data/rag/knowledge_base/Aerococcus/genus.json

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

  "overview": {
    "short": "Aerococcus species are Gram-positive cocci that often appear in clusters or tetrads and resemble streptococci or staphylococci on initial examination.",
    "clinical_context": "Associated with urinary tract infections, bacteremia, endocarditis, and invasive infections, particularly in elderly or immunocompromised patients."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Cocci",
    "Motility": "Negative",
    "Capsule": "Variable",
    "Spore Formation": "Negative",
    "Haemolysis": "Variable",
    "Haemolysis Type": "Variable",
    "Media Grown On": [
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Small",
      "Grey",
      "Alpha-haemolytic or Non-haemolytic"
    ],
    "Oxygen Requirement": "Facultative Anaerobe",
    "Growth Temperature": "30//37",
    "Catalase": "Negative",
    "Oxidase": "Negative",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Unknown",
    "VP": "Unknown",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Unknown",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Negative",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Unknown",
    "Ornithine Decarboxylase": "Unknown",
    "Ornitihine Decarboxylase": "Unknown",
    "Arginine dihydrolase": "Negative",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Variable",
    "Sucrose Fermentation": "Variable",
    "Maltose Fermentation": "Variable",
    "Mannitol Fermentation": "Negative",
    "Sorbitol Fermentation": "Negative",
    "Xylose Fermentation": "Negative",
    "Rhamnose Fermentation": "Unknown",
    "Arabinose Fermentation": "Negative",
    "Raffinose Fermentation": "Unknown",
    "Trehalose Fermentation": "Variable",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Negative",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "field_notes": {
    "Catalase": "Typically catalase-negative, but weak or pseudo-positive reactions may occur.",
    "Haemolysis": "Most species are alpha-haemolytic or non-haemolytic on blood agar.",
    "Shape": "Often described as cocci in tetrads or clusters, which can mimic staphylococci."
  },

  "key_differentiators": [
    {
      "field": "Catalase",
      "expected": "Negative",
      "distinguishes_from": ["Staphylococcus"],
      "notes": "Catalase negativity helps separate Aerococcus from staphylococci."
    },
    {
      "field": "NaCl Tolerant (>=6%)",
      "expected": "Negative",
      "distinguishes_from": ["Enterococcus"],
      "notes": "Lack of growth in high salt differentiates Aerococcus from enterococci."
    },
    {
      "field": "Haemolysis",
      "expected": "Variable",
      "distinguishes_from": ["Streptococcus"],
      "notes": "Haemolysis pattern combined with colony morphology aids differentiation."
    }
  ],

  "common_confusions": [
    {
      "genus": "Streptococcus",
      "reason": "Similar Gram-positive cocci morphology and haemolysis patterns."
    },
    {
      "genus": "Enterococcus",
      "reason": "Overlapping biochemical reactions in urinary isolates."
    },
    {
      "genus": "Staphylococcus",
      "reason": "Clustered cocci appearance on Gram stain may be misleading."
    }
  ],

  "when_to_question_identification": [
    "Catalase-positive reaction suggests Staphylococcus.",
    "Growth in 6.5% NaCl suggests Enterococcus.",
    "Beta-haemolysis with streptococcal morphology suggests Streptococcus."
  ],

  "recommended_next_tests": [
    {
      "test": "Catalase test (repeat)",
      "reason": "Weak reactions may require confirmation."
    },
    {
      "test": "NaCl tolerance (6.5%)",
      "reason": "Useful for exclusion of Enterococcus."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Preferred method for accurate genus and species identification."
    }
  ],

  "supported_species": [
    "urinae",
    "viridans",
    "sanguinicola",
    "christensenii"
  ]
}