data/rag/knowledge_base/Anaerococcus/genus.json

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

  "overview": {
    "short": "Anaerococcus species are Gram-positive anaerobic cocci, commonly isolated from skin, soft tissue, and genitourinary tract infections.",
    "clinical_context": "Frequently recovered from polymicrobial anaerobic infections, including abscesses, wound infections, and genital tract specimens."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Cocci",
    "Motility": "Negative",
    "Capsule": "Variable",
    "Spore Formation": "Negative",
    "Haemolysis": "Variable",
    "Haemolysis Type": "Variable",
    "Media Grown On": [
      "Blood Agar",
      "Anaerobic Blood Agar"
    ],
    "Colony Morphology": [
      "Small",
      "Grey",
      "Smooth"
    ],
    "Oxygen Requirement": "Anaerobic",
    "Growth Temperature": "35//37",
    "Catalase": "Negative",
    "Oxidase": "Negative",
    "Indole": "Variable",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Unknown",
    "VP": "Unknown",
    "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": "Positive",
    "Lactose Fermentation": "Variable",
    "Sucrose Fermentation": "Variable",
    "Maltose Fermentation": "Variable",
    "Mannitol Fermentation": "Negative",
    "Sorbitol Fermentation": "Negative",
    "Xylose Fermentation": "Negative",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Negative",
    "Raffinose Fermentation": "Negative",
    "Trehalose Fermentation": "Variable",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Variable",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Unknown"
  },

  "field_notes": {
    "Oxygen Requirement": "Strict anaerobes; growth in oxygenated conditions argues against Anaerococcus.",
    "Catalase": "Typically negative, helping differentiate from some other Gram-positive cocci.",
    "Shape": "Often seen as cocci in clusters, pairs, or short chains."
  },

  "key_differentiators": [
    {
      "field": "Oxygen Requirement",
      "expected": "Anaerobic",
      "distinguishes_from": ["Staphylococcus", "Streptococcus"],
      "notes": "Strict anaerobic growth differentiates Anaerococcus from most aerobic cocci."
    },
    {
      "field": "Catalase",
      "expected": "Negative",
      "distinguishes_from": ["Staphylococcus"],
      "notes": "Catalase negativity supports anaerobic cocci identification."
    }
  ],

  "common_confusions": [
    {
      "genus": "Finegoldia",
      "reason": "Both are Gram-positive anaerobic cocci commonly isolated from similar clinical sites."
    },
    {
      "genus": "Peptoniphilus",
      "reason": "Overlapping anaerobic coccal morphology and biochemical inactivity."
    }
  ],

  "when_to_question_identification": [
    "Growth under aerobic conditions argues against Anaerococcus.",
    "Catalase positivity suggests another Gram-positive coccus.",
    "Spore formation excludes Anaerococcus."
  ],

  "recommended_next_tests": [
    {
      "test": "Anaerobic incubation confirmation",
      "reason": "Confirms obligate anaerobic growth."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Reliable identification among anaerobic cocci with overlapping biochemistry."
    },
    {
      "test": "16S rRNA sequencing",
      "reason": "Useful for definitive identification in complex polymicrobial infections."
    }
  ],

  "supported_species": [
    "prevotii",
    "vaginalis"
  ]
}