Update data/rag/knowledge_base/Aeromonas/hydrophila.json

data/rag/knowledge_base/Aeromonas/hydrophila.json

@@ -1,52 +1,122 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Aeromonas",
   "species": "hydrophila",
-  "full_name": "Aeromonas hydrophila",
-  "clinical_significance": "A major human pathogen causing necrotizing soft tissue infections, gastroenteritis, septicemia, and severe infections following aquatic exposure. Known for potent hemolysins and cytotoxins.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Strongly β-hemolytic colonies on blood agar; non-lactose fermenting on MacConkey.",
-    "biochemical": [
-      "Oxidase positive",
-      "Indole positive",
-      "ONPG negative",
-      "Does not require NaCl",
-      "Ferments glucose with gas",
-      "Lysine decarboxylase negative or weak",
-      "Arginine dihydrolase variable",
-      "Strong β-hemolysis (key trait)"
-    ]
+
+  "overview": {
+    "short": "Aeromonas hydrophila is a Gram-negative, oxidase-positive, facultatively anaerobic rod frequently associated with wound infections and gastroenteritis, and can cause invasive disease.",
+    "clinical_context": "Often linked to water-exposure wound infections, diarrheal disease, and opportunistic septicemia."
   },
-  "differentiation": {
-    "from_close_species": [
-      "More strongly hemolytic than A. caviae and many A. veronii strains.",
-      "Indole positive (helps separate from A. caviae).",
-      "Gas production from glucose distinguishes it from many other Aeromonas species.",
-      "More strongly associated with necrotizing infections."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Positive",
+    "Haemolysis Type": "Beta",
+    "Media Grown On": [
+      "Blood Agar",
+      "MacConkey Agar"
     ],
-    "from_other_genera": [
-      "Oxidase positivity rules out Enterobacterales.",
-      "No salt requirement rules out Vibrio.",
-      "Hemolysis differentiates from Plesiomonas."
-    ]
+    "Colony Morphology": [
+      "Large",
+      "Grey",
+      "Opaque"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "4//42",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Variable",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Positive",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Positive",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Positive",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "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": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Polar"
   },
-  "virulence_factors": [
-    "Hemolysins (aerolysin, cytotoxic enterotoxin)",
-    "Actin-destabilizing toxins",
-    "Biofilm formation",
-    "Type III secretion system in some strains"
+
+  "species_markers": [
+    {
+      "field": "Haemolysis Type",
+      "value": "Beta",
+      "importance": "high",
+      "notes": "Beta haemolysis is more supportive of A. hydrophila compared with A. caviae (often non-haemolytic)."
+    },
+    {
+      "field": "Gelatin Hydrolysis",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Gelatinase positivity is commonly used in Aeromonas differentiation and supports A. hydrophila."
+    },
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Helps separate from A. caviae, which is more often ornithine positive."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Aeromonas veronii",
+      "reason": "Overlap in oxidase-positive fermentation pattern; indole and haemolysis patterns are helpful."
+    },
+    {
+      "species": "Aeromonas caviae",
+      "reason": "Both can present in gastroenteritis; ornithine and haemolysis help distinguish."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Strong β-hemolysis",
-    "Indole positivity",
-    "Glucose fermentation with gas",
-    "16S rRNA sequencing"
+
+  "when_to_question_identification": [
+    "Consistent non-haemolysis suggests A. caviae or another Aeromonas species.",
+    "Strong indole positivity suggests A. veronii or related taxa.",
+    "NaCl tolerance at >=6% suggests Vibrio rather than Aeromonas."
   ],
-  "treatment_notes": "Often resistant to ampicillin and first-generation cephalosporins. Fluoroquinolones, TMP-SMX, and advanced cephalosporins often effective.",
-  "notes": "Historically considered the most virulent Aeromonas species; common in warm freshwater environments.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Studies on Aeromonas soft tissue infections"
+
+  "recommended_next_tests": [
+    {
+      "test": "Haemolysis on Blood Agar",
+      "reason": "Supports species-level discrimination inside Aeromonas."
+    },
+    {
+      "test": "Gelatin hydrolysis",
+      "reason": "Commonly positive and useful for A. hydrophila support."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Recommended for accurate differentiation among Aeromonas species."
+    }
   ]
-}
+}