Update data/rag/knowledge_base/Actinobacillus/pleuropneumoniae.json

data/rag/knowledge_base/Actinobacillus/pleuropneumoniae.json

@@ -1,54 +1,103 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Actinobacillus",
   "species": "pleuropneumoniae",
-  "full_name": "Actinobacillus pleuropneumoniae",
-  "clinical_significance": "Actinobacillus pleuropneumoniae is the etiologic agent of porcine pleuropneumonia, a highly contagious respiratory disease in pigs characterized by severe fibrinous, necrotizing pneumonia and pleuritis. The disease causes major economic losses in swine production worldwide. It is host-adapted to pigs and is not considered a human pathogen.",
-  "phenotype_profile": {
-    "morphology": "Small Gram-negative coccobacilli; may show short rods in pairs or chains.",
-    "culture": "Grows on chocolate or enriched blood agar; many biovars are NAD (V factor) dependent and show satellitism around NAD-producing streaks. Colonies are often beta-hemolytic on blood agar, especially in virulent serovars. Growth is enhanced in CO₂-enriched atmospheres.",
-    "biochemical": [
-      "Facultative anaerobe",
-      "Oxidase positive",
-      "Catalase positive",
-      "Ferments glucose (acid without gas)",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Non-motile",
-      "NAD (V factor) dependency in most biovars (defining trait)",
-      "Indole negative",
-      "Urease negative or weak (helps differentiate from A. suis)",
-      "Nitrate reduction positive"
-    ]
+
+  "overview": {
+    "short": "Actinobacillus pleuropneumoniae is a Gram-negative coccobacillus causing severe respiratory disease in swine.",
+    "clinical_context": "A major cause of porcine pleuropneumonia; not considered a human pathogen."
   },
-  "differentiation": {
-    "from_close_species": [
-      "A. pleuropneumoniae is typically NAD dependent and strongly hemolytic; A. suis is NAD independent and also hemolytic but associated with septicemia rather than classic pleuropneumonia.",
-      "Pasteurella multocida from pigs may cause pneumonia but is usually non-hemolytic and NAD independent.",
-      "Mannheimia haemolytica is a ruminant pathogen; A. pleuropneumoniae is specific for pigs."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Short Rods",
+    "Motility": "Negative",
+    "Capsule": "Positive",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Positive",
+    "Haemolysis Type": "Beta",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "from_other_genera": [
-      "NAD dependency with porcine origin distinguishes it from many other Pasteurellaceae.",
-      "Enterobacterales from lung tissue ferment glucose with gas and may grow in higher salt concentrations; A. pleuropneumoniae does not.",
-      "True Haemophilus species from humans require both X and V factors, while A. pleuropneumoniae is primarily V dependent and animal associated."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "35//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "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": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "virulence_factors": [
-    "RTX toxins (ApxI, ApxII, ApxIII) causing cytotoxicity and tissue necrosis",
-    "Capsule aiding in evasion of host immunity",
-    "LPS endotoxin contributing to inflammation and vascular damage",
-    "Outer membrane proteins involved in adhesion and iron acquisition"
+
+  "species_markers": [
+    {
+      "field": "Oxidase",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Helps distinguish from other Actinobacillus species."
+    },
+    {
+      "field": "Host specificity",
+      "value": "Swine",
+      "importance": "high",
+      "notes": "Strongly associated with porcine hosts."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Actinobacillus suis",
+      "reason": "Shared haemolysis and overlapping veterinary context."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS from pure culture",
-    "Demonstration of NAD dependency and beta-hemolysis on blood agar",
-    "Species-specific PCR assays and serovar-specific PCRs targeting apx and capsule genes",
-    "16S rRNA sequencing or other molecular typing methods"
+
+  "when_to_question_identification": [
+    "Isolation from human samples suggests misidentification.",
+    "Non-haemolytic isolates are inconsistent with A. pleuropneumoniae."
   ],
-  "treatment_notes": "Control relies on antimicrobial therapy, vaccination, and herd management. Resistance to commonly used antimicrobials (e.g., tetracyclines, macrolides) is increasingly reported. Therapy must be guided by susceptibility testing and local veterinary guidelines.",
-  "notes": "Biovars differ in NAD dependency and toxin profiles. Chronic carriers in tonsils and upper airways can seed outbreaks when pigs are stressed or mixing occurs.",
-  "references": [
-    "Veterinary microbiology and swine disease texts on A. pleuropneumoniae.",
-    "Manual of Clinical Microbiology, veterinary sections.",
-    "Recent reviews on RTX toxins and porcine pleuropneumonia pathogenesis."
+
+  "recommended_next_tests": [
+    {
+      "test": "Veterinary PCR panels",
+      "reason": "Gold standard for definitive identification."
+    }
   ]
-}
+}