Update data/rag/knowledge_base/Achromobacter/xylosoxidans.json

data/rag/knowledge_base/Achromobacter/xylosoxidans.json

@@ -1,52 +1,112 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Achromobacter",
   "species": "xylosoxidans",
-  "full_name": "Achromobacter xylosoxidans",
-  "clinical_significance": "The most clinically important Achromobacter species. Commonly isolated from respiratory specimens in cystic fibrosis patients and associated with chronic colonization. It also causes bacteremia, catheter-associated infections, pneumonia, and opportunistic hospital outbreaks.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods; non-fermenting.",
-    "culture": "Grows well on blood and MacConkey agar as smooth, grey, non-lactose-fermenting colonies.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Non-fermenter",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Xylose oxidation positive (definitive trait)",
-      "Glucose oxidation positive",
-      "Nitrate reduction positive",
-      "Motile"
-    ]
+
+  "overview": {
+    "short": "Achromobacter xylosoxidans is a Gram-negative, aerobic, non-fermenting rod and the most commonly isolated species of the genus in clinical microbiology.",
+    "clinical_context": "Frequently associated with respiratory infections in cystic fibrosis patients, as well as bloodstream and device-associated infections."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Strongly xylose-positive, unlike A. inosolitus and A. denitrificans.",
-      "More robust growth and oxidation profile compared to A. inosolitus.",
-      "Nitrate reduction helps distinguish from xylose-positive Burkholderia species."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "MacConkey Agar"
     ],
-    "from_other_genera": [
-      "Burkholderia may ferment glucose weakly, unlike A. xylosoxidans.",
-      "Delftia produces orange insoluble pigment in OF glucose medium; Achromobacter does not.",
-      "Alcaligenes is typically asaccharolytic, unlike xylose-positive A. xylosoxidans."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Non-lactose fermenting"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Positive",
+    "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": "Polar"
   },
-  "virulence_factors": [
-    "Biofilm formation, especially in cystic fibrosis lung environment",
-    "Efflux pump–mediated multidrug resistance",
-    "Environmental persistence and disinfectant tolerance"
+
+  "species_markers": [
+    {
+      "field": "Arginine dihydrolase",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Key defining feature of A. xylosoxidans among non-fermenting Gram-negative rods."
+    },
+    {
+      "field": "Nitrate Reduction",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Supports differentiation from closely related Achromobacter species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Pseudomonas",
+      "reason": "Shared oxidase positivity and non-fermentative metabolism."
+    },
+    {
+      "genus": "Burkholderia",
+      "reason": "Overlap in biochemical profile and environmental association."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS (best method)",
-    "Xylose oxidation test",
-    "Glucose oxidation pattern",
-    "16S rRNA sequencing",
-    "Nitrate reduction test"
+
+  "when_to_question_identification": [
+    "Oxidase-negative result argues against Achromobacter.",
+    "Carbohydrate fermentation suggests Enterobacterales.",
+    "Pigment production suggests Pseudomonas."
   ],
-  "treatment_notes": "Frequently multidrug-resistant. Piperacillin–tazobactam, carbapenems, and TMP-SMX are often active, but susceptibility testing is required. Chronic infection in CF patients may require combination therapy.",
-  "notes": "Most clinically encountered Achromobacter isolates belong to the xylosoxidans complex. Very commonly misidentified as Alcaligenes by older biochemical systems.",
-  "references": [
-    "CF Foundation pathogen surveillance data.",
-    "Koneman's Diagnostic Microbiology.",
-    "Manual of Clinical Microbiology, 12th Edition."
+
+  "recommended_next_tests": [
+    {
+      "test": "Arginine dihydrolase",
+      "reason": "Confirms Achromobacter lineage."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Gold standard for non-fermenter species differentiation."
+    }
   ]
-}
+}