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

data/rag/knowledge_base/Aerococcus/genus.json

@@ -1,79 +1,137 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Aerococcus",
-  "taxonomy": {
-    "family": "Aerococcaceae",
-    "order": "Lactobacillales",
-    "class": "Bacilli"
+
+  "overview": {
+    "short": "Aerococcus species are Gram-positive cocci that often appear in clusters or tetrads and resemble streptococci or staphylococci on initial examination.",
+    "clinical_context": "Associated with urinary tract infections, bacteremia, endocarditis, and invasive infections, particularly in elderly or immunocompromised patients."
   },
-  "overview": "Aerococcus is a genus of Gram-positive cocci arranged in tetrads, clusters, or irregular groups. They are catalase negative, facultatively anaerobic, and alpha-hemolytic on blood agar. Aerococcus species are increasingly recognized as human pathogens, particularly in urinary tract infections and infective endocarditis among older adults.",
-  "key_traits": [
-    "Gram-positive cocci forming tetrads, clusters, or pairs",
-    "Catalase negative (key differentiator from Staphylococcus)",
-    "Alpha-hemolytic or non-hemolytic",
-    "Non-motile",
-    "Facultative anaerobes",
-    "Grow on blood agar; may be mistaken for viridans streptococci",
-    "Do not grow in 6.5% NaCl (distinguishes from Enterococcus)",
-    "ONPG negative",
-    "LAP positive",
-    "PYR negative"
-  ],
-  "ecology": "Aerococcus species are found in air, dust, environmental samples, and human skin and mucosa, particularly in the urinary tract and perineal region.",
-  "pathogenicity": "Aerococcus urinae and Aerococcus sanguinicola are significant causes of urinary tract infections, bacteremia, and infective endocarditis, especially in older men with urinary tract abnormalities. Aerococcus viridans is less commonly associated with invasive disease but has been implicated in opportunistic infections.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Catalase negative (unlike staphylococci)",
-      "Alpha-hemolytic colonies resembling viridans streptococci",
-      "ONPG negative",
-      "No growth in 6.5% NaCl",
-      "LAP positive (helps separate from some streptococci)",
-      "Non-fermentative appearance on some biochemical panels due to weak reactivity"
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Cocci",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate fermentation profiles are inconsistent across strains.",
-      "Hemolysis alone cannot distinguish species."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Staphylococcus is catalase positive; Aerococcus is catalase negative despite coccoid clustering.",
-      "Enterococcus grows in 6.5% NaCl and is PYR positive; Aerococcus does neither.",
-      "Streptococcus forms chains, not tetrads, and often has stronger fermentation profiles.",
-      "Micrococcus forms tetrads but is catalase positive and strictly aerobic.",
-      "Granulicatella is nutritionally variant and will not grow well on routine media unless supplemented."
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Alpha-haemolytic or Non-haemolytic"
     ],
-    "key_rag_filters": [
-      "Gram-positive cocci in tetrads + catalase negative → strongly favors Aerococcus.",
-      "Alpha-hemolytic + negative catalase + LAP positive → eliminates Staph, most Streptococcus.",
-      "No growth in 6.5% NaCl → rules out Enterococcus.",
-      "Urine isolate from older male → strong push toward Aerococcus urinae or sanguinicola."
-    ]
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "30//37",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Unknown",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Unknown",
+    "Ornithine Decarboxylase": "Unknown",
+    "Ornitihine Decarboxylase": "Unknown",
+    "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": "Unknown",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Unknown",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Gram-positive cocci in tetrads or clusters",
-      "Catalase negative",
-      "Alpha-hemolytic colonies resembling viridans streptococci",
-      "LAP positive, PYR negative",
-      "Weak or variable biochemical reactivity"
-    ],
-    "important_tests": [
-      "Gram stain morphology (tetrads)",
-      "Catalase test",
-      "LAP test",
-      "MALDI-TOF MS",
-      "16S rRNA sequencing when needed"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (high accuracy for Aerococcus spp.)",
-      "16S rRNA sequencing",
-      "Tetrad formation on Gram stain combined with catalase negativity"
-    ]
+
+  "field_notes": {
+    "Catalase": "Typically catalase-negative, but weak or pseudo-positive reactions may occur.",
+    "Haemolysis": "Most species are alpha-haemolytic or non-haemolytic on blood agar.",
+    "Shape": "Often described as cocci in tetrads or clusters, which can mimic staphylococci."
   },
-  "notes": "Aerococcus is frequently misidentified as streptococci or staphylococci without MALDI-TOF. Clinically important species are A. urinae and A. sanguinicola.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Recent research on Aerococcus infective endocarditis",
-    "Koneman's Diagnostic Microbiology"
+
+  "key_differentiators": [
+    {
+      "field": "Catalase",
+      "expected": "Negative",
+      "distinguishes_from": ["Staphylococcus"],
+      "notes": "Catalase negativity helps separate Aerococcus from staphylococci."
+    },
+    {
+      "field": "NaCl Tolerant (>=6%)",
+      "expected": "Negative",
+      "distinguishes_from": ["Enterococcus"],
+      "notes": "Lack of growth in high salt differentiates Aerococcus from enterococci."
+    },
+    {
+      "field": "Haemolysis",
+      "expected": "Variable",
+      "distinguishes_from": ["Streptococcus"],
+      "notes": "Haemolysis pattern combined with colony morphology aids differentiation."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Streptococcus",
+      "reason": "Similar Gram-positive cocci morphology and haemolysis patterns."
+    },
+    {
+      "genus": "Enterococcus",
+      "reason": "Overlapping biochemical reactions in urinary isolates."
+    },
+    {
+      "genus": "Staphylococcus",
+      "reason": "Clustered cocci appearance on Gram stain may be misleading."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Catalase-positive reaction suggests Staphylococcus.",
+    "Growth in 6.5% NaCl suggests Enterococcus.",
+    "Beta-haemolysis with streptococcal morphology suggests Streptococcus."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Catalase test (repeat)",
+      "reason": "Weak reactions may require confirmation."
+    },
+    {
+      "test": "NaCl tolerance (6.5%)",
+      "reason": "Useful for exclusion of Enterococcus."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Preferred method for accurate genus and species identification."
+    }
+  ],
+
+  "supported_species": [
+    "urinae",
+    "viridans",
+    "sanguinicola",
+    "christensenii"
   ]
-}
+}