Update data/rag/knowledge_base/Erysipelothrix/tonsillarum.json

data/rag/knowledge_base/Erysipelothrix/tonsillarum.json

@@ -1,48 +1,119 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Erysipelothrix",
   "species": "tonsillarum",
-  "full_name": "Erysipelothrix tonsillarum",
-  "clinical_significance": "Primarily an animal-associated species commonly found in the tonsils of swine, poultry, and other mammals. Rarely causes human infection; when it does, disease is usually milder than that caused by E. rhusiopathiae.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive thin rods with variable staining.",
-    "culture": "Small, gray colonies; sometimes smoother and less filamentous than E. rhusiopathiae.",
-    "biochemical": [
-      "Catalase negative",
-      "Non-motile",
-      "H2S weak or absent (less consistent than E. rhusiopathiae)",
-      "Indole negative",
-      "Urease negative",
-      "Ferments glucose"
-    ]
+
+  "overview": {
+    "short": "Erysipelothrix tonsillarum is a Gram-positive, non-spore-forming, non-motile short rod most commonly associated with animals and environmental exposure rather than classic erysipeloid.",
+    "clinical_context": "More often isolated from animals (e.g., tonsils/oropharynx) and may appear in mixed cultures; human disease is less commonly described than E. rhusiopathiae."
   },
-  "differentiation": {
-    "from close species": [
-      "Typically weaker H2S production vs strong H2S of E. rhusiopathiae.",
-      "Primarily recovered from animals; human isolates uncommon.",
-      "Lower virulence and not strongly associated with erysipeloid."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Short Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Catalase negative + slender rods + weak H2S supports identification.",
-      "Lack of motility differentiates from Listeria."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Translucent",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "20//42",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Variable",
+    "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": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "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": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "virulence_factors": [
-      "Less well characterized than E. rhusiopathiae",
-      "Likely surface adhesins and enzymes contributing to colonization in animals"
+
+  "species_markers": [
+    {
+      "field": "H2S",
+      "value": "Variable",
+      "importance": "high",
+      "notes": "Compared with E. rhusiopathiae, H2S may be less consistently observed; treat as supportive rather than definitive."
+    },
+    {
+      "field": "Clinical Context",
+      "value": "Animal-associated / commensal-leaning",
+      "importance": "medium",
+      "notes": "Frequently associated with animal reservoirs; human clinical relevance may require correlation."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "16S rRNA sequencing",
-      "H2S profile on TSI"
+
+  "common_confusions": [
+    {
+      "species": "Erysipelothrix rhusiopathiae",
+      "reason": "Very close overlap in routine phenotypic testing; separation often requires MALDI-TOF or molecular identification."
+    },
+    {
+      "genus": "Listeria",
+      "reason": "Short rod appearance; motility and catalase help separate."
+    }
   ],
-  "treatment_notes": [
-      "Generally penicillin susceptible.",
-      "Vancomycin resistance intrinsic to the genus.",
-      "Treatment guided by clinical significance (rare pathogen)."
+
+  "when_to_question_identification": [
+    "Clear and reproducible H2S positivity plus classic erysipeloid context favors E. rhusiopathiae.",
+    "Motility suggests non-Erysipelothrix short rods.",
+    "Catalase positivity argues against Erysipelothrix."
   ],
-  "notes": "More relevant in veterinary microbiology; human infection extremely rare.",
-  "references": [
-      "Veterinary microbiology literature on Erysipelothrix",
-      "Taxonomic studies differentiating E. tonsillarum"
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Most practical method to separate E. tonsillarum from E. rhusiopathiae in routine workflows.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "H2S detection on TSI or iron-containing media",
+      "reason": "Use as a supportive feature; interpret cautiously due to variability.",
+      "api_kit": "API Coryne"
+    },
+    {
+      "test": "Molecular identification (e.g., sequencing)",
+      "reason": "Useful where MALDI libraries are limited or when clinical stakes are high.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}