Update data/rag/knowledge_base/Chromobacterium/haemolyticum.json

data/rag/knowledge_base/Chromobacterium/haemolyticum.json

@@ -1,48 +1,102 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Chromobacterium",
   "species": "haemolyticum",
-  "full_name": "Chromobacterium haemolyticum",
-  "clinical_significance": "A pathogenic Chromobacterium species associated with fulminant sepsis, severe skin and soft tissue infection, and high mortality. Unlike C. violaceum, it does NOT produce violacein pigment, making it easy to misidentify. Often more hemolytic and potentially more virulent.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "β-hemolytic colonies on blood agar. No violet pigment. Grows well on routine media.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Indole negative",
-      "ONPG negative",
-      "Nitrate reduction positive",
-      "Motile",
-      "No growth in 6.5% NaCl"
-    ]
+
+  "overview": {
+    "short": "Chromobacterium haemolyticum is a Gram-negative, motile rod distinguished by strong haemolytic activity and absence of violacein pigment.",
+    "clinical_context": "Rarely associated with human infection; differentiation from C. violaceum is clinically relevant due to differing virulence."
   },
-  "differentiation": {
-    "from close species": [
-      "Non-pigmented and strongly β-hemolytic (C. violaceum is pigmented and less hemolytic).",
-      "More invasive disease documented in case reports.",
-      "Requires molecular confirmation due to lack of distinctive pigment."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Positive",
+    "Haemolysis Type": "Beta",
+    "Media Grown On": [
+      "Blood Agar",
+      "Nutrient Agar"
     ],
-    "from other genera": [
-      "Aeromonas may be β-hemolytic but typically indole positive.",
-      "Pseudomonas aeruginosa often produces pigments (pyocyanin), unlike C. haemolyticum.",
-      "Burkholderia pseudomallei has wrinkled colonies and different epidemiology."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Haemolytic"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Positive",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Variable",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Variable",
+    "Ornitihine Decarboxylase": "Variable",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "Hemolysins",
-    "Type III secretion system",
-    "Cytotoxins distinct from violacein",
-    "Invasive systemic spread"
+
+  "species_markers": [
+    {
+      "field": "Haemolysis",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Consistent beta haemolysis differentiates C. haemolyticum from non-haemolytic Chromobacterium species."
+    },
+    {
+      "field": "Pigment",
+      "value": "None",
+      "importance": "high",
+      "notes": "Absence of violacein distinguishes it from C. violaceum."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "β-hemolysis with oxidase positivity",
-    "16S sequencing"
+
+  "common_confusions": [
+    {
+      "species": "Chromobacterium violaceum",
+      "reason": "Shared oxidase positivity and motility, but violacein pigment is absent in C. haemolyticum."
+    }
   ],
-  "treatment_notes": "Similar antibiotic pattern to C. violaceum. Often susceptible to fluoroquinolones, carbapenems, and TMP-SMX; resistant to penicillins and many cephalosporins.",
-  "notes": "Considered an emerging Chromobacterium pathogen with severe clinical outcomes. Easy to overlook due to lack of pigmentation.",
-  "references": [
-    "Chromobacterium haemolyticum clinical case reports",
-    "Environmental GNR infection reviews"
+
+  "recommended_next_tests": [
+    {
+      "test": "Blood agar haemolysis assessment",
+      "reason": "Confirms strong beta haemolysis pattern."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Definitive species-level confirmation for rare isolates."
+    }
   ]
-}
+}