Update data/rag/knowledge_base/Alcaligenes/genus.json

data/rag/knowledge_base/Alcaligenes/genus.json

@@ -1,76 +1,121 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Alcaligenes",
-  "taxonomy": {
-    "family": "Alcaligenaceae",
-    "order": "Burkholderiales",
-    "class": "Betaproteobacteria"
+
+  "overview": {
+    "short": "Alcaligenes species are Gram-negative, aerobic, non-fermentative rods commonly found in environmental sources and occasionally associated with opportunistic infections.",
+    "clinical_context": "Rarely pathogenic but may be isolated from respiratory specimens, blood, or hospital environments."
   },
-  "overview": "Alcaligenes is a genus of aerobic, oxidase-positive, non-fermenting Gram-negative rods commonly isolated from soil, water, and environmental sources. They are motile, nonsaccharolytic organisms that rarely cause human infections except as opportunistic pathogens in immunocompromised or hospitalized individuals.",
-  "key_traits": [
-    "Gram-negative rods",
-    "Obligate aerobes",
-    "Oxidase positive",
-    "Catalase positive",
-    "Non-fermentative and typically asaccharolytic",
-    "Motile with peritrichous flagella",
-    "Grow on MacConkey agar (non-lactose fermenting)",
-    "Do not require NaCl",
-    "ONPG negative",
-    "Environmental organisms"
-  ],
-  "ecology": "Common in water, soil, and moist environments. Often associated with contamination of medical devices, fluids, and solutions.",
-  "pathogenicity": "Low virulence. Occasionally implicated in catheter-associated infections, bacteremia, peritonitis in dialysis patients, and opportunistic infections in immunocompromised hosts.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Strongly asaccharolytic (key trait).",
-      "Oxidase positive and catalase positive.",
-      "Non-fermenting rods that do not utilize carbohydrates.",
-      "Motile with peritrichous flagella.",
-      "ONPG negative.",
-      "No growth in 6.5% NaCl."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Nutrient Agar"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate oxidation patterns are absent or extremely weak.",
-      "Biochemical kits often misidentify Alcaligenes due to nonsaccharolytic metabolism."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Achromobacter species oxidize some carbohydrates; Alcaligenes are strictly asaccharolytic.",
-      "Comamonas is oxidase positive but has more consistent carbohydrate oxidation patterns.",
-      "Delftia produces yellow pigment or 'Delftia reaction', unlike Alcaligenes.",
-      "Ralstonia and Burkholderia show stronger oxidative metabolism and distinct biochemical profiles.",
-      "Bordetella species are usually non-motile (except B. bronchiseptica)."
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Grey-White"
     ],
-    "key_rag_filters": [
-      "Oxidase positive + asaccharolytic + motile → strong push toward Alcaligenes.",
-      "No pigment production → excludes Delftia.",
-      "Weak or absent carbohydrate oxidation → separates from Achromobacter."
-    ]
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "20//42",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Variable",
+    "Ornitihine Decarboxylase": "Variable",
+    "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": "Peritrichous"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Oxidase positive, non-fermenting rods",
-      "Asaccharolytic metabolism",
-      "Non-lactose fermenting colonies on MacConkey",
-      "Motility positive"
-    ],
-    "important_tests": [
-      "Oxidase test",
-      "Motility determination",
-      "Carbohydrate utilization testing (absence supports identification)",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (most accurate)",
-      "16S rRNA sequencing",
-      "Asaccharolytic biochemical profile"
-    ]
+
+  "field_notes": {
+    "Oxidase": "Strong oxidase positivity is characteristic.",
+    "Glucose Fermentation": "Alcaligenes species are non-fermentative."
   },
-  "notes": "Alcaligenes xylosoxidans was reclassified into Achromobacter (Achromobacter xylosoxidans). Older literature may still refer to it as Alcaligenes.",
-  "references": [
-    "Manual of Clinical Microbiology, 12th Edition",
-    "Koneman’s Diagnostic Microbiology",
-    "Taxonomic studies on Alcaligenaceae"
+
+  "key_differentiators": [
+    {
+      "field": "Oxidase",
+      "expected": "Positive",
+      "distinguishes_from": ["Enterobacter", "Escherichia"],
+      "notes": "Separates Alcaligenes from oxidase-negative Enterobacterales."
+    },
+    {
+      "field": "Glucose Fermentation",
+      "expected": "Negative",
+      "distinguishes_from": ["Aeromonas"],
+      "notes": "Non-fermentative metabolism is genus-defining."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Achromobacter",
+      "reason": "Both are oxidase-positive, non-fermentative Gram-negative rods."
+    },
+    {
+      "genus": "Pseudomonas",
+      "reason": "Shared aerobic growth and non-fermentative metabolism."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Oxidase negativity suggests another genus.",
+    "Glucose fermentation argues against Alcaligenes.",
+    "Pigment production suggests Pseudomonas."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Oxidase test",
+      "reason": "Key screening test for non-fermentative Gram-negative rods."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Recommended due to limited biochemical resolution."
+    }
+  ],
+
+  "supported_species": [
+    "faecalis",
+    "denitrificans"
   ]
-}
+}