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

data/rag/knowledge_base/Anaerococcus/genus.json

@@ -1,79 +1,126 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Anaerococcus",
-  "taxonomy": {
-    "family": "Peptoniphilaceae",
-    "order": "Tissierellales",
-    "class": "Clostridia",
-    "phylum": "Firmicutes"
+
+  "overview": {
+    "short": "Anaerococcus species are Gram-positive anaerobic cocci, commonly isolated from skin, soft tissue, and genitourinary tract infections.",
+    "clinical_context": "Frequently recovered from polymicrobial anaerobic infections, including abscesses, wound infections, and genital tract specimens."
   },
-  "overview": "Anaerococcus is a genus of Gram-positive anaerobic cocci (GPAC) commonly isolated from skin, oral cavity, gastrointestinal tract, and the urogenital tract. They are frequently involved in polymicrobial infections, especially soft tissue infections, abscesses, and infections associated with mucosal surfaces. They are part of the former Peptostreptococcus group.",
-  "key_traits": [
-    "Gram-positive cocci in pairs, clusters, or tetrads",
-    "Strict anaerobes",
-    "Catalase negative or weakly positive",
-    "Indole negative (important GPAC distinction)",
-    "Non-motile",
-    "Do not grow in 6.5% NaCl",
-    "ONPG negative",
-    "Often isolated in polymicrobial infections",
-    "Butyric acid production on gas chromatography"
-  ],
-  "ecology": "Found in normal flora of the skin, oral cavity, gastrointestinal tract, and urogenital tract. They frequently participate in biofilm and abscess formation alongside other anaerobes such as Bacteroides, Peptoniphilus, and Finegoldia.",
-  "pathogenicity": "Anaerococcus species are opportunistic pathogens causing abscesses, wound infections, diabetic foot infections, osteomyelitis, pelvic infections, and bacteremia. Rarely pathogenic on their own, but significant contributors to polymicrobial disease.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Indole negative (helps distinguish from Finegoldia magna which is indole positive).",
-      "Ferments peptones and amino acids rather than carbohydrates.",
-      "ONPG negative.",
-      "No growth in 6.5% NaCl.",
-      "Produces short-chain fatty acids (SCFAs) including butyrate.",
-      "Catalase variable but usually negative."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Cocci",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "Anaerobic Blood Agar"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate fermentation patterns are unreliable in GPAC.",
-      "Hemolysis patterns vary and are not species-defining."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Finegoldia magna is indole positive; Anaerococcus is indole negative.",
-      "Peptoniphilus species often produce acid from certain sugars and show different GC fatty acid profiles.",
-      "Parvimonas micra forms Gram-positive cocci in chains, not clusters.",
-      "Atopobium and other Gram-positive anaerobic rods have different morphology and metabolic profiles.",
-      "Anaerococcus does not grow in 6.5% NaCl, unlike Enterococcus."
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Smooth"
     ],
-    "key_rag_filters": [
-      "Gram-positive cocci + strict anaerobe → narrows to GPAC group.",
-      "Clusters/tetrads + indole negative → strongly supports Anaerococcus.",
-      "Involvement in soft tissue abscess → high likelihood of Anaerococcus or Finegoldia.",
-      "Gas chromatography showing butyrate → supportive for Anaerococcus."
-    ]
+    "Oxygen Requirement": "Anaerobic",
+    "Growth Temperature": "35//37",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Variable",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "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": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Unknown"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Gram-positive cocci in clusters or pairs on Gram stain",
-      "Strictly anaerobic growth",
-      "Indole negative",
-      "Characteristic butyrate production on GC",
-      "Small, local soft tissue abscess associations"
-    ],
-    "important_tests": [
-      "Indole test",
-      "Anaerobic culture methods",
-      "Gas chromatography of fatty acids",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (highly accurate for GPAC)",
-      "16S rRNA sequencing",
-      "Fatty acid profile via GC",
-      "Morphology + indole negativity"
-    ]
+
+  "field_notes": {
+    "Oxygen Requirement": "Strict anaerobes; growth in oxygenated conditions argues against Anaerococcus.",
+    "Catalase": "Typically negative, helping differentiate from some other Gram-positive cocci.",
+    "Shape": "Often seen as cocci in clusters, pairs, or short chains."
   },
-  "notes": "Species were historically classified under Peptostreptococcus. Now placed within Peptoniphilaceae with clearer biochemical and genomic boundaries.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Recent taxonomic studies of GPAC",
-    "Anaerobic bacteriology literature"
+
+  "key_differentiators": [
+    {
+      "field": "Oxygen Requirement",
+      "expected": "Anaerobic",
+      "distinguishes_from": ["Staphylococcus", "Streptococcus"],
+      "notes": "Strict anaerobic growth differentiates Anaerococcus from most aerobic cocci."
+    },
+    {
+      "field": "Catalase",
+      "expected": "Negative",
+      "distinguishes_from": ["Staphylococcus"],
+      "notes": "Catalase negativity supports anaerobic cocci identification."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Finegoldia",
+      "reason": "Both are Gram-positive anaerobic cocci commonly isolated from similar clinical sites."
+    },
+    {
+      "genus": "Peptoniphilus",
+      "reason": "Overlapping anaerobic coccal morphology and biochemical inactivity."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Growth under aerobic conditions argues against Anaerococcus.",
+    "Catalase positivity suggests another Gram-positive coccus.",
+    "Spore formation excludes Anaerococcus."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Anaerobic incubation confirmation",
+      "reason": "Confirms obligate anaerobic growth."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable identification among anaerobic cocci with overlapping biochemistry."
+    },
+    {
+      "test": "16S rRNA sequencing",
+      "reason": "Useful for definitive identification in complex polymicrobial infections."
+    }
+  ],
+
+  "supported_species": [
+    "prevotii",
+    "vaginalis"
   ]
-}
+}