data/rag/knowledge_base/Alcaligenes/genus.json

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

  "overview": {
    "short": "Alcaligenes species are Gram-negative, aerobic, non-fermentative rods commonly found in environmental sources and occasionally associated with opportunistic infections.",
    "clinical_context": "Rarely pathogenic but may be isolated from respiratory specimens, blood, or hospital environments."
  },

  "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": [
      "Small",
      "Smooth",
      "Grey-White"
    ],
    "Oxygen Requirement": "Aerobe",
    "Growth Temperature": "20//42",
    "Catalase": "Positive",
    "Oxidase": "Positive",
    "Indole": "Negative",
    "Urease": "Variable",
    "Citrate": "Negative",
    "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": "Variable",
    "Ornitihine Decarboxylase": "Variable",
    "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": "K/K",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Peritrichous"
  },

  "field_notes": {
    "Oxidase": "Strong oxidase positivity is characteristic.",
    "Glucose Fermentation": "Alcaligenes species are non-fermentative."
  },

  "key_differentiators": [
    {
      "field": "Oxidase",
      "expected": "Positive",
      "distinguishes_from": ["Enterobacter", "Escherichia"],
      "notes": "Separates Alcaligenes from oxidase-negative Enterobacterales."
    },
    {
      "field": "Glucose Fermentation",
      "expected": "Negative",
      "distinguishes_from": ["Aeromonas"],
      "notes": "Non-fermentative metabolism is genus-defining."
    }
  ],

  "common_confusions": [
    {
      "genus": "Achromobacter",
      "reason": "Both are oxidase-positive, non-fermentative Gram-negative rods."
    },
    {
      "genus": "Pseudomonas",
      "reason": "Shared aerobic growth and non-fermentative metabolism."
    }
  ],

  "when_to_question_identification": [
    "Oxidase negativity suggests another genus.",
    "Glucose fermentation argues against Alcaligenes.",
    "Pigment production suggests Pseudomonas."
  ],

  "recommended_next_tests": [
    {
      "test": "Oxidase test",
      "reason": "Key screening test for non-fermentative Gram-negative rods."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Recommended due to limited biochemical resolution."
    }
  ],

  "supported_species": [
    "faecalis",
    "denitrificans"
  ]
}