Update data/rag/knowledge_base/Anaerococcus/vaginalis.json

data/rag/knowledge_base/Anaerococcus/vaginalis.json

@@ -1,42 +1,101 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Anaerococcus",
   "species": "vaginalis",
-  "full_name": "Anaerococcus vaginalis",
-  "clinical_significance": "Anaerococcus vaginalis is part of the normal vaginal and perineal microbiota. It is associated with bacterial vaginosis, pelvic infections, postpartum infections, and polymicrobial urogenital abscesses.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive cocci occurring in pairs, tetrads, or small clusters.",
-    "culture": "Slow-growing on anaerobic blood agar. May exhibit slight yellowish pigmentation.",
-    "biochemical": [
-      "Indole negative",
-      "Catalase variable",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Produces butyrate and isovalerate on GC (distinctive)",
-      "Non-motile"
-    ]
+
+  "overview": {
+    "short": "Anaerococcus vaginalis is a Gram-positive anaerobic coccus associated primarily with the female genitourinary tract.",
+    "clinical_context": "Most frequently isolated from vaginal and pelvic infections, often as part of mixed anaerobic flora."
   },
-  "differentiation": {
-    "from_close_species": [
-      "More commonly isolated from urogenital infections than A. prevotii.",
-      "Distinct SCFA profile (butyrate + isovalerate) helps differentiate from A. prevotii.",
-      "A. prevotii lacks association with bacterial vaginosis."
+
+  "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"
     ],
-    "from_other_genera": [
-      "Indole negativity separates from Finegoldia magna.",
-      "Cluster/tetrad morphology separates from chain-forming Parvimonas.",
-      "Strict anaerobiosis differentiates from facultative staphylococci."
-    ]
+    "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"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "SCFA analysis with GC",
-    "16S rRNA sequencing",
-    "Anaerobic culture morphology"
+
+  "species_markers": [
+    {
+      "field": "Clinical Source",
+      "value": "Genitourinary tract",
+      "importance": "medium",
+      "notes": "Isolation from vaginal specimens supports A. vaginalis."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Anaerococcus prevotii",
+      "reason": "Very similar biochemical behavior; clinical context often required."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Indole consistently negative isolates may fit better with A. prevotii.",
+    "Aerobic growth argues against Anaerococcus."
   ],
-  "treatment_notes": "Typically susceptible to metronidazole and β-lactams. Clindamycin resistance increasingly reported in vaginal anaerobes.",
-  "notes": "Often co-isolated with Gardnerella, Mobiluncus, and anaerobic Gram-negative rods in BV-associated microbiota.",
-  "references": [
-    "Bacterial vaginosis microbiome studies",
-    "Manual of Clinical Microbiology"
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Preferred method for accurate species-level identification."
+    },
+    {
+      "test": "16S rRNA sequencing",
+      "reason": "Useful in ambiguous anaerobic coccal identifications."
+    }
   ]
-}
+}