurate genus-level and species-level identification.",
      "api_kit": "Not applicable"
    },
    {
      "test": "Molecular identification",
      "reason": "Useful for rare or clinically significant isolates.",
      "api_kit": "Not applicable"
    }
  ],

  "supported_species": [
    "kerstersii",
    "testosteroni"
  ]
}