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

data/rag/knowledge_base/Acinetobacter/genus.json

@@ -1,78 +1,135 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Acinetobacter",
-  "taxonomy": {
-    "family": "Moraxellaceae",
-    "order": "Pseudomonadales",
-    "class": "Gammaproteobacteria"
+
+  "overview": {
+    "short": "Acinetobacter species are Gram-negative, strictly aerobic, non-fermentative coccobacilli widely distributed in the environment.",
+    "clinical_context": "Clinically significant species, particularly Acinetobacter baumannii, are important causes of healthcare-associated infections."
   },
-  "overview": "Acinetobacter is a genus of aerobic, non-fermenting, oxidase-negative Gram-negative coccobacilli. They are ubiquitous environmental organisms found in soil, water, and hospital environments. Several species, especially Acinetobacter baumannii, are major opportunistic pathogens associated with multidrug resistance, ventilator-associated pneumonia, bloodstream infections, and wound infections.",
-  "key_traits": [
-    "Gram-negative coccobacilli (may appear Gram-variable)",
-    "Strict aerobes",
-    "Non-fermenters",
-    "Oxidase negative (key differentiator from most non-fermenters)",
-    "Catalase positive",
-    "Non-motile",
-    "May grow on MacConkey agar (non-lactose fermenting)",
-    "Often exhibit dry, pale colonies",
-    "Survive prolonged periods on surfaces"
-  ],
-  "ecology": "Widespread in soil, water, hospital sinks, medical devices, and skin flora. Known for environmental persistence and resistance to desiccation, enabling nosocomial spread.",
-  "pathogenicity": "A. baumannii causes severe nosocomial infections including VAP, bacteremia, wound infections, and meningitis. Other species (A. junii, A. lwoffii) are less pathogenic but may cause opportunistic infections in immunocompromised individuals or neonates.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Oxidase negative (critical genus-level trait).",
-      "Non-fermentative metabolism; some species oxidize glucose weakly.",
-      "ONPG negative.",
-      "Do not grow in 6.5% NaCl.",
-      "Non-motile (distinguishes from many non-fermenters).",
-      "Ability to grow on MacConkey agar."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Coccobacilli",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "MacConkey Agar"
     ],
-    "non_definitive_tests": [
-      "Glucose oxidation/fermentation patterns are unreliable for species identification.",
-      "Gram stain may resemble diplococci and confuse with Neisseria."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Stenotrophomonas is oxidase negative but motile and typically oxidizes maltose; Acinetobacter is non-motile.",
-      "Alcaligenes is oxidase positive; Acinetobacter is oxidase negative.",
-      "Moraxella catarrhalis is oxidase positive and asaccharolytic; Acinetobacter is oxidase negative.",
-      "Burkholderia species are oxidase positive and motile; Acinetobacter is oxidase negative and non-motile.",
-      "Neisseria and Moraxella are Gram-negative cocci but oxidase positive, unlike Acinetobacter."
+    "Colony Morphology": [
+      "Smooth",
+      "Opaque",
+      "Grey-White"
     ],
-    "key_rag_filters": [
-      "Gram-negative coccobacilli + oxidase negative → strongly favors Acinetobacter.",
-      "Non-motile + non-fermenter → rules out Burkholderia, Alcaligenes, Stenotrophomonas.",
-      "Dry pale colonies → characteristic of Acinetobacter, especially baumannii.",
-      "Resistance profile (carbapenem resistance) → strongly pushes toward A. baumannii."
-    ]
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//44",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Variable",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Variable",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Variable",
+    "Lipase Test": "Variable",
+    "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": "Variable",
+    "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"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Oxidase negative",
-      "Non-fermenting on TSI/KIA",
-      "Gram-negative coccobacilli",
-      "Non-motile",
-      "Growth on MacConkey agar"
-    ],
-    "important_tests": [
-      "Oxidase test",
-      "Motility testing",
-      "Carbohydrate oxidation panel (limited usefulness)",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (best method)",
-      "Whole-genome sequencing",
-      "16S rRNA sequencing",
-      "Multiplex PCR assays (esp. for baumannii complex)"
-    ]
+
+  "field_notes": {
+    "Motility": "Acinetobacter species are characteristically non-motile.",
+    "Oxidase": "Oxidase negativity is a key differentiator from many other non-fermenters.",
+    "Shape": "Often appear as plump coccobacilli on Gram stain."
   },
-  "notes": "Speciation of Acinetobacter based solely on biochemical testing is unreliable. Modern systems rely on MALDI-TOF or molecular identification. The A. baumannii complex includes multiple closely related species.",
-  "references": [
-    "Manual of Clinical Microbiology, 12th Edition.",
-    "Recent WHO and CDC reports on MDR Acinetobacter.",
-    "Koneman's Diagnostic Microbiology."
+
+  "key_differentiators": [
+    {
+      "field": "Oxidase",
+      "expected": "Negative",
+      "distinguishes_from": ["Pseudomonas", "Burkholderia"],
+      "notes": "Oxidase negativity is critical in separating Acinetobacter from most non-fermenters."
+    },
+    {
+      "field": "Motility",
+      "expected": "Negative",
+      "distinguishes_from": ["Stenotrophomonas", "Alcaligenes"],
+      "notes": "Non-motility supports Acinetobacter."
+    },
+    {
+      "field": "Glucose Fermentation",
+      "expected": "Negative",
+      "distinguishes_from": ["Enterobacterales"],
+      "notes": "Non-fermentative metabolism excludes Enterobacterales."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Pseudomonas",
+      "reason": "Shared non-fermentative metabolism but differs by oxidase status."
+    },
+    {
+      "genus": "Stenotrophomonas",
+      "reason": "Overlapping non-fermentative profile with variable biochemical reactions."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Oxidase positivity argues against Acinetobacter.",
+    "Motility suggests an alternative non-fermenter.",
+    "Anaerobic growth is inconsistent."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Oxidase test",
+      "reason": "Primary discriminator among non-fermenters."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable genus- and species-level identification."
+    },
+    {
+      "test": "Antimicrobial susceptibility testing",
+      "reason": "Clinically important due to frequent multidrug resistance."
+    }
+  ],
+
+  "supported_species": [
+    "baumannii",
+    "calcoaceticus",
+    "lwoffii",
+    "johnsonii",
+    "pittii"
   ]
-}
+}