Update data/rag/knowledge_base/Elizabethkingia/miricola.json

data/rag/knowledge_base/Elizabethkingia/miricola.json

@@ -1,50 +1,114 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Elizabethkingia",
   "species": "miricola",
-  "full_name": "Elizabethkingia miricola",
-  "clinical_significance": "Initially isolated from the Mir space station's water supply. Increasingly identified in clinical specimens, including bacteremia, pneumonia, and urinary infections, particularly in immunocompromised or hospitalized patients. Less common than E. anophelis but clinically relevant.",
-  "phenotype_profile": {
-    "morphology": "Slender Gram-negative rods; pale and irregularly staining.",
-    "culture": "Yellowish colonies, non-motile, non-fermenting, grows poorly on MacConkey.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Indole positive",
-      "Non-motile",
-      "Urease negative",
-      "Non-fermenter",
-      "Weak esculin hydrolysis"
-    ]
+
+  "overview": {
+    "short": "Elizabethkingia miricola is a Gram-negative, aerobic, non-fermenting rod originally isolated from environmental sources and later recognised as a rare opportunistic human pathogen.",
+    "clinical_context": "Reported in sporadic infections, often in immunocompromised hosts; clinical relevance is less well defined than other Elizabethkingia species."
   },
-  "differentiation": {
-    "from close species": [
-      "Difficult to differentiate from other Elizabethkingia without MALDI-TOF.",
-      "Genetically distinct by WGS; phenotypically extremely similar to E. anophelis.",
-      "Clinical involvement somewhat less common than anophelis."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "from other genera": [
-      "Indole-positive oxidase-positive non-motile profile limits differential to Elizabethkingia.",
-      "Weakly pigmented, slow-growing colonies unlike Pseudomonas/Burkholderia."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Non-mucoid"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//42",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Variable",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Variable",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Variable",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Negative",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "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": "K/K",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "virulence_factors": [
-      "Biofilm formation in water distribution systems",
-      "Metallo-β-lactamases conferring high drug resistance",
-      "Environmental survival in low-nutrient water"
+
+  "species_markers": [
+    {
+      "field": "Indole",
+      "value": "Variable",
+      "importance": "low",
+      "notes": "Indole reaction is less consistent and not reliable for species separation."
+    },
+    {
+      "field": "Clinical Frequency",
+      "value": "Rare",
+      "importance": "medium",
+      "notes": "Less commonly isolated from human clinical samples compared to other Elizabethkingia species."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "Whole-genome sequencing",
-      "rpoB and 16S sequencing"
+
+  "common_confusions": [
+    {
+      "species": "Elizabethkingia anophelis",
+      "reason": "Overlapping biochemical profiles and environmental origin."
+    },
+    {
+      "species": "Elizabethkingia meningoseptica",
+      "reason": "Shared genus-level characteristics; differentiation usually requires MALDI-TOF or sequencing."
+    }
   ],
-  "treatment_notes": [
-      "Resistant to carbapenems, most β-lactams, and aminoglycosides.",
-      "TMP-SMX, fluoroquinolones, and piperacillin-tazobactam have variable activity.",
-      "Therapeutic decisions should be guided by susceptibility testing."
+
+  "when_to_question_identification": [
+    "Species designation without advanced identification methods.",
+    "Strong epidemiological link to neonatal outbreaks (suggests other species).",
+    "Indole-negative result does not exclude E. miricola."
   ],
-  "notes": "Originally isolated from a space station; environmental resilience is striking.",
-  "references": [
-      "Elizabethkingia miricola genomic studies",
-      "Clinical outbreak and identification literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Primary method for confident species-level identification.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "16S rRNA sequencing",
+      "reason": "Recommended for confirmation due to rarity and database variability.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}