data/rag/knowledge_base/Aerococcus/urinae.json

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

  "overview": {
    "short": "Aerococcus urinae is a Gram-positive, catalase-negative coccus commonly isolated from urinary tract infections.",
    "clinical_context": "Frequently associated with UTIs, bacteremia, and infective endocarditis in elderly patients."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Cocci",
    "Motility": "Negative",
    "Capsule": "Variable",
    "Spore Formation": "Negative",
    "Haemolysis": "Positive",
    "Haemolysis Type": "Alpha",
    "Media Grown On": [
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Small",
      "Grey",
      "Alpha-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"
  },

  "species_markers": [
    {
      "field": "Clinical Source",
      "value": "Urinary tract",
      "importance": "high",
      "notes": "Strong association with urinary isolates."
    },
    {
      "field": "Haemolysis Type",
      "value": "Alpha",
      "importance": "medium",
      "notes": "Typically alpha-haemolytic on blood agar."
    }
  ],

  "common_confusions": [
    {
      "species": "Aerococcus sanguinicola",
      "reason": "Similar biochemical profile and haemolysis pattern."
    },
    {
      "genus": "Enterococcus",
      "reason": "Shared UTI association and Gram-positive cocci morphology."
    }
  ],

  "when_to_question_identification": [
    "Growth in 6.5% NaCl suggests Enterococcus.",
    "Catalase positivity suggests Staphylococcus.",
    "Beta-haemolysis suggests Streptococcus."
  ],

  "recommended_next_tests": [
    {
      "test": "MALDI-TOF MS",
      "reason": "Gold standard for distinguishing Aerococcus species."
    },
    {
      "test": "16S rRNA sequencing",
      "reason": "Useful when MALDI-TOF is inconclusive."
    }
  ]
}