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

data/rag/knowledge_base/Comamonas/genus.json

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+{
+  "genus": "Comamonas",
+  "taxonomy": {
+    "family": "Comamonadaceae",
+    "order": "Burkholderiales",
+    "class": "Betaproteobacteria",
+    "phylum": "Proteobacteria"
+  },
+  "overview": "Comamonas is a genus of aerobic, motile, oxidase-positive Gram-negative rods found in soil, freshwater, and wastewater environments. They are non-fermenters and generally considered low-virulence organisms, although Comamonas kerstersii has recently emerged as a human pathogen associated with intra-abdominal infections, particularly appendicitis.",
+  "key_traits": [
+    "Gram-negative rods",
+    "Motile with polar flagella",
+    "Oxidase positive",
+    "Catalase positive",
+    "Non-fermenters (oxidize glucose but do not ferment)",
+    "Nitrate reduction positive",
+    "Grow well on routine aerobic media",
+    "Do not grow in 6.5% NaCl",
+    "Indole negative",
+    "ONPG negative"
+  ],
+  "ecology": "Widely distributed in water, soil, sewage, and biofilms. Some species colonize hospital water systems. Human infection occurs through contaminated water or disrupted mucosal barriers.",
+  "pathogenicity": "Most species are environmental and rarely cause infection. Comamonas kerstersii is increasingly reported in appendicitis, peritonitis, bacteremia, and pelvic infections. Comamonas testosteronii is usually a contaminant or colonizer but may cause opportunistic infections in immunocompromised hosts.",
+  "genus_level_biochemistry": {
+    "general_tendencies": [
+      "Oxidase positive aerobic rods.",
+      "Do not ferment carbohydrates; use oxidative metabolism.",
+      "Motile by polar flagella.",
+      "ONPG negative, urease negative.",
+      "Nitrate to nitrite reduction positive."
+    ],
+    "non_definitive_tests": [
+      "Colony morphology overlaps with Delftia and Acidovorax.",
+      "Carbohydrate utilization tests limited for speciation."
+    ]
+  },
+  "genus_differentiation": {
+    "from_close_genera": [
+      "Delftia acidovorans forms characteristic 'orange peel' surface and is DNase positive, unlike most Comamonas.",
+      "Acidovorax species are often less motile and differ in assimilation reactions.",
+      "Burkholderia are typically more resistant and may be oxidase variable.",
+      "Pseudomonas aeruginosa produces pigments and grows in high salt; Comamonas does not.",
+      "Ralstonia are oxidase positive but often nonmotile and more water-system associated."
+    ],
+    "key_rag_filters": [
+      "Oxidase positive + non-fermenting + motile = Comamonas/Delftia/Burkholderia group.",
+      "Appendicitis-associated isolate → strongly suggests Comamonas kerstersii.",
+      "Environmental water isolate + low virulence → suggests Comamonas testosteronii.",
+      "No pigment + no DNase activity → favors Comamonas over Delftia."
+    ]
+  },
+  "diagnostics": {
+    "typical_lab_findings": [
+      "Motile oxidase-positive GNR",
+      "Non-fermenter on TSI/KIA",
+      "Growth on MacConkey (NLF)",
+      "No pigment production"
+    ],
+    "important_tests": [
+      "Oxidase test",
+      "Glucose oxidation vs fermentation",
+      "Nitrate reduction",
+      "MALDI-TOF MS"
+    ],
+    "confirmation_methods": [
+      "MALDI-TOF MS (high accuracy)",
+      "16S rRNA sequencing",
+      "Whole-genome sequencing for rare species"
+    ]
+  },
+  "notes": "Historically under-recognized due to misidentification by older biochemical systems.",
+  "references": [
+    "Manual of Clinical Microbiology",
+    "Comamonas infection case series",
+    "Burkholderiales taxonomy studies"
+  ]
+}