Update data/rag/knowledge_base/Aerococcus/sanguinicola.json

data/rag/knowledge_base/Aerococcus/sanguinicola.json

@@ -1,44 +1,96 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Aerococcus",
   "species": "sanguinicola",
-  "full_name": "Aerococcus sanguinicola",
-  "clinical_significance": "Aerococcus sanguinicola is a significant urinary pathogen and cause of bacteremia and infective endocarditis, similar to A. urinae. It is strongly associated with urinary tract disease in older men and is frequently underdiagnosed without MALDI-TOF.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive cocci in tetrads or clusters.",
-    "culture": "Alpha-hemolytic colonies; sometimes slightly larger or smoother than A. urinae on blood agar.",
-    "biochemical": [
-      "Catalase negative",
-      "Non-motile",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "LAP positive",
-      "PYR negative",
-      "Arginine dihydrolase negative (helps distinguish from A. urinae)",
-      "Generally weak biochemical reactions"
-    ]
+
+  "overview": {
+    "short": "Aerococcus sanguinicola is a Gram-positive, catalase-negative coccus associated with bloodstream and urinary tract infections.",
+    "clinical_context": "Often isolated from bacteremia or invasive infections in elderly or hospitalized patients."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Arginine dihydrolase negative (A. urinae is positive).",
-      "Some strains form slightly larger colonies than A. urinae.",
-      "Both cause UTIs and endocarditis, but A. sanguinicola often shows more robust bloodstream invasion."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Cocci",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Positive",
+    "Haemolysis Type": "Alpha",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "Catalase negative: eliminates staphylococci and micrococci.",
-      "Tetrads distinguish from streptococci.",
-      "Growth characteristics differ from enterococci (no salt tolerance)."
-    ]
+    "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"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS (excellent accuracy)",
-    "16S rRNA sequencing",
-    "Arginine dihydrolase negativity",
-    "Tetrad formation + alpha-hemolysis"
+
+  "species_markers": [
+    {
+      "field": "Clinical Source",
+      "value": "Bloodstream",
+      "importance": "high",
+      "notes": "More frequently isolated from blood cultures than other Aerococcus species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Aerococcus urinae",
+      "reason": "Overlapping biochemical profile and haemolysis pattern."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "UTI-only presentation suggests Aerococcus urinae.",
+    "Beta-haemolysis suggests Streptococcus."
   ],
-  "treatment_notes": "Usually susceptible to beta-lactams. Similar management to A. urinae bacteremia and endocarditis.",
-  "notes": "Commonly misidentified as A. urinae or viridans streptococci without molecular/MALDI methods.",
-  "references": [
-    "Aerococcus bacteremia and endocarditis studies",
-    "Manual of Clinical Microbiology"
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Essential for distinguishing Aerococcus species."
+    }
   ]
-}
+}