Update data/rag/knowledge_base/Edwardsiella/tarda.json

data/rag/knowledge_base/Edwardsiella/tarda.json

@@ -1,54 +1,118 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Edwardsiella",
   "species": "tarda",
-  "full_name": "Edwardsiella tarda",
-  "clinical_significance": "The major Edwardsiella species causing human disease, including gastroenteritis, systemic infections, liver abscess, wound infections, and bacteremia. Associated with freshwater exposure, aquatic animals, and consumption of raw or undercooked seafood.",
-  "phenotype_profile": {
-    "morphology": "Motile Gram-negative rods.",
-    "culture": "Non-lactose fermenter on MacConkey. Produces H2S on TSI/HE agar.",
-    "biochemical": [
-      "Indole positive",
-      "H2S positive",
-      "Lysine decarboxylase positive",
-      "Ornithine decarboxylase negative (key differentiator)",
-      "ONPG negative",
-      "Gas from glucose variable (often negative)",
-      "Nitrate reduction positive",
-      "Urease negative",
-      "Non-pigmented"
-    ]
+
+  "overview": {
+    "short": "Edwardsiella tarda is a Gram-negative, facultatively anaerobic rod and the most clinically significant species of the genus.",
+    "clinical_context": "Associated with gastroenteritis, wound infections, and invasive disease following aquatic exposure."
   },
-  "differentiation": {
-    "from close species": [
-      "Ornithine negative → distinguishes from E. hoshinae and E. ictaluri (both ornithine positive).",
-      "More frequently isolated from humans than other Edwardsiella species.",
-      "Clinical spectrum includes both gastrointestinal and extraintestinal infections."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "MacConkey Agar"
     ],
-    "from other genera": [
-      "Indole + H2S combination excludes most Salmonella.",
-      "ONPG negative helps eliminate Citrobacter.",
-      "PAD negative differentiates from Proteus."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Positive",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Positive",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Negative",
+    "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": "K/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-      "Type III secretion system",
-      "Hemolysins",
-      "Adhesins enabling intestinal colonization",
-      "Invasion factors allowing systemic spread"
+
+  "species_markers": [
+    {
+      "field": "Indole",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Primary discriminator for Edwardsiella tarda."
+    },
+    {
+      "field": "H2S",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Characteristic feature separating E. tarda from E. ictaluri."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "Biochemical identification (indole+, H2S+, ornithine–)",
-      "16S sequencing"
+
+  "common_confusions": [
+    {
+      "species": "Edwardsiella hoshinae",
+      "reason": "Shared H2S production but differs by indole reaction."
+    },
+    {
+      "genus": "Salmonella",
+      "reason": "Both produce H2S and are Enterobacterales."
+    }
   ],
-  "treatment_notes": [
-      "Generally susceptible to fluoroquinolones, TMP-SMX, aminoglycosides, and cephalosporins.",
-      "Resistance rare but documented; susceptibility testing recommended.",
-      "Severe disease requires systemic therapy."
+
+  "when_to_question_identification": [
+    "Indole negativity suggests another Edwardsiella species.",
+    "Strong lactose fermentation is inconsistent with E. tarda."
   ],
-  "notes": "Historically lumped with E. ictaluri and E. hoshinae in early taxonomy; now firmly separated.",
-  "references": [
-      "Human edwardsiellosis case reports",
-      "Marine and freshwater microbiology literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "Indole test",
+      "reason": "Definitive species-level discriminator.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "H2S detection (TSI or KIA)",
+      "reason": "Confirms sulfur reduction capability.",
+      "api_kit": "API 20E"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable confirmation.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}