Update data/rag/knowledge_base/Acinetobacter/johnsonii.json

data/rag/knowledge_base/Acinetobacter/johnsonii.json

@@ -1,44 +1,97 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Acinetobacter",
-  "species": "junii",
-  "full_name": "Acinetobacter junii",
-  "clinical_significance": "A less pathogenic species compared to A. baumannii. Often isolated in neonates and immunocompromised patients, causing bacteremia, meningitis, and wound infections. Generally more susceptible to antibiotics.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative coccobacilli; may appear slightly longer than baumannii.",
-    "culture": "Smooth, moist colonies on blood agar. Non-lactose fermenting on MacConkey agar.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase positive",
-      "Non-fermenter",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Non-motile",
-      "Does NOT grow at 44°C",
-      "Weak or absent glucose oxidation"
-    ]
+  "species": "johnsonii",
+
+  "overview": {
+    "short": "Acinetobacter johnsonii is a Gram-negative, aerobic, non-fermentative coccobacillus commonly recovered from environmental sources.",
+    "clinical_context": "Rarely associated with human infection and typically considered of low pathogenic potential."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Does not grow at 44°C, unlike A. baumannii.",
-      "More antibiotic susceptible than A. baumannii.",
-      "Colony morphology more moist and less adherent.",
-      "Genetic identification required for reliable distinction."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Coccobacilli",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "MacConkey Agar"
     ],
-    "from_other_genera": [
-      "Oxidase negative non-motile phenotype differentiates from Stenotrophomonas and Alcaligenes.",
-      "Coccobacillary morphology may mimic Neisseria, but oxidase negative result rules them out."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Dry"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "15//37",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Negative",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Negative",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Negative",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "K/K",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "16S rRNA sequencing",
-    "Inability to grow at 44°C (supports species assignment)",
-    "Genome-based identification for high accuracy"
+
+  "species_markers": [
+    {
+      "field": "Growth Temperature",
+      "value": "37//37",
+      "importance": "medium",
+      "notes": "Does not tolerate higher temperatures typical of A. baumannii."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Acinetobacter lwoffii",
+      "reason": "Similar low biochemical activity and environmental presence."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Isolation from severe clinical infections may indicate another species.",
+    "Growth at elevated temperatures argues against A. johnsonii."
   ],
-  "treatment_notes": "Typically susceptible to more antibiotics than baumannii. Standard beta-lactams, fluoroquinolones, and aminoglycosides may be effective.",
-  "notes": "Commonly isolated from neonatal intensive care units; pathogenicity lower than baumannii but still clinically relevant.",
-  "references": [
-    "Manual of Clinical Microbiology.",
-    "NICU infection surveillance literature."
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Definitive species-level identification."
+    }
   ]
-}
+}