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

data/rag/knowledge_base/Aerococcus/viridans.json

@@ -1,43 +1,96 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Aerococcus",
   "species": "viridans",
-  "full_name": "Aerococcus viridans",
-  "clinical_significance": "Aerococcus viridans is primarily an environmental species occasionally isolated from human skin or mucosa. It is less clinically significant than A. urinae or A. sanguinicola but has been associated with rare cases of bacteremia, endocarditis, and wound infections.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive cocci forming tetrads or irregular clusters.",
-    "culture": "Alpha-hemolytic or non-hemolytic colonies on blood agar; growth similar to viridans streptococci.",
-    "biochemical": [
-      "Catalase negative",
-      "Non-motile",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "LAP positive",
-      "PYR negative",
-      "Typically weak fermentation activity",
-      "Variable hippurate hydrolysis"
-    ]
+
+  "overview": {
+    "short": "Aerococcus viridans is a Gram-positive, catalase-negative coccus historically associated with environmental and opportunistic infections.",
+    "clinical_context": "Less frequently isolated than other Aerococcus species; may be recovered from blood or wound cultures."
   },
-  "differentiation": {
-    "from_close_species": [
-      "A. viridans has weaker pathogenicity and is less likely to cause UTIs compared to A. urinae or A. sanguinicola.",
-      "Often more environmental; less strongly associated with urine isolates.",
-      "Some strains show slightly larger, more spreading colonies than A. urinae."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Cocci",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Alpha",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "Catalase negativity distinguishes it from staphylococci.",
-      "Tetrad arrangement helps differentiate from streptococci.",
-      "Weak biochemical reactions differentiate from enterococci."
-    ]
+    "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",
-      "16S rRNA sequencing",
-      "Colony morphology + tetrads + catalase negative pattern"
+
+  "species_markers": [
+    {
+      "field": "Clinical Relevance",
+      "value": "Lower",
+      "importance": "medium",
+      "notes": "Less commonly implicated in invasive disease."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Streptococcus",
+      "reason": "Alpha-haemolytic colonies may mimic viridans streptococci."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Strong clinical UTI association suggests Aerococcus urinae.",
+    "Growth in high salt suggests Enterococcus."
   ],
-  "treatment_notes": "Generally susceptible to beta-lactams; clinical significance should be carefully interpreted as many isolates represent contamination.",
-  "notes": "Frequently misidentified as viridans streptococci without MALDI-TOF.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Case reports of A. viridans bacteremia"
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Required for reliable species-level identification."
+    }
   ]
-}
+}